Evolutionary divergence times in the Annonaceae: evidence of a late Miocene origin of Pseuduvaria in Sundaland with subsequent diversification in New Guinea

<p>Abstract</p> <p>Background</p> <p>Phylogenetic analyses of the Annonaceae consistently identify four clades: a basal clade consisting of <it>Anaxagorea</it>, and a small 'ambavioid' clade that is sister to two main clades, the 'long branch clade' (LBC) and 'short branch clade' (SBC). Divergence times in the family have previously been estimated using non-parametric rate smoothing (NPRS) and penalized likelihood (PL). Here we use an uncorrelated lognormal (UCLD) relaxed molecular clock in BEAST to estimate diversification times of the main clades within the family with a focus on the Asian genus <it>Pseuduvaria </it>within the SBC. Two fossil calibration points are applied, including the first use of the recently discovered Annonaceae fossil <it>Futabanthus</it>. The taxonomy and morphology of <it>Pseuduvaria </it>have been well documented, although no previous dating or biogeographical studies have been undertaken. Ancestral areas at internal nodes within <it>Pseuduvaria </it>are determined using dispersal-vicariance analysis (DIVA) and weighted ancestral area analysis (WAAA).</p> <p>Results</p> <p>The divergence times of the main clades within the Annonaceae were found to deviate slightly from previous estimates that used different calibration points and dating methods. In particular, our estimate for the SBC crown (55.2-26.9 Mya) is much younger than previous estimates (62.5-53.1 ± 3.6 Mya and ca. 58.76 Mya). Early diversification of <it>Pseuduvaria </it>was estimated to have occurred 15-8 Mya, possibly associated with the 'mid-Miocene climatic optimum.' <it>Pseuduvaria </it>is inferred to have originated in Sundaland in the late Miocene, ca. 8 Mya; subsequent migration events were predominantly eastwards towards New Guinea and Australia, although several migratory reversals are also postulated. Speciation of <it>Pseuduvaria </it>within New Guinea may have occurred after ca. 6.5 Mya, possibly coinciding with the formation of the Central Range orogeny from ca. 8 Mya.</p> <p>Conclusion</p> <p>Our divergence time estimates within the Annonaceae are likely to be more precise as we used a UCLD clock model and calibrated the phylogeny using new fossil evidence. <it>Pseuduvaria </it>is shown to have dispersed from Sundaland after the late Miocene. The present-day paleotropical distribution of <it>Pseuduvaria </it>may have been achieved by long-distance dispersal, and speciation events might be explained by global climatic oscillations, sea level fluctuations, and tectonic activity.</p

Early evolutionary history of the flowering plant family Annonaceae : steady diversification and boreotropical geodispersal

Aim : Rain forest-restricted plant families show disjunct distributions between the three major tropical regions: South America, Africa and Asia. Explaining these disjunctions has become an important challenge in biogeography. The pantropical plant family Annonaceae is used to test hypotheses that might explain diversification and distribution patterns in tropical biota: the museum hypothesis (low extinction leading to steady accumulation of species); and dispersal between Africa and Asia via Indian rafting versus boreotropical geodispersal. Location : Tropics and boreotropics. Methods : Molecular age estimates were calculated using a Bayesian approach based on 83% generic sampling representing all major lineages within the family, seven chloroplast markers and two fossil calibrations. An analysis of diversification was carried out, which included lineage-through-time (LTT) plots and the calculation of diversification rates for genera and major clades. Ancestral areas were reconstructed using a maximum likelihood approach that implements the dispersal-extinction-cladogenesis model. Results : The LTT plots indicated a constant overall rate of diversification with low extinction rates for the family during the first 80 Ma of its existence. The highest diversification rates were inferred for several young genera such as Desmopsis, Uvariopsis and Unonopsis. A boreotropical migration route was supported over Indian rafting as the best fitting hypothesis to explain present-day distribution patterns within the family. Main conclusions : Early diversification within Annonaceae fits the hypothesis of a museum model of tropical diversification, with an overall steady increase in lineages possibly due to low extinction rates. The present-day distribution of species within the two largest clades of Annonaceae is the result of two contrasting biogeographic histories. The 'long-branch clade' has been diversifying since the beginning of the Cenozoic and underwent numerous geodispersals via the boreotropics and several more recent long-distance dispersal events. In contrast, the 'short-branch clade' dispersed once into Asia via the boreotropics during the Early Miocene and further dispersal was limited

Cencurut virus: A novel Orthonairovirus from Asian house shrews (Suncus murinus) in Singapore

Orthonairovirus is a genus of viruses in the family Nairoviridae, order Bunyavirales, with a segmented circular RNA genome. They typically infect birds and mammals and are primarily transmitted by ectoparasites such as ticks. Four of nine Orthonairovirus genogroups can infect humans, with Crimean-Congo hemorrhagic fever virus infections displaying case fatality rates up to 40%. Here, we discover and describe a novel Orthonairovirus as Cencurut virus (CENV). CENV was detected in 34 of 37 Asian house shrews (Suncus murinus) sampled in Singapore and in a nymphal Amblyomma helvolum tick collected from an infected shrew. Pairwise comparison of CENV S, M, and L segments had 95.0 to 100% nucleotide and 97.5 to 100% amino acid homology within CENV genomes, suggesting a diverse viral population. Phylogenetic analysis of the individual gene segments showed that CENV is related to Erve, Lamgora, Lamusara, and Thiafora viruses, with only 49.0 to 58.2% nucleotide and 41.7 to 61.1% amino acid homology, which has previously been detected in other shrew species from France, Gabon, and Senegal respectively. The high detection frequency suggests that CENV is endemic among S. murinus populations in Singapore. The discovery of CENV, from a virus family with known zoonotic potential, underlines the importance of surveillance of synanthropic small mammals that are widely distributed across Southeast Asia

Host specificity of Hepatocystis infection in short-nosed fruit bats (Cynopterus brachyotis) in Singapore

Haemosporidians infect a wide diversity of bat genera and species, yet little is known about their transmission cycles or epidemiology. Though several recent studies have focused on the genus Hepatocystis, an Old World parasite primarily infecting bats, monkeys, and squirrels, this group is still understudied with little known about its transmission and molecular ecology. These parasites lack an asexual erythrocytic stage, making them unique from the Plasmodium vertebrate life cycle. In this study, we detected a prevalence of 31% of Hepatocystis in short-nosed fruit bats (Cynopterus brachyotis) in Singapore. Phylogenetic reconstruction with a partial cytochrome b sequence revealed a monophyletic group of Hepatocystis from C. brachyotis in Malaysia, Singapore, and Thailand. There was no relationship with infection and bat age, sex, location, body condition or monsoon season. The absence of this parasite in the five other bat species sampled in Singapore indicates this Hepatocystis species may be host restricted

Characteristics of acute febrile illness and determinants of illness recovery among adults presenting to Singapore primary care clinics

Abstract Background Undifferentiated acute febrile illness (AFI) is a common presentation among adults in primary care settings in Singapore but large gaps exist in the understanding of the characteristics of these patients. We studied clinical and epidemiological characteristics of AFI patients and factors associated with delayed recovery from AFI. Methods We performed a secondary data analysis using data from the Early DENgue infection and outcome (EDEN) study on 2046 adult patients presenting at 5 Singapore polyclinics between December 2007 and February 2013 with a history of fever (≥38 °C) for less than 72 h. We used an accelerated failure time model to investigate factors associated with delayed recovery from AFI. Results The mean age of patients was 36.6 years, 65 % were male, 51 % were of Chinese ethnicity, and 75 % lived in public housing. Median illness duration was 5 days (interquartile range, 3–7). In multivariable analysis, the unemployed and white collar workers had longer illness duration compared with blue collar workers (time ratio (TR), 1.10; 95 % confidence interval (CI), 1.03–1.17 and TR, 1.08; 95 % CI, 1.02–1.15, respectively). Patients with more symptoms at initial consultation had slower recovery (TR, 1.03 per additional symptom; 95 % CI, 1.02–1.03). Other clinical factors were also associated with longer duration of illness, including use of analgesics (TR, 1.21; 95 % CI, 1.15–1.28); use of cough medicines (TR, 1.14; 95 % CI, 1.08–1.20); use of antibiotics (TR, 1.14; 95 % CI, 1.07–1.21); and hospitalization (TR, 1.59; 95 % CI, 1.39–1.82). Compared to patients with normal WBC count at first consultation, those with low WBC count had slower recovery (TR, 1.14; 95 % CI, 1.07–1.21), while the reverse was observed among patients with high WBC count (TR, 0.94; 95 % CI, 0.88–1.00). Conclusions Differences in illness duration among different types of employment may reflect differences in their underlying general health status. Early identification of factors delaying recovery could help triage management in a primary care setting. In-depth characterization of fever etiology in Singapore will improve surveillance and control activities

Effects of a major deletion in the SARS-CoV-2 genome on the severity of infection and the inflammatory response: an observational cohort study

10.1016/S0140-6736(20)31757-8LANCET39610251603-61