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Previous phylogenies of extant short-faced bats (Chiroptera: Stenodermatina) supported either two colonization events from the mainland to the Antilles, or reverse colonization, but lacked both fossil data and statistical modelling of biogeography. Recent multi-locus phylogenies of noctilionoid bats and likelihood modelling of ancestral ranges support a continental origin for the clade. We include all known extinct and extant stenodermatina species and apply statistical modelling to test competing biogeographical hypotheses. Location: The Neotropics, including the Antilles. Methods: We combined mitochondrial and nuclear sequences with 302 new morphological characters to infer phylogenies. Bayesian tip-dating analyses applied codon models to protein-coding genes, with relaxed molecular clocks fitting a compound Poisson process. The combined maximum clade credibility tree was used in comparisons of alternative biogeographical models. Results: The new phylogenies support the fossil Cubanycteris silvai as sister to all extant species of short-faced bats. Among Artibeus (the sister group to short-faced bats), the Antillean fossil A. anthonyi has distinctive characters and is nested within the subgenus Artibeus. The common ancestor of all short-faced bats is inferred to be Antillean, as a mainland origin is unlikely. Founder-event speciation is the most probable process explaining the distribution of these highly divergent fossil lineages. Main conclusions: Dated, character-based phylogenies of fossil species are indispensable for biogeographical inference: without fossils, biogeographical analyses find a mainland origin for short-faced bats. The rate of founder speciation in this clade is twice as high as the estimate from noctilionoids in general, highlighting the role of founder events in the diversification of island taxa. Although rare, reverse colonization contributes key species to continental communities. Short-faced bats, including Cubanycteris, share biomechanical adaptations for a strong bite conferring access to harder figs. We hypothesize these adaptations and characters related to roosting ecology enabled ancestral lineages to successfully establish and diversify on the mainland.

The Japanese greater horseshoe bat (Rhinolophus nippon) is distributed widely in East Asia. Within the species, R. nippon in Northeast Asia is regarded as the lineage that diverged most recently. However, the monophyly of the Japanese populations is unclear due to insufficient data about phylogenetic relationship of the western Japanese populations. To test the monophyly of the Japanese populations of R. nippon, we sampled R. nippon from western Japan and performed a phylogeographic analysis based on mitochondrial DNA cytochrome b and the D‐loop. The Northeast Asian lineage consisted of three main clades in eastern Japan (clade I), western Japan (clade II), and the continent as well as the Kumamoto population in westernmost Japan (clade III). The results of this study do not support the monophyly of the Japanese population. The findings suggest the “reverse colonization” of R. nippon from the Japanese Archipelago to the Eurasian continent, and provide important insight into the role of the island system in creation and supply of diversity to the continent. We performed a phylogeographic analysis of the Japanese greater horseshoe bat (Rhinolophus nippon) in Northeast Asia based on mitochondrial DNA cytochrome b and the D‐loop. The results revealed that the Japanese populations are not monophyletic, and the continental populations are imbedded within the Japanese population. The findings support the \"reverse colonization\" of R. nippon from the Japanese Archipelago to the Eurasian continent.

AIM: Why some groups of species radiate, when others appear not to have done so, remains a fundamental question in evolutionary biology. Here, we investigate why island endemism, a common surrogate of speciation rate, reaches its lowest levels among land plants in bryophytes. Using molecular phylogeographical analyses in the moss genus Rhynchostegiella, we contrast the hypotheses (1) that the small size of oceanic islands and moderate genetic isolation in island populations with high dispersal capacities promote lower anagenetic diversification rates than in continental populations, and (2) that island and continental speciation rates do not differ, but island endemics quickly colonize continents. LOCATION: Macaronesia, Europe and Africa. METHODS: A time‐calibrated multilocus species tree for 80 populations, representing the nine species of Rhynchostegiella across their entire distribution range, was constructed using beast. Based on this dated tree, ancestral ranges were estimated in BioGeoBears and speciation rates using bamm. RESULTS: Although island‐endemic Rhynchostegiella species evolved anagenetically, speciation rates did not significantly differ between island and continental lineages. Seven episodes of colonization from islands to continental regions were inferred from ancestral‐area estimations, which identified the Canary Islands as the ancestral distribution area of the genus, lending support to our second hypothesis. MAIN CONCLUSIONS: Our findings reinforce the view of north‐eastern Atlantic archipelagos as ‘departure gates’ for the colonization of western Europe during the late Pleistocene. They further show that, over longer evolutionary time‐scales, the colonization of continents from island ancestors can lead to speciation and contribute to extant patterns of continental diversity.

This chapter presents commonly used terms in the study of postcolonialism. The terms listed begin with the alphabet “R”. Detailed explanation is provided for several terms, including race, refugee and reverse colonization. Each entry includes the origin of the term; a detailed explanation of its perceived meaning; and examples of the term's use in literary‐cultural texts. Postcolonialism as a mode of interpretation tracks race and its cognates, racial difference and racism, as an organizing principle of literary texts and history‐writing but, more than anything else, of colonialism. Race theory was responsible for the generation of endless stereotypes, where these stereotypes then perpetuated themselves and furthered race theory in a kind of vicious colonial cycle. The refugee is also constructed as a category in opposition to the citizen. Reverse colonization as a process was anticipated in the writings of several English poets.

Significance Animals form associations with bacteria that play important roles in host development and fitness. The mechanisms by which animals horizontally acquire their bacterial partners from the environment are poorly understood. To address this question, we take advantage of a natural symbiosis between the luminous Gram-negative bacterium Vibrio fischeri and its squid host, Euprymna scolopes . We applied the insertion sequencing global approach and identified 380 colonization determinants in V. fischeri . Characterization of the factors revealed novel biofilm regulation and beneficial colonization factors at the cell envelope. To our knowledge, our study is the first global functional analysis in V. fischeri and expands opportunities for systems biology approaches at the host microbe interface in a valuable reductionist model of microbiota colonization. Animal epithelial tissue becomes reproducibly colonized by specific environmental bacteria. The bacteria (microbiota) perform critical functions for the host’s tissue development, immune system development, and nutrition; yet the processes by which bacterial diversity in the environment is selected to assemble the correct communities in the host are unclear. To understand the molecular determinants of microbiota selection, we examined colonization of a simplified model in which the light organ of Euprymna scolopes squid is colonized exclusively by Vibrio fischeri bacteria. We applied high-throughput insertion sequencing to identify which bacterial genes are required during host colonization. A library of over 41,000 unique transposon insertions was analyzed before and after colonization of 1,500 squid hatchlings. Mutants that were reproducibly depleted following squid colonization represented 380 genes, including 37 that encode known colonization factors. Validation of select mutants in defined competitions against the wild-type strain identified nine mutants that exhibited a reproducible colonization defect. Some of the colonization factors identified included genes predicted to influence copper regulation and secretion. Other mutants exhibited defects in biofilm development, which is required for aggregation in host mucus and initiation of colonization. Biofilm formation in culture and in vivo was abolished in a strain lacking the cytoplasmic chaperone DnaJ, suggesting an important role for protein quality control during the elaboration of bacterial biofilm in the context of an intact host immune system. Overall these data suggest that cellular stress responses and biofilm regulation are critical processes underlying the reproducible colonization of animal hosts by specific microbial symbionts.

Staphylococcus aureus is the major cause of skin diseases, and its increased prevalence in skin colonization and infections present a need to understand its physiology in this environment. The work presented here outlines S. aureus upregulation of colonization and virulence factors using a newly developed medium that strives to replicate the human skin surface environment and demonstrates roles for adhesins clumping factor A (ClfA), serine-rich repeat glycoprotein adhesin (SraP), and the fibronectin binding proteins (Fnbps) in human corneocyte adherence.

Host glycans are paramount in regulating the symbiotic relationship between humans and their gut bacteria. The constant flux of host-secreted mucin at the mucosal layer creates a steady niche for bacterial colonization. Mucin degradation by keystone species subsequently shapes the microbial community. This study investigated the transcriptional response during mucin-driven trophic interaction between the specialised mucin-degrader Akkermansia muciniphila and a butyrogenic gut commensal Anaerostipes caccae. A. muciniphila monocultures and co-cultures with non-mucolytic A. caccae from the Lachnospiraceae family were grown anaerobically in minimal media supplemented with mucin. We analysed for growth, metabolites (HPLC analysis), microbial composition (quantitative reverse transcription PCR), and transcriptional response (RNA-seq). Mucin degradation by A. muciniphila supported the growth of A. caccae and concomitant butyrate production predominantly via the acetyl-CoA pathway. Differential expression analysis (DESeq 2) showed the presence of A. caccae induced changes in the A. muciniphila transcriptional response with increased expression of mucin degradation genes and reduced expression of ribosomal genes. Two putative operons that encode for uncharacterised proteins and an efflux system, and several two-component systems were also differentially regulated. This indicated A. muciniphila changed its transcriptional regulation in response to A. caccae. This study provides insight to understand the mucin-driven microbial ecology using metatranscriptomics. Our findings show that the expression of mucolytic enzymes by A. muciniphila increases upon the presence of a community member. This could indicate its role as a keystone species that supports the microbial community in the mucosal environment by increasing the availability of mucin sugars.

Abstract Background More than 2 months separated the initial description of SARS-CoV-2 and discovery of its widespread dissemination in the United States. Despite this lengthy interval, implementation of specific quantitative reverse transcription (qRT)-PCR-based SARS-CoV-2 tests in the US has been slow, and testing is still not widely available. Metagenomic sequencing offers the promise of unbiased detection of emerging pathogens, without requiring prior knowledge of the identity of the responsible agent or its genomic sequence. Methods To evaluate metagenomic approaches in the context of the current SARS-CoV-2 epidemic, laboratory-confirmed positive and negative samples from Seattle, WA were evaluated by metagenomic sequencing, with comparison to a 2019 reference genomic database created before the emergence of SARS-CoV-2. Results Within 36 h our results showed clear identification of a novel human Betacoronavirus, closely related to known Betacoronaviruses of bats, in laboratory-proven cases of SARS-CoV-2. A subset of samples also showed superinfection or colonization with human parainfluenza virus 3 or Moraxella species, highlighting the need to test directly for SARS-CoV-2 as opposed to ruling out an infection using a viral respiratory panel. Samples negative for SARS-CoV-2 by RT-PCR were also negative by metagenomic analysis, and positive for Rhinovirus A and C. Unlike targeted SARS-CoV-2 qRT-PCR testing, metagenomic analysis of these SARS-CoV-2 negative samples identified candidate etiological agents for the patients’ respiratory symptoms. Conclusion Taken together, these results demonstrate the value of metagenomic analysis in the monitoring and response to this and future viral pandemics.

Bifidobacteria are important members of human gut microbiota; however, quantitative data on their early-life dynamics is limited. Here, using a sensitive reverse transcription-qPCR approach, we demonstrate the carriage of eight signature infant-associated Bifidobacterium species ( B. longum, B. breve, B. bifidum, B. catenulatum group , B. infantis, B. adolescentis, B. angulatum and B. dentium ) in 76 healthy full-term vaginally-born infants from first day to three years of life. About 21% babies carry bifidobacteria at first day of life (6.2 ± 1.9 log 10  cells/g feces); and this carriage increases to 64% (8.0 ± 2.2), 79% (8.5 ± 2.1), 97% (9.3 ± 1.8), 99% (9.6 ± 1.6), and 100% (9.7 ± 0.9) at age 7 days, 1, 3 and 6 months, and 3 years, respectively. B. longum, B. breve, B. catenulatum group and B. bifidum are among the earliest and abundant bifidobacterial clades. Interestingly, infants starting formula-feed as early as first week of life have higher bifidobacterial carriage compared to exclusively breast-fed counterparts. Bifidobacteria demonstrate an antagonistic correlation with enterobacteria and enterococci. Further analyses also reveal a relatively lower/ delayed bifidobacterial carriage in cesarean-born babies. The study presents a quantitative perspective of the early-life gut Bifidobacterium colonization and shows how factors such as birth and feeding modes could influence this acquisition even in healthy infants.