Phylogenetic Clustering Research Articles

Genomic Analysis of Clostridioides difficile Recovered from Horses in Western Australia.

Clostridioides difficile poses an ongoing threat as a cause of gastrointestinal disease in humans and animals. Traditionally considered a human healthcare-related disease, increases in community-associated C. difficile infection (CDI) and growing evidence of inter-species transmission suggest a wider perspective is required for CDI control. In horses, C. difficile is a major cause of diarrhoea and life-threatening colitis. This study aimed to better understand the epidemiology of CDI in Australian horses and provide insights into the relationships between horse, human and environmental strains. A total of 752 faecal samples from 387 Western Australian horses were collected. C. difficile was isolated from 104 (30.9%) horses without gastrointestinal signs and 19 (37.8%) with gastrointestinal signs. Of these, 68 (55.3%) harboured one or more toxigenic strains, including C. difficile PCR ribotypes (RTs) 012 (n = 14), 014/020 (n = 10) and 087 (n = 7), all prominent in human infection. Whole-genome analysis of 45 strains identified a phylogenetic cluster of 10 closely related C. difficile RT 012 strains of equine, human and environmental origin (0-62 SNP differences; average 23), indicating recent shared ancestry. Evidence of possible clonal inter-species transmission or common-source exposure was identified for a subgroup of three horse and one human isolates, highlighting the need for a One Health approach to C. difficile surveillance.

Identification of taxon through classification with partial reject options

Abstract Identification of taxa can significantly be assisted by statistical classification based on trait measurements either individually or by phylogenetic (clustering) methods. In this article, we present a general Bayesian approach for classifying species individually based on measurements of a mixture of continuous and ordinal traits, and any type of covariates. The trait vector is derived from a latent variable with a multivariate Gaussian distribution. Decision rules based on supervised learning are presented that estimate model parameters through blocked Gibbs sampling. These decision regions allow for uncertainty (partial rejection), so that not necessarily one specific category (taxon) is output when new subjects are classified, but rather a set of categories including the most probable taxa. This type of discriminant analysis employs reward functions with a set-valued input argument, so that an optimal Bayes classifier can be defined. We also present a way of safeguarding against outlying new observations, using an analogue of a p-value within our Bayesian setting. We refer to our Bayesian set-valued classifier as the Karlsson–Hössjer method, and it is illustrated on an original ornithological data set of birds. We also incorporate model selection through cross-validation, exemplified on another original data set of birds.

Effects of evolutionary history on assembly of flowering plants in regions across Africa

The global cooling beginning in the Eocene has caused the coverage of tropical forests to contract from covering nearly all of Africa during the early Tertiary to about one tenth of Africa at the present time. Accompanying the climate cooling and drying was the evolution of traits tolerating cold and drought, particularly extreme drought in the Sahara. Here, we analyze a comprehensive data set of angiosperms to determine the effects of evolutionary history on assembly of angiosperms in regional floras in Africa. In particular, using phylogenetic metrics accounting for different depths of evolutionary history, we assess whether drought has caused stronger phylogenetic clustering relative to cold. We divided Africa into 27 regions, and collated species lists of angiosperms for each region. We used different phylogenetic metrics (tip‐ vs basal‐weighted) reflecting different evolutionary depths to quantify phylogenetic structure, and related phylogenetic structure metrics to climatic variables representing average, extreme and seasonality conditions of climate. Variations of phylogenetic structure across Africa were well explained by climate, with R2values being ~ 0.84 for each phylogenetic metric when all climatic variables used in this study were considered. Angiosperm assemblages with the strongest phylogenetic clustering are located in temperate regions, rather than in tropical desert regions of Africa. Minimum temperature explained much more variation in phylogenetic metrics than did minimum precipitation, suggesting that evolution of traits conferring cold tolerance is more phylogenetically constrained compared to those conferring drought tolerance. Temperature seasonality also explained much more variation in phylogenetic metrics than did precipitation seasonality. When mean annual temperature and precipitation are considered or when all temperature‐related variables and all precipitation‐related variables are considered, temperature variables are more important than precipitation variables in driving tip‐weighted phylogenetic structure of angiosperms in Africa but the pattern is reversed when basal‐weighted phylogenetic structure is considered.

A novel blight and root rot of chickpea: A new host for Neoscytalidiumdimidiatum

In the southeastern province of Mardin in Turkey, a severe and novel fungal infection affected all chickpea plant parts, resulting in blight symptoms on stem, petiole, branch, and leaf, defoliation, seed and root rot, and death. Neoscytalidium dimidiatum was identified as the agent responsible for this new blight and root rot using sequence analysis of the ITS, tef1, and tub2 loci as well as morphological data. The pathogen was found in all surveyed districts and fields, with varying incidences of blight and root rot, blight being nearly twice (40%) as common as root rot (21%), and root-rotted and blighted plants co-occurring in the majority of instances. All 92 N. dimidiatum isolates from various tissues induced necrotic lesions on the inoculated plants, indicating they were pathogenic for chickpea. Conidia exhibited germination across a temperature range, with increasing temperatures positively influencing germination rates, and mycelial growth was significantly influenced by temperature, with the optimal growth temperature observed to be 35 °C. The response of 25 Turkish chickpea cultivars and three other genotypes when subjected to inoculation with Ciar 12 and Ciar 78 isolates, representative of phylogenetic clusters, was evaluated based on the severity of blight and root rot. The majority of cultivars and genotypes displayed high susceptibility and suffered mortality when exposed to either soil or spray inoculation with each isolate. Among the assessed cultivars and genotypes, Çağatay had the lowest severity of root rot. This study is the first to report a natural infection of chickpea plants by N. dimidiatum. Under global warming, this may be detrimental to chickpea cultivation and habitat in southeastern Turkey, which is the origin of chickpeas.

Hepatitis C virus transmission between eight high-income countries among men who have sex with men: a whole-genome analysis

Microelimination of the hepatitis C virus (HCV) among men who have sex with men (MSM) could be complicated by continuous external introductions and the emergence of phylogenetic clusters harbouring clinically significant resistance-associated substitutions (RAS). To investigate international clustering and the prevalence and transmission of RAS, we aimed to analyse whole-genome HCV sequences from MSM with a recently acquired infection who participated in a large, international HCV treatment trial. For this whole-genome analysis, we obtained HCV sequences from 128 MSM who had acquired HCV within the past 12 months and were participating in the REACT trial. The participants from whom sequences were obtained were recruited at 24 sites in eight countries. We inferred maximum-likelihood phylogenies and identified transmission clusters for HCV genotypes separately. We constructed time-scaled phylogenies to estimate cluster introduction dates and used a Bayesian Skygrid approach to estimate the effective population size over the past 50 years. We calculated the prevalence of RAS and the extent of RAS transmission in the study population. The majority of recent HCV infections were part of international networks that arose in the late 1990s and early 2000s. Sequences obtained in the same country clustered frequently, and in 36% of subclusters since 2015 we found evidence of international transmission. European MSM were more likely than non-European MSM to be in a cluster (odds ratio 11·9 [95% CI 3·6-43·4], p<0·0001). The effective population size decreased rapidly since around 2015 in Europe. RAS associated with substantially diminished cure rates were infrequently detected and transmission of highly resistant viruses was not observed. Despite antiviral treatment becoming widely available, international transmission of HCV among MSM has still occurred over the past 8 years, which could complicate microelimination of the virus in this population. RAS-enriched clusters and widespread RAS transmission are currently not a threat to elimination goals. These findings support an international approach for HCV microelimination among MSM. National Institutes of Health and Dr. C.J. Vaillant Fonds.

Looking similar but all different: Phylogenetic signature of Brazilian rocky outcrops and the influence of temperature variability on their phylogenetic structure

Abstract Old, climatically buffered, infertile landscapes (OCBILs) have a disjunct yet wide distribution worldwide. Old lineages, rare and geographically restricted species, generally characterise these landscapes. Although the last decade provided evidence supporting the OCBIL theory, many studies are biased towards local scales, woody plants and specific OCBILs. Therefore, broad‐scale investigations across different types of OCBILs are needed. We used 5186 flowering plant species (woody and herbaceous) distributed across 129 rocky outcrop sites in Brazil to investigate (1) the relative influence of climate on the phylogenetic diversity and structure of OCBILs; (2) their phylogenetic signature; (3) whether vegetation type influences phylogenetic diversity and structure of OCBILs after controlling for climate; and (4) the OCBILs' evolutionary median community age. We found that rocky outcrops exhibit lower than expected phylogenetic diversity and are home to plant communities composed of closely related species (i.e. phylogenetic clustering) relative to the reference species pool, primarily due to temperature seasonality. Each rocky outcrop shows a distinct phylogenetic signature, indicated by plant families with more descendant species than expected by chance. Even after controlling for climate, phylogenetic diversity and structure remain low and clustered in most rocky outcrops. The median community age estimated at the species level is lower in campos de altitude than in other rocky outcrops. Synthesis. We show that the influence of climate seasonality is pervasive in the phylogenetic diversity and structure of Brazilian rocky outcrops at different taxonomic levels. We also show that the phylogenetic signature of rocky outcrops comprises a mix of relatively old and young overrepresented plant families whose descendants contribute to their low phylogenetic diversity and phylogenetic clustering. Overall, the combination of low phylogenetic diversity, phylogenetic clustering and comparably low median community age across Brazilian rocky outcrops indicates that, on average, these OCBILs are subjected to strong environmental constraints and serve as arenas of recent diversification rather than a steady accumulation of taxa. Therefore, these findings indicate different OCBILs as hotspots for various plant lineages and species.

Canine Distemper Virus Infection in the Free-Living Wild Canines, the Red Fox (Vulpes vulpes) and Jackal (Canis aureus moreoticus), in Croatia.

The canine distemper virus (CDV), a paramyxovirus that is closely related to the human measles virus and rinderpest virus of cattle, is a highly contagious viral disease in dogs and wild carnivores worldwide. CDV represents a serious threat to domestic and wild animals, especially to the conservation of endangered wild carnivores. Our study aims to investigate the occurrence of CDV in free-living wild canines in Croatia. For this purpose, 176 red foxes and 24 jackal brain samples collected in the frame of the active surveillance of rabies during winter 2021/2022 were tested. This study provided the first comprehensive overview of the prevalence and spatial distribution of CDV in the wildlife of Croatia, including the molecular phylogenetic analysis of the H gene sequence of field CDV strains circulating in red fox and jackal populations of Croatia. The molecular characterization of hemagglutinin gene genomic regions confirmed the phylogenetic clustering of obtained sequences into the Europa 1 genotype. The obtained CDV red fox sequences were mutually very similar (97.60%). This study indicates the high genetic similarity of Croatian CDV red fox sequences and CDV red fox sequences from Italy and Germany, badger sequences from Germany, polecat sequences from Hungary, and dog sequences from Hungary and Germany.

Geographic distribution of C4 species and its phylogenetic structure across China

Over the past fifty years, the distribution patterns of C 4 species, across large spatial scales, are largely ignored. Here, we endeavored to examine patterns in the taxonomic and phylogenetic diversity of species with C 4 photosynthetic pathways across the broad spatial extent of China and relate those to climatic gradients. We built a database of all plants with the C 4 photosynthetic pathway in China. We analyzed the geographic distributions, taxonomic diversity, phylogenetic diversity, and phylogenetic structure of all C 4 species, as well as the three families with the most C 4 species (Poaceae, Amaranthaceae and Cyperaceae), and compared their values along temperature and precipitation gradients at two scales—the level of the province and at the 100 x 100 km grid cell. We found 644 C 4 plants (belonging to 23 families 165 genera) in China, with Poaceae (57%), Amaranthaceae (17%), Cyperaceae (13%) accounting for the majority of species. Standardized effect size values of phylogenetic distances were negative overall, indicating that C 4 species showed a phylogenetic clustering pattern. Southern China had the highest species richness and the highest degree of phylogenetic clustering. C 4 tended to be more phylogenetically over-dispersed in regions with colder and/or drier climates, but more clustered in warmer and/or wetter climates. Patterns within individual families were more nuanced. The distribution of C 4 species and its phylogenetic structure across China was constrained by temperature and precipitation. C 4 species showed a phylogenetic clustering pattern across China, while different families showed more nuanced responses to climate variation, suggesting a role for evolutionary history.

Functional Diversity of Homologous Oxidoreductases-Tuning of Substrate Specificity by a FAD-Stacking Residue for Iron Acquisition and Flavodoxin Reduction.

Although bacterial thioredoxin reductase-like ferredoxin/flavodoxin NAD(P)+ oxidoreductases (FNRs) are similar in terms of primary sequences and structures, they participate in diverse biological processes by catalyzing a range of different redox reactions. Many of the reactions are critical for the growth, survival of, and infection by pathogens, and insight into the structural basis for substrate preference, specificity, and reaction kinetics is crucial for the detailed understanding of these redox pathways. Bacillus cereus (Bc) encodes three FNR paralogs, two of which have assigned distinct biological functions in bacillithiol disulfide reduction and flavodoxin (Fld) reduction. Bc FNR2, the endogenous reductase of the Fld-like protein NrdI, belongs to a distinct phylogenetic cluster of homologous oxidoreductases containing a conserved His residue stacking the FAD cofactor. In this study, we have assigned a function to FNR1, in which the His residue is replaced by a conserved Val, in the reduction of the heme-degrading monooxygenase IsdG, ultimately facilitating the release of iron in an important iron acquisition pathway. The Bc IsdG structure was solved, and IsdG-FNR1 interactions were proposed through protein-protein docking. Mutational studies and bioinformatics analyses confirmed the importance of the conserved FAD-stacking residues on the respective reaction rates, proposing a division of FNRs into four functionally unique sequence similarity clusters likely related to the nature of this residue.

Capturing patterns of evolutionary relatedness with reflectance spectra to model and monitor biodiversity

Biogeographic history can set initial conditions for vegetation community assemblages that determine their climate responses at broad extents that land surface models attempt to forecast. Numerous studies have indicated that evolutionarily conserved biochemical, structural, and other functional attributes of plant species are captured in visible-to-short wavelength infrared, 400 to 2,500 nm, reflectance properties of vegetation. Here, we present a remotely sensed phylogenetic clustering and an evolutionary framework to accommodate spectra, distributions, and traits. Spectral properties evolutionarily conserved in plants provide the opportunity to spatially aggregate species into lineages (interpreted as "lineage functional types" or LFT) with improved classification accuracy. In this study, we use Airborne Visible/Infrared Imaging Spectrometer data from the 2013 Hyperspectral Infrared Imager campaign over the southern Sierra Nevada, California flight box, to investigate the potential for incorporating evolutionary thinking into landcover classification. We link the airborne hyperspectral data with vegetation plot data from 1372 surveys and a phylogeny representing 1,572 species. Despite temporal and spatial differences in our training data, we classified plant lineages with moderate reliability (Kappa = 0.76) and overall classification accuracy of 80.9%. We present an assessment of classification error and detail study limitations to facilitate future LFT development. This work demonstrates that lineage-based methods may be a promising way to leverage the new-generation high-resolution and high return-interval hyperspectral data planned for the forthcoming satellite missions with sparsely sampled existing ground-based ecological data.

Global patterns of phylogenetic relatedness of invasive flowering plants

AbstractAimThe ability of predicting which naturalized non‐native species are likely to become invasive can help manage and prevent species invasions. The goal of this study is to test whether invasive angiosperm (flowering plant) species are a phylogenetically clustered subset of naturalized species at global, continental and regional scales, and to assess the relationships of phylogenetic relatedness of invasive species with climate condition (temperature and precipitation).LocationGlobal.Time periodCurrent.TaxonAngiosperms (flowering plants).MethodsThe globe is divided into 290 regions, which are grouped into seven biogeographic (continental) regions. Two phylogenetic metrics (net relatedness index and nearest taxon index), which represent different evolutionary depths, are used to quantify phylogenetic relatedness of invasive angiosperms, with respect to different tailor‐made species pools. Phylogenetic relatedness of invasive angiosperms is related to climatic variables.ResultsThe global assemblage of invasive angiosperm species is a strongly phylogenetically clustered subset of the species of the entire global angiosperm flora. Most invasive angiosperm assemblages are a phylogenetically clustered subset of their respective naturalized species pools, and phylogenetic clustering reflecting shallow evolutionary history is greater than that reflecting deep evolutionary history. In general, the phylogenetic relatedness of invasive species is greater in regions with lower temperature and precipitation across the world.Main conclusionsThe finding that invasive angiosperm assemblages across the globe are, in general, phylogenetically clustered subsets of their respective naturalized species pools has significant implications in biological conservation, particularly in predicting and controlling invasive species based on phylogenetic relatedness among naturalized species.

Comparison of predicted T cell epitopes in porcine circovirus type 2 isolates from 2017 to 2021 and selected vaccines (EpiCC analysis) confirms the global relevance of a bivalent vaccine approach

Porcine circovirus type 2 (PCV2) is a globally important pathogen of swine with a high capacity for genetic change, potentially including evolution of strains less susceptible to vaccine induced immunity. Starting with DNA sequences, in silico tools can be used to predict the T cell epitope content of the PCV2 capsid protein in vaccines and field strains, allowing calculation of Epitope Content Comparison (EpiCC) scores reflecting the number of T-cell epitopes held in common. Previous work has shown that a bivalent PCV2a and PCV2b vaccine gave greater T cell epitope coverage (higher EpiCC scores) than either PCV2a or PCV2b as a monovalent, with the more complete match potentially helping to preserve or enhance vaccine efficacy. This study extends the above, using refined methodology to compare the putative T-cell epitope content of 4 PCV2 vaccines (3 based on PCV2a, and one a PCV2a and PCV2b bivalent) to a larger and more contemporary global sample of PCV2 field strains. 746 PCV2, ORF2 nucleotide sequences from diagnostic submissions dating from 2017 to 2021 were included. These comprised PCV2a (129), PCV2b (109) and PCV2d (508), and originated from Asia (185), Europe (269), North America (235) and South America (57). Phylogenetic classification confirmed the predominance of PCV2d in all regions, but with continuing presence of PCV2a and PCV2b. An interesting regional divergence was noted for PCV2a, with all strains from Europe grouped within a single phylogenetic cluster (cluster 10) and all but one from North America being in a different phylogenetic cluster (cluster 6). EpiCC scores for the bivalent vaccine were significantly higher than for the monovalents for all genotypes in all regions, showing the global relevance of the bivalent approach. Calculation of the relative contributions of the PCV2a and PCV2b components showed that, while most T-cell epitopes were present in both, each also made substantial unique contributions. Of most practical relevance, given that most commercial vaccines are based on PCV2a, the addition of PCV2b increased T-cell epitope coverage by 33% and 21% for PCV2b and PCV2d respectively.

The microbiome of buried soils demonstrates significant shifts in taxonomic structure and a general trend towards mineral horizons

Burial mounds represent a challenge for microbiologists. Could ancient buried soils preserve microbiomes as they do archaeological artifacts? To investigate this question, we studied the soil microbiome under a burial mound dating from 2500 years ago in Western Kazakhstan. Two soil profile cuts were established: one under the burial mound and another adjacent to the mound surface steppe soil. Both soils represented the same dark chestnut soil type and had the same horizontal stratification (A, B, C horizons) with slight alterations. DNA samples isolated from all horizons were studied with molecular techniques including qPCR and high throughput sequencing of amplicon libraries of the 16S rRNA gene fragment. The taxonomic structure of the microbiome of the buried horizons demonstrated a deep divergence from ones of the surface, comparable to the variation between different soil types (representatives of the soil types were included in the survey). The cause of this divergence could be attributed to diagenetic processes characterized by the reduction of organic matter content and changes in its structure. Corresponding trends in the microbiome structure are obvious from the beta-diversity pattern: the A and B horizons of the buried soils form one cluster with the C horizons of both buried and surface soil. This trend could generally be designated as ‘mineralization’. Statistically significant changes between the buried and surface soils microbiomes were detected in the number of phylogenetic clusters, the biology of which is in the line of diagenesis. The trend of ‘mineralization’ was also supported by PICRUSt2 functional prediction, demonstrating a higher occurrence of the processes of degradation in the buried microbiome. Our results show a profound shift in the buried microbiome relatively the “surface” microbiome, indicating the deep difference between the original and buried microbiomes.

Molecular Assessment of Kappaphycus alvarezii Cultivated in Tarakan based on cox2-3 Spacer

The seaweed Kappaphycus alvarezii is a leading aquaculture commodity possessing high economic value that has been used as a raw material for various natural products, food, and pharmaceutical industries. The main challenge regarding its production, escpecially in Tarakan is the supply of superior seeds. Therefore, this study aims to obtain phylogenetic information and the cultivation performance of the selected seeds by identifying genetic sources based on molecular markers. DNA sequencing analysis was carried out using the molecular marker cox2-3 spacer on a collection comprising 16 cultivars from all over the country (Indonesia). The four haplotypes representing K. alvarezii to be cultivated in the city were produced by phylogenetic clustering and further molecular analysis using cox2-3 intergenic spacer mitochondrial DNA marker. These include the Kupang varieties and Natuna, also referred to as Lampung seedlings, which is a tissue culture plantlet used for development at SEAMEO-BIOTROP Bogor and propagated by the Lampung Marine Aquaculture Center (BBPBL), Tarakan. These varieties were genetically distances (pairwise comparisons based on mean Kimura 2-parameter model) ranging from 0.00-0.23 unit. The cultivation was carried out for 30 days in the waters of Tanjung Batu (Tj. Batu) Mamburungan, Tarakan, North Kalimantan, for 30 days. The result showed that the Natuna* as Lampung cultivar has superior performance compared to local cultivars (Takalar as Mamburungan Tanjung Batu, Tarakan, and Kupang). Furthermore, the genetic analysis with cox2-3 spacer markers had the potential as an effective seed selection tool for tracing genetic information in the development of superior seedlings in aquaculture activities.

Molecular Assessment of Kappaphycus alvarezii Cultivated in Tarakan based on cox2-3 Spacer

The seaweed Kappaphycus alvarezii is a leading aquaculture commodity possessing high economic value that has been used as a raw material for various natural products, food, and pharmaceutical industries. The main challenge regarding its production, escpecially in Tarakan is the supply of superior seeds. Therefore, this study aims to obtain phylogenetic information and the cultivation performance of the selected seeds by identifying genetic sources based on molecular markers. DNA sequencing analysis was carried out using the molecular marker cox2-3 spacer on a collection comprising 16 cultivars from all over the country (Indonesia). The four haplotypes representing K. alvarezii to be cultivated in the city were produced by phylogenetic clustering and further molecular analysis using cox2-3 intergenic spacer mitochondrial DNA marker. These include the Kupang varieties and Natuna, also referred to as Lampung seedlings, which is a tissue culture plantlet used for development at SEAMEO-BIOTROP Bogor and propagated by the Lampung Marine Aquaculture Center (BBPBL), Tarakan. These varieties were genetically distances (pairwise comparisons based on mean Kimura 2-parameter model) ranging from 0.00-0.23 unit. The cultivation was carried out for 30 days in the waters of Tanjung Batu (Tj. Batu) Mamburungan, Tarakan, North Kalimantan, for 30 days. The result showed that the Natuna* as Lampung cultivar has superior performance compared to local cultivars (Takalar as Mamburungan Tanjung Batu, Tarakan, and Kupang). Furthermore, the genetic analysis with cox2-3 spacer markers had the potential as an effective seed selection tool for tracing genetic information in the development of superior seedlings in aquaculture activities.

Integrated analysis of how gender and body weight affect the intestinal microbial diversity of Gymnocypris chilianensis

Intestinal microorganisms that living in the mucosa and contents of the gastrointestinal tract of animals, have close links with their hosts over a long evolutionary history. The community structure of the fish intestinal microbiota is associated with food, living environment, and the growth stage. To screen for potential probiotics that can be used for regulating breeding behaviors, this study focused on the diversity of fish intestinal microorganisms. This study aimed to investigate the effects of sex and body weight on the intestinal microbial diversity of Gymnocypris chilianensis in the wild. The results showed that the significant high diversity and richness of intestinal microbiota were fould in heavier individuals, and males. The dominant bacterial phyla of G. chilianensis were Proteobacteria, Firmicutes, and Bacteroidetes. In addition, the abundance of Firmicutes varied significantly among different body weights. The genus profile revealed that small individuals were dominated by Weissella, while females were dominated by Aeromonas, and both large individuals and males were dominated by other genera. Phylogenetic relationships and UPGMA clustering analysis showed significant differences among the groups. In general, the two main factors that have an effect on the intestinal microbiota diversity of wild G. chilianensis are sex and body weight.

Seasonal and spatial dynamics of phylogenetic structure of fish communities in coastal waters

Understanding community assembly has long attracted the attention of ecologists. There are a lot of studies on how community assembly mechanisms work through phylogenetic analysis. Nevertheless, phylogenetic structures have generally been assumed to be stable over time in most studies, and little attention has been paid to seasonal shifts in phylogenetic structure, which is important to mobile animals. In this study, phylogenetic distance was measured as the mean pairwise distance (MPD) and as mean nearest taxon distance (MNTD). The phylogenetic structures of fish communities in different regions, subregions and at sampling stations were examined using the standardized effect sizes of MPD and MNTD (SES.MPD and SES.MNTD) under null model independent swap over four seasons in the coastal waters of Shandong Province, China. Generalized additive model (GAM) was used to detect which environmental factors have an important impact on phylogenetic structure indices at each sampling station. The fish communities were phylogenetically clustered in most seasons in the whole survey waters, indicating environmental filtering tended to shape the whole fish assemblage. Two phylogenetic indices indicated that the phylogenetic structure (phylogenetic over-dispersion or phylogenetic clustering) was inconsistent on the different regions and subregions. For fish assemblages at each sampling station, the phylogenetic structure of fish communities presented patchy distribution patterns in different seasons. GAM analysis showed that phylogenetic structure responded differently to different environmental factors over four seasons, and the change in phylogenetic structure indices was significantly associated with environmental factors, especially in autumn and winter. SES.MPD can better respond to environmental changes than SES.MNTD. Spatial factors (longitude and latitude) were important factors influencing fish community assembly, indicating that fish communities at offshore stations with low latitude exhibit a relatively high degree of phylogenetic overdispersion. It was difficult to draw consistent conclusions about seasonal changes in phylogenetic structure of fish communities on different temporal and spatial scales. It is possible that seasonal variations and spatial scales in assembly mechanisms contribute to maintaining marine fish diversity in temperate waters, resulting in different phylogenetic structures in fish community.

Mutation rates and adaptive variation among the clinically dominant clusters of Mycobacterium abscessus

Mycobacterium abscessus (Mab) is a multidrug-resistant pathogen increasingly responsible for severe pulmonary infections. Analysis of whole-genome sequences (WGS) of Mab demonstrates dense genetic clustering of clinical isolates collected from disparate geographic locations. This has been interpreted as supporting patient-to-patient transmission, but epidemiological studies have contradicted this interpretation. Here, we present evidence for a slowing of the Mab molecular clock rate coincident with the emergence of phylogenetic clusters. We performed phylogenetic inference using publicly available WGS from 483 Mab patient isolates. We implement a subsampling approach in combination with coalescent analysis to estimate the molecular clock rate along the long internal branches of the tree, indicating a faster long-term molecular clock rate compared to branches within phylogenetic clusters. We used ancestry simulation to predict the effects of clock rate variation on phylogenetic clustering and found that the degree of clustering in the observed phylogeny is more easily explained by a clock rate slowdown than by transmission. We also find that phylogenetic clusters are enriched in mutations affecting DNA repair machinery and report that clustered isolates have lower spontaneous mutation rates in vitro. We propose that Mab adaptation to the host environment through variation in DNA repair genes affects the organism's mutation rate and that this manifests as phylogenetic clustering. These results challenge the model that phylogenetic clustering in Mab is explained by person-to-person transmission and inform our understanding of transmission inference in emerging, facultative pathogens.

Spatial genetic structure of 2009 H1N1 pandemic influenza established as a result of interaction with human populations in mainland China.

Identifying the spatial patterns of genetic structure of influenza A viruses is a key factor for understanding their spread and evolutionary dynamics. In this study, we used phylogenetic and Bayesian clustering analyses of genetic sequences of the A/H1N1pdm09 virus with district-level locations in mainland China to investigate the spatial genetic structure of the A/H1N1pdm09 virus across human population landscapes. Positive correlation between geographic and genetic distances indicates high degrees of genetic similarity among viruses within small geographic regions but broad-scale genetic differentiation, implying that local viral circulation was a more important driver in the formation of the spatial genetic structure of the A/H1N1pdm09 virus than even, countrywide viral mixing and gene flow. Geographic heterogeneity in the distribution of genetic subpopulations of A/H1N1pdm09 virus in mainland China indicates both local to local transmission as well as broad-range viral migration. This combination of both local and global structure suggests that both small-scale and large-scale population circulation in China is responsible for viral genetic structure. Our study provides implications for understanding the evolution and spread of A/H1N1pdm09 virus across the population landscape of mainland China, which can inform disease control strategies for future pandemics.

Genetic differences of dengue virus 2 in patients with distinct clinical outcome.

The genetic diversity of the dengue virus is characterized by four circulating serotypes, several genotypes, and an increasing number of existing lineages that may have differences in the potential to cause epidemics and disease severity. Accurate identification of the genetic variability of the virus is essential to identify lineages responsible for an epidemic and understanding the processes of virus spread and virulence. Here, we characterize, using portable nanopore genomic sequencing, different lineages of dengue virus 2 (DENV-2) detected in 22 serum samples from patients with and without dengue warning signs attended at Hospital de Base of São José do Rio Preto (SJRP) in 2019, during a DENV-2 outbreak. Demographic, epidemiological, and clinical data were also analyzed. The phylogenetic reconstruction and the clinical data showed that two lineages belonging to the American/Asian genotype of DENV-2-BR3 and BR4 (BR4L1 and BR4L2)-were co-circulating in SJRP. Although preliminary, these results indicate no specific association between clinical form and phylogenetic clustering at the virus consensus sequence level. Studies with larger sample sizes and which explore single nucleotide variants are needed. Therefore, we showed that portable nanopore genome sequencing could generate quick and reliable sequences for genomic surveillance to monitor viral diversity and its association with disease severity as an epidemic unfolds.