Restriction Site-associated DNA Sequencing Research Articles

Successive cycles of allopatric differentiation and secondary contact shape phylogeographical structure in an Indo-West Pacific reef fish

Abstract Geographical barriers and sea-level fluctuations have significantly influenced the population genetic structure and evolutionary history of Indo-West Pacific (IWP) reef species. This study examines these effects in Abudefduf septemfasciatus (banded sergeant), a widely distributed egg-brooding IWP damselfish. Using 4700 genome-wide single nucleotide polymorphisms obtained from double-digest restriction site-associated DNA sequencing and a 1638-bp mitochondrial gene fragment from 106 samples across six IWP locations, we identified two main genetic clusters: one in the Indian Ocean and another in the Pacific Ocean. Within the Pacific, two distinct subclusters were detected, with overlapping ranges in Taiwan. Demographic analysis of the dataset using two-population genetic models in ∂a∂I, based on diffusion approximation, revealed asymmetric gene flow, with stronger migration from the Indian Ocean to the Pacific. Recurrent episodes of isolation and secondary contact during Pleistocene glacial cycles further shaped these genetic patterns. Our findings provide new insights into the complex phylogeography and evolutionary dynamics of banded sergeants, contributing to a broader understanding of how historical environmental changes have driven the diversification of IWP reef fishes.

Isolation by environment is more important than isolation by distance along a tropical gradient in direct developing frogs

Abstract Abiotic factors are important for defining population structure and limiting gene flow, especially in ectotherm species. In amphibians, abiotic factors like temperature and precipitation can facilitate or restrict gene flow. The challenge is identifying if these factors can lead to a pattern of isolation by environment. Our study aims to quantify the extent to which divergence is driven by abiotic factors such as temperature, precipitation and elevation. To do so, we used a direct-developing frog species, Craugastor loki that occurs along a steep elevation gradient. Using restriction-site associated DNA sequencing (RADseq) from individuals collected from 100 m to 2250 m of elevation across 13 localities at Sierra Madre de Chiapas in southern Mexico, we described population structure using a variety of model-based clustering and landscape genomics approaches. We found that populations sampled at higher elevation probably correspond to an undescribed new species of Craugastor, and that populations from Craugastor loki between 120 m and 1500 m are clustered in two different genetic groups: a Pacific slope group and a Central Depression slope group. We found signatures of isolation by environment more important than isolation by distance in contributing to genetic divergence in this group of frogs at a fine scale. The environmental variables such as: mean temperature of wettest and warmest quarter, annual mean temperature, and seasonality in temperature and precipitation play an important role on population differentiation. Our results underscore the importance of abiotic factors as drivers of genetic differentiation and highlight the use of different approaches to illuminate fine scale population divergence given the complexity of disentangling the contribution of both patterns of isolation.

Environmental gradients shape genetic variation in the desert moss, Syntrichia caninervis Mitt. (Pottiaceae)

The moss Syntrichia caninervis Mitt. is distributed throughout drylands globally, and often anchors ecologically significant communities known as biological soil crusts (biocrusts). The species occupies a variety of dryland habitats with varying levels of drought and temperature stress, suggesting the potential for ecological specialization within S. caninervis. Here, we sampled S. caninervis from sites along two elevation gradients and used restriction site associated DNA sequencing to compare the relative impacts of environmental factors and geospatial distances on genetic differentiation in S. caninervis populations. While we found no evidence of isolation by distance in our data, one environmental variable, mean annual precipitation (MAP), was found to be a positive predictor of FST. An ecological association analysis identified 32 SNP alleles that covary significantly with MAP, 15 of which fall within the exonic regions of genes with annotations suggesting diverse roles in response to dehydration stress. Understanding the degree to which genetic variation in S. caninervis is associated with environmental factors is key to predicting its potential for persistence in the face of global climate change, which is predicted to be especially detrimental to desert organisms already living at their physiological limits.

Comparing microsatellites and single nucleotide polymorphisms to evaluate genetic structure and diversity in wolverines (Gulo gulo) across Alaska and western Canada

Abstract The Wolverine (Gulo gulo) is a cold-adapted species of conservation interest because it is sensitive to human development, disturbance, exploitation, and climate warming. Wolverine populations have been studied across much of their distributional range to evaluate patterns of genetic diversity, genetic structure, and gene flow. Little population structure has been detected in northwestern North America with microsatellite loci, but low genomic diversity in wolverines may limit detection of genetic differences in this highly vagile species. Here, we genotyped a relatively large sample of wolverines from across Alaska (US) and adjacent Yukon (Canada) with 12 microsatellite loci (n = 501) and 4,222 single nucleotide polymorphisms (SNPs; n = 201) identified using restriction-site associated DNA sequencing. We compared the relative ability of our microsatellite and SNP datasets to evaluate population genetic structure, genetic diversity, differentiation, and isolation by distance (IBD). We predicted that the SNP dataset would detect a higher degree of genetic structure and provide more significant support for IBD. We found evidence for multiple genetic clusters, including genetic distinctiveness of wolverines in southeast Alaska and on the Kenai Peninsula. The SNP dataset detected additional genetic clusters that align largely with ecoregions, and the SNP dataset showed stronger evidence of IBD, while the 2 datasets were generally consistent in estimates of genetic diversity and differentiation among regional groups. Our results highlight the importance of genomic methods to assess gene flow in wolverines. Identifying population genetic structure allows an assessment of the potential impacts of conservation threats and is an important precursor for designing population monitoring programs.

High-Density Genetic Map Construction and QTL Detection for Cotyledon Color in Faba Bean Based on Double Digest Restriction-Site Associated DNA Sequencing (ddRAD-Seq)

Cotyledon color is one of the important indices for identifying faba bean variety purity and measuring processing quality. Therefore, an in-depth study of the genetic mechanism of cotyledon color is vital for promoting faba bean industry development. We used the yellow cotyledon variety Qingcan 16 and the green cotyledon variety Qingcan 17 as parent plants to construct hybrid combinations. F1-, F2-, BC1F1-, and BC2F1-generation single-plant cotyledon colors were counted to clarify cotyledon color inheritance. F2-generation individuals were genotyped using ddRAD-Seq to construct a genetic linkage map and identify QTLs for cotyledon color. Green cotyledons were controlled by one pair of recessive nuclear genes. Using the screened 1991 SNP markers, a high-density linkage map was constructed, with a coverage length of 1476.95 cM and an average map distance of 0.96 cM. The green cotyledon trait was located using WinQTL Cart, and a vfGC candidate interval explaining 34.30 to 49.40% of the phenotypic variation was identified at LG02 (101.952 cM to 115.493 cM) and at LOD = 16.0, corresponding to chr1L 1,077,051,302 bp to 1,636,400,339 bp (559.35 Mb). The above interval contained 2021 genes, 20 of which were involved in photosynthesis, but no SGR or genes with similar functions were identified. However, the published faba bean vfSGR was located within the vfGC candidate interval, confirming that our localization interval was reliable. The above findings provided further clues for the fine localization of genes regulating green cotyledons and the development of molecular linked markers in faba bean.

Genetic Variation for Wild Populations of the Rare and Endangered Plant Glyptostrobus pensilis Based on Double-Digest Restriction Site-Associated DNA Sequencing.

Glyptostrobus pensilis is an endangered tree species, and detecting its genetic diversity can reveal the mechanisms of endangerment, providing references for the conservation of genetic resources. Samples of 137 trees across seven populations within Fujian Province were collected and sequenced using double-digest restriction site-associated DNA (ddRAD-seq). A total of 3,687,189 single-nucleotide polymorphisms (SNPs) were identified, and 15,158 high-quality SNPs were obtained after filtering. The genetic diversity in the populations was found to be low (Ho = 0.08630, He = 0.03475, π = 0.07239), with a high genetic differentiation coefficient (Fst). When K = 4, the coefficient of variation (CV) error value was minimized, suggesting that the 137 individuals could be divided into four groups, with frequent gene flow between them. Principal component analysis (PCA) divided the seven populations into two major categories based on their north-south geographic location. The clustering was consistent with those obtained from the PCA. The main reasons for the endangerment of G. pensilis are likely to be poor natural regeneration, human disturbances, and climatic factors. It is recommended that methods such as in situ conservation, ex situ conservation, and the establishment of germplasm banks be implemented to maintain the genetic diversity of G. pensilis populations.

High-density genetic map construction and QTL analysis of the first flower node in kenaf using RAD-seq

BackgroundIn kenaf (Hibiscus cannabinus L.) which is an important natural fiber crop, the first flower node is closely linked to fiber yield. However, the genetic mechanisms controlling the first flower node remain poorly understood.ResultsIn this study, we constructed a high-density genetic linkage map using Restriction-site associated DNA sequencing (RAD-seq) technology based on 148 individual hybrid kenaf progeny. The map contained 3418 bin markers unevenly on 18 linkage groups and spanned a total of 864.607 cM with an average distance of 0.253 cM. Based on the genetic map, two major QTLs, FFN6.1 and FFN6.2, were detected on LG6 and were strongly associated with the first flower node. Based on annotation information in the GO, KEGG and NR public databases, 373 candidate genes were predicted in the FFN6.1 and FFN6.2 regions. Finally, using RT-qPCR, three genes related to the first flower node were identified.ConclusionThe study provides a good foundation for understanding the molecular mechanisms of the first flower node trait in kenaf.

QTL mapping provides new insights into emamectin benzoate resistance in salmon lice, Lepeophtheirus salmonis

BackgroundThe salmon louse (Lepeophtheirus salmonis) is a parasite of wild and farmed salmonid fish, causing huge economic damage to the commercial farming of Atlantic salmon (Salmo salar) in the northern hemisphere. The avermectin emamectin benzoate (EMB) is widely used for salmon delousing. While resistance to EMB is widespread in Atlantic populations of L. salmonis, the molecular mechanisms of resistance remain to be elucidated. The aim of the present work was to obtain insights into potential EMB resistance mechanisms by identifying genetic and transcriptomic markers associated with EMB resistance.ResultsCrosses were performed between EMB-susceptible and -resistant L. salmonis, sourced from two parental strains isolated in Scotland, producing fully pedigreed families. The EMB susceptibility of individual parasites was characterised using time-to-response bioassays. Parasites of two families were subjected to double digest restriction site-associated DNA sequencing (ddRAD-seq) for simultaneous discovery of single nucleotide polymorphisms (SNPs) and genotyping. Data analysis revealed that EMB resistance is associated with one quantitative trait locus (QTL) region on L. salmonis chromosome 5. Marker-trait association was confirmed by genotyping assays for 7 SNPs in two additional families. Furthermore, the transcriptome of male parasites of the EMB-susceptible and -resistant L. salmonis parental strains was assessed. Among eighteen sequences showing higher transcript expression in EMB-resistant as compared to drug-susceptible lice, the most strongly up-regulated gene is located in the above QTL region and shows high homology to β spectrin, a cytoskeleton protein that has roles in neuron architecture and function. Further genes differentially regulated in EMB-resistant lice include a glutathione S-transferase (GST), and genes coding for proteins with predicted roles in mitochondrial function, intracellular signalling or transcription.ConclusionsMajor determinants of EMB resistance in L. salmonis are located on Chromosome 5. Resistance can be predicted using a limited number of genetic markers. Genes transcriptionally up-regulated in EMB resistant parasites include a β spectrin, a cytoskeletal protein with still incompletely understood roles in neuron structure and function, as well as glutathione S-transferase, an enzyme with potential roles in the biochemical defence against toxicants.

Runs of homozygosity assessment using reduced representation sequencing highlight the evidence of random mating in emu (Dromaius novaehollandiae).

The domestication of emu (Dromaius novaehollandiae) began in the 1970s, but their productive characteristics have not undergone significant genetic enhancement. This study investigated the inbreeding and genetic diversity of 50 emus from various farms in Japan using Double digest restriction-site associated DNA sequencing (ddRAD-seq) markers. Single nucleotide polymorphism (SNP) calling revealed 171 975 high-quality SNPs while runs of homozygosity (ROH) analysis identified 1843 homozygous segments, with an average of 36.86 ROH per individual and a mean genome length of 27 Mb under ROH. The majority (86%) of ROH were short (0.5-1 Mb), indicating ancient or remote inbreeding. The average genomic inbreeding coefficient (FROH) was 0.0228, suggesting nearly no inbreeding. Overlapping ROH regions were identified, with top consensus regions found on chromosomes 8 and Z. Seven candidate genes related to egg production, feather development, and energy metabolism were annotated in these regions. The findings highlight the prevalence of genetic diversity and low inbreeding levels in the studied emu population. This research highlights the potentiality of random mating in genetic management and conservation of emus. Further studies should focus on enhancing productive traits through selective breeding while preserving genetic diversity to ensure the sustainable growth of the emu farming.

Evidence of Extensive Home Range Sharing Among Mother-Daughter Bobcat Pairs in the Wildland-Urban Interface of the Tucson Mountains.

Urbanization impacts the structure and viability of wildlife populations. Some habitat generalists, such as bobcats (Lynx rufus), maintain populations at the intersection of wild and urban habitats (wildland urban interface, WUI), but impacts of urbanization on bobcat social structure are not well understood. Although commonly thought to establish exclusive home ranges among females, instances of mother-daughter home range sharing have been documented. We combined GPS localities with genomic relatedness inferences from double-digest restriction site associated DNA sequencing (ddRADseq) to investigate mother-daughter home range sharing in bobcats (n = 38) at the WUI in the Tucson Mountains, Arizona, USA. We found the highest relatedness among females, which showed stronger isolation by distance than males and the population as a whole. Using mother-daughter relationships inferred from pedigree reconstruction, we found extensive mother-daughter home range sharing, compared to other females. Every mother identified as having at least one daughter, shared home ranges with one daughter, while other confirmed daughters established adjacent home ranges. Our results provide substantial support for the mother-daughter home range sharing hypothesis, as well as evidence of spatiotemporal overlap between mothers and daughters, adding to the body of research complicating the solitary felid paradigm. These results additionally challenge the notion of home range partitioning by prior rights land tenure, suggesting a role of matrilineal land tenure in home range establishment of daughters. Habitat fragmentation due to human population growth and urbanization thus has the potential to alter landscape genetic structure and social dynamics in bobcats.

Genetic diversity analysis and core collection construction of tea plant from the Yunnan Province of China using ddRAD sequencing

Tea plants are economically important woody plants that originated in southwestern China. The Yunnan Province in China is regarded as the central origin of tea plants owing to the abundance and diversity of the tea germplasm present in this region. However, there is a lack of knowledge regarding the genetic diversity and evolutionary relationships among tea plants in this region. Here, a total of 266,397 high-quality single nucleotide polymorphisms were obtained using double digest restriction-site associated DNA sequencing from 468 tea accessions collected from Yunnan. The phylogenetic relationship and population structure of the 468 tea accessions revealed remarkable inter- and intraspecific introgression across different sect. Thea species. We found that Camellia taliensis (W. W. Smith) Melchior is the main genetic donor that greatly contributed to the domestication of C. sinensis (L.) O. Kuntze, as evidenced by the frequent generation of genetic intermediates derived from the hybridization between C. sinensis and C. taliensis in Lincang, Xishuangbanna, and Pu’er. Notable genetic differences were observed across the populations from distinct regions of Yunnan. Additionally, the Lancang River may have attenuated the genetic interflow between Lincang and Pu’er. Finally, a core collection of 50 tea accessions was constructed based on the genetic diversity of the 468 tea accessions. Our results provide novel insights into the evolutionary and domestication history of tea plants in Yunnan Province and can facilitate the development of strategies for the conservation, breeding, and utilization of the core collection.

Seascape Genomics of the Smooth Hammerhead Shark Sphyrna zygaena Reveals Regional Adaptive Clinal Variation.

Globally, hammerhead sharks have experienced severe declines owing to continued overexploitation and anthropogenic change. The smooth hammerhead shark Sphyrna zygaena remains understudied compared to other members of the family Sphyrnidae. Despite its vulnerable status, a comprehensive understanding of its genetic landscape remains lacking in many regions worldwide. The present study aimed to conduct a fine-scale genomic assessment of Sphyrna zygaena within the highly dynamic marine environment of South Africa's coastline, using thousands of single nucleotide polymorphisms (SNPs) derived from restriction site-associated DNA sequencing (3RAD). A combination of differentiation-based outlier detection methods and genotype-environment association (GEA) analysis was employed in Sphyrna zygaena. Subsequent assessments of putatively adaptive loci revealed a distinctive south to east genetic cline. Among these, notable correlations between adaptive variation and sea-surface dissolved oxygen and salinity were evident. Conversely, analysis of 111,243 neutral SNP markers revealed a lack of regional population differentiation, a finding that remained consistent across various analytical approaches. These results provide evidence for the presence of differential selection pressures within a limited spatial range, despite high gene flow implied by the selectively neutral dataset. This study offers notable insights regarding the potential impacts of genomic variation in response to fluctuating environmental conditions in the circumglobally distributed Sphyrna zygaena.

Construction of a high-density genetic map and QTL mapping of growth traits in kiwifruit

Construction of a high-density genetic map and QTL mapping of growth traits in kiwifruit

Divergent Population Structure in Five Common Rockfish Species of Puget Sound, WA Suggests the Need for Species-Specific Management.

Quantifying connectivity between endangered or threatened marine populations is critical information for management and conservation, especially where abundance and productivity differ among such populations. Spatial patterns of such connectivity depend not only on extrinsic factors such as oceanography and bathymetry but also on intrinsic species-specific factors such as life history, demography and the location of glacial refugia. Nevertheless, population structure is often inferred from related or ecologically similar species. For example, the population structure in most rockfish species (Sebastes spp.) in the Salish Sea and the US West Coast is currently inferred from genetic data of three species that are known to hybridise in Puget Sound. Here, we determined the population structure and connectivity in five Puget Sound Rockfish species (Black [Sebastes melanops], Yellowtail [S. flavidus], Redstripe [S. proriger], Greenstriped [S. elongatus], and Puget Sound Rockfish [S. emphaeus]) from over 12,000 restriction-site associated DNA sequencing (RADseq) loci. We found species-specific patterns of genetic differentiation, attributable to both extrinsic and intrinsic factors. Specifically, Black and Puget Sound rockfishes showed no genetic differentiation; Yellowtail and Greenstriped rockfishes were structured according to known geographic barriers; and Redstripe Rockfish revealed evidence for temporal genetic differentiation, suggesting irregular recruitment influences population structure. Only Yellowtail Rockfish followed the federal DPS boundaries generally assumed for rockfish, further emphasizing the importance of species-specific management for the effective recovery and management of these rockfish populations and of marine species in general.

High Crimean-Congo hemorrhagic fever incidence linked to greater genetic diversity and differentiation in Hyalomma marginatum populations in Türkiye

BackgroundTicks are crucial vectors of a wide range of pathogens, posing significant threats to human and animal health globally. Understanding the genetic basis of tick biology and host–parasite interactions is essential for developing effective control programs. This study investigates the fine-scale genetic structure of Hyalomma marginatum Koch, 1844, the primary vector of Crimean-Congo hemorrhagic fever (CCHF) in Türkiye. Despite its significant public health importance, information regarding its population structure and genetic diversity is quite limited.MethodsWe used restriction site-associated DNA sequencing (RAD-Seq) to obtain genome-wide sequence data from 10 tick populations in Türkiye, collected from regions with low, moderate, and high incidence rates of CCHF. Based on these data, we determined population structure and diversity of populations using principal component analysis (PCA) and admixture analysis. Furthermore, we calculated pairwise FST and utilized discriminant analysis of principal components (DAPC) to understand genetic differentiation between populations.ResultsPCA and admixture analysis indicated minimal genetic structure between populations, but we detected notable genetic differentiation and high genetic diversity from regions with high CCHF rates. Furthermore, our DAPC identified 31 significant single-nucleotide polymorphisms (SNPs) associated with regions with high CCHF incidence, with 25 SNPs located near genes involved in critical biological functions such as nucleic acid binding, transmembrane transport, and proteolysis. These findings suggest that genetic variations in these regions may confer adaptive advantages in environments with high pathogen loads.ConclusionsThis study provides the first comprehensive analysis of H. marginatum genetic diversity in Türkiye, revealing significant differentiation in populations from CCHF-endemic regions. These results underscore the importance of considering fine-scale genetic diversity to fully understand the drivers of genetic variation in ticks and their implications for vectorial capacity.Graphical

Population connectivity of the European squid Loligo vulgaris along the West Iberian Peninsula coast: comparing mtDNA and SNPs

Understanding genetic diversity and population connectivity in marine organisms is essential for fisheries management. In the present study, we examined the population genetics of the European squid, Loligo vulgaris, along the western Iberian Peninsula at two genetic resolutions using the mitochondrial cytochrome oxidase subunit I gene (COI) and genomic markers obtained via double digest restriction-site associated DNA sequencing (ddRADseq). The results obtained revealed 79 haplotypes out of 160 COI sequences, while the SNP data set included 86,431 loci after filtering for 38 individuals with 86,319 neutral data. Mitochondrial COI analyses revealed high haplotype (0.961) and nucleotide (0.010) diversities, and the haplotype network reveals complex sub-structure in Turkish waters within a panmictic population. Both Tajima’s D and Fu’s Fs tests suggest that the population of L. vulgaris analysed is evolving neutrally. Pairwise Fst for neutral SNPs were low (0 < Fst<0.002) and not significant showing high homogeneity among populations, while pairwise comparations for candidate adaptive SNPs (112 loci) showed Fst values ranging from 0.026 to 0.234. While neutral SNPs showed admixture, the candidate adaptive SNPs showed a moderate significant structure with a latitudinal discrimination. Overall, both genetic approaches showed homogeneity and strong genetic flux identifying a unique population along the Western Iberian Peninsula.

Morphological and molecular data demonstrate the existence of Betula fruticosa and B. middendorffii and the absence of B. ovalifolia in northeastern China

Abstract Shrub birches are important components of massive wetlands in Northeast China, although much of these habitats have been lost over the past two decades. However, the taxonomy of shrub birches has been ambiguous owing to their morphological variation. In this study, we incorporated morphological and molecular data to address the taxonomic challenges associated with shrub birches. We characterized the morphological variation in the leaves, seeds, and bracts of 11 shrub birch populations in Northeast China and a population of Betula ovalifolia in northern Japan. We genotyped birch individuals from Northeast China at 15 microsatellite loci as well as a subset of individuals, using restriction site-associated DNA sequencing (RAD-seq). The populations in Northeast China consisted of B. fruticosa and B. middendorffii. These two species and B. ovalifolia differ in the width of their seed wings and the angle between the side lobes of their bracts, despite substantial intraspecific variation. Our genetic data revealed two distinct clusters, corresponding to B. fruticosa and B. middendorffii. Ploidy level assessment via RAD-seq revealed that B. fruticosa is diploid and B. middendorffii is tetraploid. Phylogenetic analysis revealed that B. fruticosa formed a sister clade to diploid B. humilis, and B. middendorffii formed a clade with diploid B. nana. Our results indicate the existence of B. fruticosa and B. middendorffii and the probable absence of B. ovalifolia in the northern Daxing’an Range, as all the tetraploid individuals sampled there represented B. middendorffii. In addition, our results suggest that B. humilis and B. nana may have served as diploid parents of the tetraploid species B. ovalifolia and B. middendorffii, respectively.

A pilot study to directly estimate radiation-induced mutation in large Japanese field mouse duo sample, mother and offspring, excluding unknown father, using ddRAD sequencing.

DNA mutations are one of the effects of radiation exposure. A large amount of radioactive materials was released into the environment from the Fukushima Daiichi Nuclear Power Plant after a major earthquake and tsunami. Wild animals and plants living in highly radiation-contaminated areas are constantly exposed to high doses of radiation, and concerns occur about its effects on their health and the next generations. As a pilot study, double-digest restriction site-associated DNA (ddRAD) sequencing was conducted to assess the incidence of mutations in wild large Japanese field mice collected from the evacuation area. The optimal combination of restriction enzymes, encompassing the functionally important coding regions, was selected using in silico analysis. These enzymes were used for ddRAD sequence analysis of females and their fetuses to evaluate mutation rates. The results indicated that no significant differences were observed in mutation rates between mothers and fetuses in the study areas.

Critically ill patients will benefit from single isolated laminar-air-flow wards by improving the environmental microbial composition

BackgroundHospital-associated infection (HAI) is an important issue in intensive care units (ICUs). We still lack direct evidence on whether the ICU patients and/or the medical system can benefit from single isolated laminar-air-flow (LAF) wards.MethodsHigh-touched-surface (HTS) swabs from 5 sites in two kinds of wards with different ventilation systems were longitudinally collected for 16 S rRNA sequencing and Type IIB restriction site-associated DNA sequencing for Microbiome (2bRAD-M). Samples were collected for 3 months. The clinical data of patients admitted to different wards during the sampling time and the whole year were collected and compared.ResultsThe α-diversity of single wards with isolated LAF was significantly higher than open regions without LAF (p<0.01). β-diversity analysis showed differences between different wards and similarities among the same region. We also identified 3 genera attributed to the most difference between the two kinds of wards. 2bRAD-M analysis further revealed community divergence among different HTS sites. There was an overlap between HTS microbiome profiling and the clinically cultivated pathogens of patients with HAI. People in single wards had a better outcome than those in open regions (p<0.05), indicating that single wards had a protective effect for critically ill patients.ConclusionOverall, there was a prominent difference in the microbiome community between single wards and open regions. Single wards had more balanced communities which may lead to better outcomes for patients. For critically ill patients, single ward is recommended when arranging and constructing.

Human Activity Changed the Genetic Pattern of the Orchid Phaius flavus Population

Human activity often has profound effects on plant growth and evolution. Orchids are the most diverse group of flowering plants and are threatened by habitat fragmentation, over-harvesting, and urbanization. A population of Phaius flavus from Beikengding Mount (BM) in the Fujian Province of China was divided into two patches by road construction. This study evaluated its genetic characteristics using restriction site-associated DNA sequencing (RAD-seq) data, more than seven years post-road construction. The purpose of this study was to explore the impact of road construction on the evolution of isolated patches within a population. The analysis revealed that the genetic diversity of patch B was slightly higher than that of patch A in the BM population of P. flavus. Principal component and phylogenetic analyses, genetic structure and genetic differentiation analysis, and bottleneck detection indicated relatively independent genetic differentiation between the two patches. Thus, the construction of the Y013 village road may have influenced different patches of this population on a genetic level. This study provides a case for understanding the impact of specific human activities on plant populations, and then biodiversity conservation. It is conducive to formulating more effective biological protection strategies to mitigate the damage inflicted by human activities on biodiversity.