Distribution Of Clades Research Articles

Distribution and Variation of Serotypes and Pneumococcal Surface Protein A Clades of Streptococcus pneumoniae Strains Isolated From Adult Patients With Invasive Pneumococcal Disease in Japan.

Pneumococcal surface protein A (PspA) is a surface protein of Streptococcus pneumoniae that may be a candidate antigen for new pneumococcal vaccines. This study investigates the distribution of PspA clades of the causative strains of adult invasive pneumococcal disease (IPD) in Japan. Of the 1,939 strains isolated from cases of adult IPD during 2014–2019, the PspA clades of 1,932 (99.6%) strains were determined, and no pspA was detected in the remaining 7 strains (0.4%). PspA clades 1–6 were detected in 786 (40.5%), 291 (15.0%), 443 (22.8%), 369 (19.0%), 33 (1.7%), and 6 (0.3%) strains, respectively. New PspA clades (0.2%) were identified in two non-typeable and two serotype 35B pneumococci. The proportions of clade 1 and clade 2 showed significantly decreased and increased trends, respectively. Furthermore, the PspA clade of pneumococcal strains was partially serotype- and sequence type-dependent. The majority of strains belonging to serotypes contained in both the 13-valent pneumococcal conjugate vaccine (PCV13) and the 23-valent pneumococcal polysaccharide vaccine (PPSV23) belonged to PspA clades 1 or 3. In contrast, the distribution of clades in non-vaccine serotypes was wider than that of vaccine serotype pneumococci. Our findings demonstrate that almost all pneumococcal strains from adult IPD express PspA clades 1–4, especially for non-vaccine serotypes. These results may be useful for the development of a new pneumococcal vaccine with PspA.

Reconstructing Squamate Biogeography in Afro-Arabia Reveals the Influence of a Complex and Dynamic Geologic Past.

The geographic distribution of biodiversity is central to understanding evolutionary biology. Paleogeographic and paleoclimatic histories often help to explain how biogeographic patterns unfold through time. However, such patterns are also influenced by a variety of other factors, such as lineage diversification, that may affect the probability of certain types of biogeographic events. The complex and well-known geologic and climatic history of Afro-Arabia, together with the extensive research on reptile systematics in the region, makes Afro-Arabian squamate communities an ideal system to investigate biogeographic patterns and their drivers. Here, we reconstruct the phylogenetic relationships and the ancestral geographic distributions of several Afro-Arabian reptile clades (totaling 430 species) to estimate the number of dispersal, vicariance and range contraction events. We then compare the observed biogeographic history to a distribution of simulated biogeographic events based on the empirical phylogeny and the best-fit model. This allows us to identify periods in the past where the observed biogeographic history was likely shaped by forces beyond the ones included in the model. We find an increase in vicariance following the Oligocene, most likely caused by the fragmentation of the Afro-Arabian plate. In contrast, we did not find differences between observed and expected dispersal and range contraction levels. This is consistent with diversification enhanced by environmental processes and with the establishment of a dispersal corridor connecting Africa, Arabia and Eurasia since the middle Miocene. Finally, here we show that our novel approach is useful to pinpoint events in the evolutionary history of lineages that might reflect external forces not predicted by the underlying biogeographic model. [Dispersal; diversification; model adequacy; paleogeography; reptiles; simulations; vicariance.]

Phylogenetic paleoecology: macroecology within an evolutionary framework

The burgeoning field of phylogenetic paleoecology (Lamsdell et al. 2017) represents a synthesis of the related but differently focused fields of macroecology (Brown 1995) and macroevolution (Stanley 1975). Through a combination of the data and methods of both disciplines, phylogenetic paleoecology leverages phylogenetic theory and quantitative paleoecology to explain the temporal and spatial variation in species diversity, distribution, and disparity. Phylogenetic paleoecology is ideally situated to elucidate many fundamental issues in evolutionary biology, including the generation of new phenotypes and occupation of previously unexploited environments; the nature of relationships among character change, ecology, and evolutionary rates; determinants of the geographic distribution of species and clades; and the underlying phylogenetic signal of ecological selectivity in extinctions and radiations. This is because phylogenetic paleoecology explicitly recognizes and incorporates the quasi-independent nature of evolutionary and ecological data as expressed in the dual biological hierarchies (Eldredge and Salthe 1984; Congreve et al. 2018; Fig. 1), incorporating both as covarying factors rather than focusing on one and treating the other as error within the dataset.

Genomic Surveillance of SARS-CoV-2: Distribution of Clades in the Republic of Korea in 2020.

Since a novel beta-coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was first reported in December 2019, there has been a rapid global spread of the virus. Genomic surveillance was conducted on samples isolated from infected individuals to monitor the spread of genetic variants of SARS-CoV-2 in Korea. The Korea Disease Control and Prevention Agency performed whole genome sequencing of SARS-CoV-2 in Korea for 1 year (January 2020 to January 2021). A total of 2,488 SARS-CoV-2 cases were sequenced (including 648 cases from abroad). Initially, the prevalent clades of SARS-CoV-2 were the S and V clades, however, by March 2020, GH clade was the most dominant. Only international travelers were identified as having G or GR clades, and since the first variant 501Y.V1 was identified (from a traveler from the United Kingdom on December 22nd, 2020), a total of 27 variants of 501Y.V1, 501Y.V2, and 484K.V2 have been classified (as of January 25th, 2021). The results in this study indicated that quarantining of travelers entering Korea successfully prevented dissemination of the SARS-CoV-2 variants in Korea.

Insight into early diversification of leucine-rich repeat receptor-like kinases provided by the sequenced moss and hornwort genomes.

Identification of the subfamily X leucine-rich repeat receptor-like kinases in the recently sequenced moss and hornwort genomes points to their diversification into distinct groups during early evolution of land plants. Signal transduction mediated through receptor-ligand interactions plays key roles in controlling developmental and physiological processes of multicellular organisms, and plants employ diverse receptors in signaling. Leucine-rich repeat receptor-like kinases (LRR-RLKs) represent one of the largest receptor classes in plants and are structurally classified into subfamilies. LRR-RLKs of the subfamily X are unique in the variety of their signaling roles; they include receptors for steroid or peptide hormones as well as negative regulators of signaling through binding to other LRR-RLKs, raising a question as to how they diversified. However, our understanding of diversification processes of LRR-RLKs has been hindered by the paucity of genomic data in non-seed plants and limited taxa sampling in previous phylogenetic analyses. Here we analyzed the phylogeny of LRR-RLK X sequences collected from all major land plant lineages and show that this subfamily diversified into six major clades before the divergence between bryophytes and vascular plants. Notably, we have identified homologues of the brassinosteroid receptor, BRASSINOSTEROID INSENSITIVE 1 (BRI1), in the genomes of Sphagnum mosses, hornworts, and ferns, contrary to earlier reports that postulate the origin of BRI1-like LRR-RLKs in the seed plant lineage. The phylogenetic distribution of major clades illustrates that the current receptor repertoire was shaped through lineage-specific gene family expansion and independent gene losses, highlighting dynamic changes in the evolution of LRR-RLKs.

Phylodynamic Pattern of Genetic Clusters, Paradigm Shift on Spatio-Temporal Distribution of Clades, and Impact of Spike Glycoprotein Mutations of SARS-CoV-2 Isolates from India.

Introduction:The COVID-19 pandemic is associated with high morbidity and mortality, with the emergence of numerous variants. The dynamics of SARS-CoV-2 with respect to clade distribution is uneven, unpredictable and fast changing.Methods:Retrieving the complete genomes of SARS-CoV-2 from India and subjecting them to analysis on phylogenetic clade diversity, Spike (S) protein mutations and their functional consequences such as immune escape features and impact on infectivity. Whole genome of SARS-CoV-2 isolates (n = 4,326) deposited from India during the period from January 2020 to December 2020 is retrieved from Global Initiative on Sharing All Influenza Data (GISAID) and various analyses performed using in silico tools.Results:Notable clade dynamicity is observed indicating the emergence of diverse SARS-CoV-2 variants across the country. GR clade is predominant over the other clades and the distribution pattern of clades is uneven. D614G is the commonest and predominant mutation found among the S-protein followed by L54F. Mutation score prediction analyses reveal that there are several mutations in S-protein including the RBD and NTD regions that can influence the virulence of virus. Besides, mutations having immune escape features as well as impacting the immunogenicity and virulence through changes in the glycosylation patterns are identified.Conclusions:The study has revealed emergence of variants with shifting of clade dynamics within a year in India. It is shown uneven distribution of clades across the nation requiring timely deposition of SARS-CoV-2 sequences. Functional evaluation of mutations in S-protein reveals their significance in virulence, immune escape features and disease severity besides impacting therapeutics and prophylaxis.

Reconstructions of the past distribution of Testudo graeca mitochondrial lineages in the Middle East and Transcaucasia support multiple refugia since the Last Glacial Maximum

A cycle of glacial and interglacial periods in the Quaternary caused species’ ranges to expand and contract in response to climatic and environmental changes. During interglacial periods, many species expanded their distribution ranges from refugia into higher elevations and latitudes. In the present work, we projected the responses of the five lineages of Testudo graeca in the Middle East and Transcaucasia as the climate shifted from the Last Glacial Maximum (LGM, Mid – Holocene), to the present. Under the past LGM and Mid-Holocene bioclimatic conditions, models predicted relatively more suitable habitats for some of the lineages. The most significant bioclimatic variables in predicting the present and past potential distribution of clades are the precipitation of the warmest quarter for T. g. armeniaca (95.8 %), precipitation seasonality for T. g. buxtoni (85.0 %), minimum temperature of the coldest month for T. g. ibera (75.4 %), precipitation of the coldest quarter for T. g. terrestris (34.1 %), and the mean temperature of the driest quarter for T. g. zarudyni (88.8 %). Since the LGM, we hypothesise that the ranges of lineages have either expanded (T. g. ibera), contracted (T. g. zarudnyi) or remained stable (T. g. terrestris), and for other two taxa (T. g. armeniaca and T. g. buxtoni) the pattern remains unclear. Our analysis predicts multiple refugia for Testudo during the LGM and supports previous hypotheses about high lineage richness in Anatolia resulting from secondary contact.

Elevational shifts in phylogenetic diversity of angiosperm trees across the subtropical Brazilian Atlantic Forest

AbstractElevation gradients are drivers of species diversity, and, recently, studies have considered the evolutionary process in shaping community assembly patterns. Patterns of plant species richness across elevational gradients have been studied in different parts of the Atlantic Forest; however, little is known about plant phylogenetic diversity patterns. Thus, we aimed to analyse the phylogenetic diversity of angiosperm trees along an elevation gradient in southern Brazilian Plateau, in the subtropical portion of the Atlantic Forest. We expected a decrease in phylogenetic diversity along the elevation gradient, from lowlands towards to highlands, where species may be evolutionary closely related as many tropical lineages are not capable to inhabit colder conditions. We also investigated the distribution of phylogenetic clades along the elevation gradient through principal coordinates of phylogenetic structure. Data were obtained from 28 phytosociological surveys distributed across different elevation levels, ranging from 40 to 975 m. We found a negative association between phylogenetic diversity and the elevation gradient. The representativeness of families Myrtaceae and Lauraceae increased with elevation, while most of the families decreased in species richness and are replaced by temperate families such as Winteraceae (Drimys) in higher elevations. The decrease in phylogenetic diversity with increasing elevation may be linked to niche conservatism of tropical lineages that retain their historical climatic niches and thus many species are not capable to inhabit colder environments. Most tropical clades are restricted to lower elevations; however, Myrtaceae and Lauraceae probably evolved tolerance to colder temperatures during glacial cycles. Furthermore, the probably long‐term climate stability in lowlands than highland areas may have promoted the co‐occurrence of distantly related species, resulting in higher phylogenetic diversity. Finally, we observed how historical imprints and current environmental conditions shape the phylogenetic diversity of angiosperm tree species in subtropical Atlantic Forest.

A review of soft corals (Octocorallia: Alcyonacea) and their symbionts: Distribution of clades and functionality

Even though soft corals are an integral part of the coral reef ecosystem, very little research has focused on theirendosymbiotic association with the zooxanthellae (Symbiodiniaceae). Symbiotic algae appear in soft corals from both the tropical seas as well as temperate regions across the world. The present study provides a list of soft corals along with their associated zooxanthellae using published data. By combining all the data, 52 soft coral species belonging to 21 genera were identified and their corresponding specific Symbiodiniaceae genera were analysed. It was important to initially compare soft corals and distinguish zooxanthellae at clade level to find any host specificity. The vast majority (75 %) of soft corals predominantly hosted the genus Cladocopium (Clade C) and therefore the focus of this study was to evaluate its geographical distribution. The genus Cladocopium consists of many species which are classified as subclades in this study, exhibiting high intra-clade diversity. For 40 of the 52 soft corals reviewed, 18 % had the same clade type C1 (considered as generalists and ancestral) and 13 % contained the clades C15, C64 and C1:3a, respectively. Analysis showed that some clades (C71a, C15b and C64) were confined to specific geographical regions while clade C1 was distributed worldwide. Understanding the distribution of endosymbionts may enable predictions of which symbioses will survive and exist under future climate change scenarios.

Genome sequencing and phylogenetic reconstruction reveal a potential fourth rhinovirus species and its worldwide distribution.

Genome sequences of members of a potential fourth rhinovirus (RV) species, provisionally denoted as rhinovirus A clade D, from patients with acute respiratory infection were determined. Bayesian coalescent analysis estimated that clade D emerged around the 1940s and diverged further around 2006-2007 into two distinctive sublineages (RV-A8-like and RV-A45-like) that harbored unique "clade-defining" substitutions. Similarity plots and bootscan mapping revealed a recombination breakpoint located in the 5'-UTR region of members of the RV-A8-like sublineage. Phylogenetic reconstruction revealed the distribution of clade D viruses in the Asia Pacific region and in Europe, underlining its worldwide distribution.

Afrotropics on the wing: phylogenomics and historical biogeography of awl and policeman skippers

AbstractThe Old‐World Tropics encompass many unique biomes and associated biotas shaped by drastic climate and geological changes throughout the Cenozoic. Disjunct distributions of clades between the Afrotropics and the Oriental regions are testament to these changes. Awl and policeman skippers (Hesperiidae: Coeliadinae) are disjunctly distributed with some genera endemic to the Afrotropics and others restricted to the Oriental and Australian regions. We reconstruct the phylogeny of these butterflies using target exon capture phylogenomics. We also generate a dated framework for this clade that uses the putatively oldest known butterfly fossil to estimate the historical biogeography of Coeliadinae using a model‐based approach. We infer a stable and robust phylogeny for the subfamily, with all but one Afrotropical lineage forming a derived clade. The African genus Pyrrhiades syn. nov. is placed in synonymy with Coeliades to accommodate the new phylogeny. Our comparative dating exercise casts doubt on the assignment of the fossil Protocoeliades kristenseni as a derived Coeliadinae and suggests, along with our biogeographic estimation, a split of Coeliadinae from the rest of skippers in the Palaeocene ca. 70 million years ago. The origin of crown Coeliadinae skippers is estimated in Indomalaya during the late Eocene ca. 36 million years ago, with subsequent Oligocene colonisation events toward the Australian region and the Afrotropics. Colonisation of the Afrotropics from the Indian region occurred during climatic transition, associated biome shifts, and the closure of the Tethys Ocean, which likely allowed geodispersal through the Arabian Peninsula. The current disjunct distribution of Coeliadinae in the Old World Tropics may result from the emergence of savannahs in the Miocene that progressively replaced woodlands and forests in the Arabian Peninsula and western Asia. Coeliadinae skippers are almost exclusively dicot feeders and were likely extirpated as grasslands became dominant, resulting in the present‐day disjunct distribution of these butterflies.

A genetic barcode of SARS-CoV-2 for monitoring global distribution of different clades during the COVID-19 pandemic

ObjectiveThe SARS-CoV-2 pathogen has established endemicity in humans. This necessitates the development of rapid genetic surveillance methodologies to serve as an adjunct with existing comprehensive, albeit though slower, genome sequencing-driven approaches. MethodsA total of 21,789 complete genomes were downloaded from GISAID on May 28, 2020 for analyses. We have defined the major clades and subclades of circulating SARS-CoV-2 genomes. A rapid sequencing-based genotyping protocol was developed and tested on SARS-CoV-2-positive RNA samples by next-generation sequencing. ResultsWe describe 11 major mutations which defined five major clades (G614, S84, V251, I378 and D392) of globally circulating viral populations. The clades can specifically identify using an 11-nucleotide genetic barcode. An analysis of amino acid variation in SARS-CoV-2 proteins provided evidence of substitution events in the viral proteins involved in both host entry and genome replication. ConclusionGlobally circulating SARS-CoV-2 genomes could be classified into 5 major clades based on mutational profiles defined by an 11-nucleotide barcode. We have successfully developed a multiplexed sequencing-based, rapid genotyping protocol for high-throughput classification of major clade types of SARS-CoV-2 in clinical samples. This barcoding strategy will be required to monitor decreases in genetic diversity as treatment and vaccine approaches become widely available.

Contribution of Canine‐Based Factors to the Spread of RMSF in Arizona and Mexico

Prior to 2003, the number of annual cases of Rocky Mountain spotted fever (RMSF) reported in Arizona was reliably close to zero. However, since an initial RMSF outbreak in 2003, case rates have rapidly increased in Arizona and continue to rise. This outbreak has been tied to a novel vector, Rhipicephalus sanguineus, the brown dog tick. Since then, the vectoring capacity of the brown dog tick is seemingly spreading as Northern Mexico across the border from Arizona has had over 4000 reported cases since 2008, with mortality rates as high as 38%. This discovery was somewhat unsettling considering the continental‐wide distribution of these ticks. Given this is a zoonotic disease, canines act as an amplifier for the bacterial agent Rickettsii rickettsii and then brown dog ticks pass it on to humans as an incidental host. Therefore, the need to understand the canine‐based factors that drive the spread of RMSF in this region has become more urgent.Previously, we have identified three distinct lineages of R. sanguineus within the region with variation in rickettsial infection rates between clades. This could lead to the distribution of ticks on a canine patient, the tick infection rate, and canine seroprevalence driving the human case rate that we see across Arizona and New Mexico. To test this hypothesis, we have focused on the canine as the unit of interest in our epidemiological approach. To this end, we collected all of the ticks and serum from a series of canine patients from five locations across distributed across Arizona and New Mexico. These ticks were phylogenetically categorized based on sequencing of mitochondrial genes and tested for the presence of rickettsial DNA. The serum was tested for rickettsial antibodies using immuno‐fluorescence assay.The results of this study show that the population of ticks found on an individual dog tend to be monophyletic belonging to a single clade, meaning ticks taken off the same canine are more closely related to one another than to ticks taken off other canines. This implies that the distribution of tick clades across the region plays a fundamental role in the transmission of RMSF. Moreover, while the rickettsial prevalence differs between these different tick lineages, we have found that the likelihood of one tick being infected on a canine is directly correlated to the number of other ticks infected on the canine. Therefore, transmission among feeding groups and co‐localized ticks is a major determinant of canine infection rates. Given these two factors drive the canine infection rate, it is likely they drive the human rate as well. These data were then used to evaluate the feasibility of a canine‐based vaccine by calculating the basic reproduction rate among other variables, which allows us to assess the plausibility of achieving herd immunity through vaccination campaigns. These methods will help to control the spread of RMSF to humans as well as prevent future outbreaks.Support or Funding InformationMWU One Health Award to JVB, MWU REAP Award to JVB, MWU Kenneth A. Suarez Award to SM, MWU CGS Funding to AO

Infraspecific diversification of the star cloak fern (Notholaena standleyi) in the deserts of the United States and Mexico.

Not all ferns grow in moist and shaded habitats. One well-known example is Notholaena standleyi, a species that thrives in deserts of the southwestern United States and Mexico. This species exhibits several "chemotypes" that differ in farina (flavonoid exudates) color and chemistry. By integrating data from molecular phylogenetics, cytology, biochemistry, and biogeography, we circumscribed the major evolutionary lineages within N. standleyi and reconstructed their diversification histories. Forty-eight samples were selected from across the geographic distribution of N. standleyi. Phylogenetic relationships were inferred using four plastid and five nuclear markers. Ploidy levels were inferred using spore sizes calibrated by chromosome counts, and farina chemistry was compared using thin-layer chromatography. Four clades are recognized, three of which roughly correspond to previously recognized chemotypes. The diploid clades G and Y are found in the Sonoran and Chihuahuan deserts, respectively; they are estimated to have diverged in the Pleistocene, congruent with the postulated timing of climatological events separating these two deserts. Clade P/YG is tetraploid and partially overlaps the distribution of clade Y in the eastern Chihuahuan Desert. It is apparently confined to limestone, a geologic substrate rarely occupied by members of the other clades. The cryptic (C) clade, a diploid group known only from southern Mexico and highly disjunct from the other three clades, is newly recognized here. Our results reveal a complex intraspecific diversification history of N. standleyi, traceable to a variety of evolutionary drivers including classic allopatry, parapatry with or without changes in geologic substrate, and sympatric divergence through polyploidization.

Phylogeographic history of flat periwinkles, Littorina fabalis and L. obtusata

BackgroundThe flat periwinkles, Littorina fabalis and L. obtusata, are two sister species widely distributed throughout the Northern Atlantic shores with high potential to inform us about the process of ecological speciation in the intertidal. However, whether gene flow has occurred during their divergence is still a matter of debate. A comprehensive assessment of the genetic diversity of these species is also lacking and their main glacial refugia and dispersal barriers remain largely unknown. In order to fill these gaps, we sequenced two mitochondrial genes and two nuclear fragments to perform a phylogeographic analysis of flat periwinkles across their distribution range.ResultsWe identified two main clades largely composed by species-specific haplotypes corresponding to L. obtusata and L. fabalis, with moderate to strong support, respectively. Importantly, a model of divergence with gene flow between the two species (from L. obtusata to L. fabalis) was better supported, both in Iberia and in northern-central Europe. Three mitochondrial clades were detected within L. fabalis and two within L. obtusata, with strong divergence between Iberia and the remaining populations. The largest component of the genetic variance within each species was explained by differences between geographic regions associated with these clades. Our data suggests that overall intraspecific genetic diversity is similar between the two flat periwinkle species and that populations from Iberia tend to be less diverse than populations from northern-central Europe.ConclusionsThe phylogeographic analysis of this sister-species pair supports divergence with gene flow. This system thus provides us with the opportunity to study the contribution of gene flow and natural selection during diversification. The distribution of the different clades suggests the existence of glacial refugia in Iberia and northern-central Europe for both species, with a main phylogeographic break between these regions. Although the genetic diversity results are not fully conclusive, the lower diversity observed in Iberia could reflect marginal conditions at the southern limit of their distribution range during the current interglacial period.

Spread and evolution of influenza A (H1N1) pdm09 virus in Hubei, 2015–2019

ObjectiveTo understand spread, phylogenetic characteristics, epitope and drug-resistance site of influenza A (H1N1) pdm09 virus in Hubei province during 2015–2019. MethodsThe spread period of the virus were divided according to the positive rate of influenza virus nucleic acid detection downloaded from influenza surveillance information system in China. Sequencing of 39 strains of influenza A (H1N1) pdm09 virus isolated from the positive samples in real-time fluorescence PCR in Hubei during 2015–2019 was conducted and 13 sequences of the strains isolated from Hubei were downloaded from global influenza database to analyze the distribution of phylogenetic clade, epitope and drug-resistant mutation sites by using bioinformatics software and simulate the structure of mutation sites by 3D modeling. ResultsThe annual spread of influenza A (H1N1) pdm09 virus lasted for 11–14 weeks in Hubei from 2015 to 2019, and the spread intensity increased year by year. Multiple branches of 6B.1A to 6B.1A7 evolved from 6B clade in phylogenetic tree of the HA and NA genes. Twelve epitope substitutions of HA and two drug-resistance sites of NA were detected, and there were obvious differences in D222G substitution virulence identifying marker and drug-resistance site I223V on homology in 3D modeling structure. ConclusionThe spread intensity and phylogenetic clade number of influenza A (H1N1) pdm09 virus increased In Hubei during 2015–2019. Sporadic virulence marker and drug-resistance site were detected for influenza A (H1N1) pdm09 virus. The results of this analysis can be used to improve the epidemiological research and genetic evolution surveillance of influenza virus in Hubei.

Community Structure, Abundance and Potential Functions of Bacteria and Archaea in the Sansha Yongle Blue Hole, Xisha, South China Sea.

The Sansha Yongle Blue Hole is the deepest blue hole in the world and exhibits unique environmental characteristics. In this paper, Illumina sequencing and qPCR analysis were conducted to obtain the microbial information in this special ecosystem. The results showed that the richness and diversity of bacterial communities in the hole was greater than those of archaeal communities, and bacterial and archaeal communities were dominated by Proteobacteria and Euryarchaeota, respectively. Temperature and nitrate concentration significantly contributed to the heterogeneous distribution of major bacterial clades; salinity explained most variations of the archaeal communities, but not significant. A sudden increase of bacterial 16S rRNA, archaeal 16S rRNA, ANAMMOX 16S rRNA, nirS and dsrB gene was noticed from 90 to 100 m in the hole probably due to more phytoplankton at this depth. Sulfur oxidation and nitrate reduction were the most abundant predicted ecological functions in the hole, while lots of archaea were predicted to be involved in aerobic ammonia oxidation and methanogenesis. The co-occurrence network analysis illustrated that a synergistic effect between sulfate reduction and sulfur oxidation, and between nitrogen fixation and denitrification, a certain degree of coupling between sulfur and nitrogen cycle was also observed in the hole. The comparisons of bacterial and archaeal communities between the hole and other caves in the world (or other areas of the South China Sea) suggest that similar conditions are hypothesized to give rise to similar microbial communities, and environmental conditions may contribute significantly to the bacterial and archaeal communities.

Climatic shifts drove major contractions in avian latitudinal distributions throughout the Cenozoic

Many higher level avian clades are restricted to Earth's lower latitudes, leading to historical biogeographic reconstructions favoring a Gondwanan origin of crown birds and numerous deep subclades. However, several such "tropical-restricted" clades (TRCs) are represented by stem-lineage fossils well outside the ranges of their closest living relatives, often on northern continents. To assess the drivers of these geographic disjunctions, we combined ecological niche modeling, paleoclimate models, and the early Cenozoic fossil record to examine the influence of climatic change on avian geographic distributions over the last ∼56 million years. By modeling the distribution of suitable habitable area through time, we illustrate that most Paleogene fossil-bearing localities would have been suitable for occupancy by extant TRC representatives when their stem-lineage fossils were deposited. Potentially suitable habitat for these TRCs is inferred to have become progressively restricted toward the tropics throughout the Cenozoic, culminating in relatively narrow circumtropical distributions in the present day. Our results are consistent with coarse-scale niche conservatism at the clade level and support a scenario whereby climate change over geological timescales has largely dictated the geographic distributions of many major avian clades. The distinctive modern bias toward high avian diversity at tropical latitudes for most hierarchical taxonomic levels may therefore represent a relatively recent phenomenon, overprinting a complex biogeographic history of dramatic geographic range shifts driven by Earth's changing climate, variable persistence, and intercontinental dispersal. Earth's current climatic trajectory portends a return to a megathermal state, which may dramatically influence the geographic distributions of many range-restricted extant clades.

The Mesozoic Biogeographic History of Gondwanan Terrestrial Vertebrates: Insights from Madagascar's Fossil Record

The Mesozoic plate tectonic and paleogeographic history of Gondwana had a profound effect on the distribution of terrestrial vertebrates. As the supercontinent fragmented into a series of large landmasses (South America, Africa-Arabia, Antarctica, Australia, New Zealand, the Indian subcontinent, and Madagascar), particularly during the Late Jurassic and Cretaceous, its terrestrial vertebrates became progressively isolated, evolving into unique faunal assemblages. We focus on four clades that, during the Mesozoic, had relatively low ability for dispersal across oceanic barriers—crocodyliforms, sauropod dinosaurs, nonavian theropod dinosaurs, and mammals. Their distributions reveal patterns that are critically important in evaluating various biogeographic hypotheses, several of which have been informed by recent discoveries from the Late Cretaceous of Madagascar. We also examine the effects of lingering, intermittent connections, or reconnections, of Gondwanan landmasses with Laurasia (through the Caribbean, Mediterranean, and Himalayan regions) on the distributions of different clades. ▪ This article reviews the biogeographic history of terrestrial vertebrates from the Mesozoic of the southern supercontinent Gondwana. ▪ Relatively large, terrestrial animals—including crocodyliforms, sauropod and nonavian theropod dinosaurs, and mammals—are the focus of this review. ▪ Most patterns related to vicariance occurred during the Late Jurassic and Cretaceous, the intervals of most active Gondwanan fragmentation. ▪ Recent discoveries of vertebrates from the Late Cretaceous of Madagascar have played a key role in formulating and testing various biogeographic hypotheses.

The Emergence and Decennary Distribution of Clade 2.3.4.4 HPAI H5Nx

Reassortment events among influenza viruses occur naturally and may lead to the development of new and different subtypes which often ignite the possibility of an influenza outbreak. Between 2008 and 2010, highly pathogenic avian influenza (HPAI) H5 of the N1 subtype from the A/goose/Guangdong/1/96-like (Gs/GD) lineage generated novel reassortants by introducing other neuraminidase (NA) subtypes reported to cause most outbreaks in poultry. With the extensive divergence of the H5 hemagglutinin (HA) sequences of documented viruses, the WHO/FAO/OIE H5 Evolutionary Working Group clustered these viruses into a systematic and unified nomenclature of clade 2.3.4.4 currently known as “H5Nx” viruses. The rapid emergence and circulation of these viruses, namely, H5N2, H5N3, H5N5, H5N6, H5N8, and the regenerated H5N1, are of great concern based on their pandemic potential. Knowing the evolution and emergence of these novel reassortants helps to better understand their complex nature. The eruption of reports of each H5Nx reassortant through time demonstrates that it could persist beyond its usual seasonal activity, intensifying the possibility of these emerging viruses’ pandemic potential. This review paper provides an overview of the emergence of each novel HPAI H5Nx virus as well as its current epidemiological distribution.