Phylogenomics and the rise of the angiosperms

Angiosperms are the cornerstone of most terrestrial ecosystems and human livelihoods1,2. A robust understanding of angiosperm evolution is required to explain their rise to ecological dominance. So far, the angiosperm tree of life has been determined primarily by means of analyses of the plastid genome3,4. Many studies have drawn on this foundational work, such as classification and first insights into angiosperm diversification since their Mesozoic origins5-7. However, the limited and biased sampling of both taxa and genomes undermines confidence in the tree and its implications. Here, we build the tree of life for almost 8,000 (about 60%) angiosperm genera using a standardized set of 353 nuclear genes8. This 15-fold increase in genus-level sampling relative to comparable nuclear studies9 provides a critical test of earlier results and brings notable change to key groups, especially in rosids, while substantiating many previously predicted relationships. Scaling this tree to time using 200 fossils, we discovered that early angiosperm evolution was characterized by high gene tree conflict and explosive diversification, giving rise to more than 80% of extant angiosperm orders. Steady diversification ensued through the remaining Mesozoic Era until rates resurged in the Cenozoic Era, concurrent with decreasing global temperatures and tightly linked with gene tree conflict. Taken together, our extensive sampling combined with advanced phylogenomic methods shows the deep history and full complexity in the evolution of a megadiverse clade.

The origin and speciation of orchids

Orchids constitute one of the most spectacular radiations of flowering plants. However, their origin, spread across the globe, and hotspots of speciation remain uncertain due to the lack of an up-to-date phylogeographic analysis. We present a new Orchidaceae phylogeny based on combined high-throughput and Sanger sequencing data, covering all five subfamilies, 17/22 tribes, 40/49 subtribes, 285/736 genera, and c. 7% (1921) of the 29 524 accepted species, and use it to infer geographic range evolution, diversity, and speciation patterns by adding curated geographical distributions from the World Checklist of Vascular Plants. The orchids' most recent common ancestor is inferred to have lived in Late Cretaceous Laurasia. The modern range of Apostasioideae, which comprises two genera with 16 species from India to northern Australia, is interpreted as relictual, similar to that of numerous other groups that went extinct at higher latitudes following the global climate cooling during the Oligocene. Despite their ancient origin, modern orchid species diversity mainly originated over the last 5 Ma, with the highest speciation rates in Panama and Costa Rica. These results alter our understanding of the geographic origin of orchids, previously proposed as Australian, and pinpoint Central America as a region of recent, explosive speciation.

[Association between gestational diabetes mellitus and preterm birth subtypes]

Objective: To investigate the association between gestational diabetes mellitus (GDM) and preterm birth subtypes. Methods: Based on the cohort of pregnant women in Anqing Prefectural Hospital, the pregnant women who received prenatal screening in the first or second trimesters were recruited into baseline cohorts; and followed up for them was conducted until delivery, and the information about their pregnancy status and outcomes were obtained through electronic medical record system and questionnaire surveys. The log-binomial regression model was used to explore the association between GDM and preterm birth [iatrogenic preterm birth, spontaneous preterm birth (preterm premature rupture of membranes and preterm labor)]. For multiple confounding factors, the propensity score correction model was used to compute the adjusted association. Results: Among the 2 031 pregnant women with a singleton delivery, the incidence of GDM and preterm birth were 10.0% (204 cases) and 4.4% (90 cases) respectively. The proportions of iatrogenic preterm birth and spontaneous preterm birth in the GDM group (n=204) were 1.5% and 5.9% respectively, while the proportions in non-GDM group (n=1 827) were 0.9% and 3.2% respectively, and the difference in the proportion of spontaneous preterm birth between the two groups was significant (P=0.048). Subtypes of spontaneous preterm were further analyzed, and the results showed that the proportions of preterm premature rupture of membranes and preterm labor in the GDM group were 4.9% and 1.0% respectively, while the proportions in the non-GDM group were 2.1% and 1.1% respectively. It showed that the risk of preterm premature rupture of membranes in GDM pregnant women was 2.34 times (aRR=2.34, 95%CI: 1.16-4.69) higher than that in non-GDM pregnant women. Conclusions: Our results showed that GDM might increase the risk of preterm premature rupture of membranes. No significant increase in the proportion of preterm labor in pregnant women with GDM was found.

Diversification Slowdown in the Cirrhopetalum Alliance (Bulbophyllum, Orchidaceae): Insights From the Evolutionary Dynamics of Crassulacean Acid Metabolism

Evolutionary slowdowns in diversification have been inferred in various plant and animal lineages. Investigation based on diversification models integrated with environmental factors and key characters could provide critical insights into this diversification trend. We evaluate diversification rates in the Cirrhopetalum alliance (Bulbophyllum, Orchidaceae subfam. Epidendroideae) using a time-calibrated phylogeny and assess the role of Crassulacean acid metabolism (CAM) as a hypothesised key innovation promoting the spectacular diversity of orchids, especially those with an epiphytic habit. An explosive early speciation in the Cirrhopetalum alliance is evident, with the origin of CAM providing a short-term advantage under the low atmospheric CO2 concentrations (pCO2) associated with cooling and aridification in the late Miocene. A subsequent slowdown of diversification in the Cirrhopetalum alliance is possibly explained by a failure to keep pace with pCO2 dynamics. We further demonstrate that extinction rates in strong CAM lineages are ten times higher than those of C3 lineages, with CAM not as evolutionarily labile as previously assumed. These results challenge the role of CAM as a "key innovation" in the diversification of epiphytic orchids.

[Observation and experiment: a causal perspective]

Observation and experiment and their related connotations and concepts remain vague, which affects the correct understanding of research design and the judgment of the validity of causal inference. This article borrows the concept of phase transition in physics, combines causal thinking and causal diagrams, firstly establishes the relationships among the attribute, state, event, and phenomenon, and then identifies two ways with the opposite causal structures to acquire phenomena-human observations and human manipulated experiments. In causal inference, the ways mentioned above, intervention and assignment of exposure are affected by their own causal mechanisms. Finally, intervention is a causal concept, a core link among known phenomena, unknown phenomena available for measurement, and natural causality. Based on this, the two strategies in classifying research design are analyzed, and intervention method and non-intervention method are proposed, as is comprehensive and concise. Observations and experiments provide the basis for all scientific knowledge and should be viewed as concepts with a unified connotation. The accurate classification of research designs based on the law of causality and measurement process may be one of the best options worthy of in-depth study.

Plastome Evolution in the Hyperdiverse Genus Euphorbia (Euphorbiaceae) Using Phylogenomic and Comparative Analyses: Large-Scale Expansion and Contraction of the Inverted Repeat Region

With c. 2,000 species, Euphorbia is one of the largest angiosperm genera, yet a lack of chloroplast genome (plastome) resources impedes a better understanding of its evolution. In this study, we assembled and annotated 28 plastomes from Euphorbiaceae, of which 15 were newly sequenced. Phylogenomic and comparative analyses of 22 plastome sequences from all four recognized subgenera within Euphorbia revealed that plastome length in Euphorbia is labile, presenting a range of variation c. 42 kb. Large-scale expansions of the inverted repeat (IR) region were identified, and at the extreme opposite, the near-complete loss of the IR region (with only 355 bp left) was detected for the first time in Euphorbiaceae. Other structural variations, including gene inversion and duplication, and gene loss/pseudogenization, were also observed. We screened the most promising molecular markers from both intergenic and coding regions for phylogeny-based utilities, and estimated maximum likelihood and Bayesian phylogenies from four datasets including whole plastome sequences. The monophyly of Euphorbia is supported, and its four subgenera are recovered in a successive sister relationship. Our study constitutes the first comprehensive investigation on the plastome structural variation in Euphorbia and it provides resources for phylogenetic research in the genus, facilitating further studies on its taxonomy, evolution, and conservation.

Six new species of Begonia from Guangxi, China

BACKGROUND

With currently 1980 described species, the mega-diverse Begonia is now perhaps the 5th largest flowering plant genus, expanding rapidly from ca. 900 species in 1997 to its current size in merely two decades. In continuation of our studies of Asian Begonia, we report six additional new species from Guangxi, the region/province harboring the second richest Begonia flora of China.

RESULTS

Based on morphological and molecular data, the new species B. aurora belongs to Begonia sect. Platycentrum, while the other five new species (viz. B. larvata, B. longiornithophylla, B. lui, B. scabrifolia, and B. zhuoyuniae) are members of Sect. Coelocentrum. Somatic chromosome numbers of B. longiornithophylla and B. zhuoyuniae at metaphase were counted as 2n = 30, consistent with previously reports for Sect. Coelocentrum.

CONCLUSIONS

With the addition of the six new species, the total number of Begonia species in Guangxi increases from 86 to 92. Detailed description, line drawings, and color plates are provided to aid in identification.

[Association and interaction of pre-pregnant body mass index and gestational weight gain of women on neonatal birthweight]

Objective: To investigate the association between maternal pre-pregnant body mass index and gestational weight gain, as well as their interaction on neonatal birthweight. Methods: We built a cohort in Anqing Municipal Hospital from January 2014 to March 2015, enrolling pregnant women who decided to give birth in this hospital. All women were asked to fill a questionnaire for basic information collection. Medical information of both pregnant women and their newborns were obtained through electronic medical record. Chi-square analysis, multinomial logistic regression, multiplicative and additive interaction methods were used to analyze the association between pre-pregnant body mass index and gestational weight gain as well as their interactions on birth weight of the neonates. Results: A total of 2 881 pregnant women were included in this study. Of the 2 881 newborns, 359 (12.46%) were small for gestational age (SGA) and 273 (9.48%) were large for gestational age (LGA). After adjusting the possible confounding factors, results from the multinomial logistic regression showed that pre-pregnancy underweight women were more possible to deliver SGA (aRR=1.33, 95%CI: 1.02-1.73). If the gestational weight gain was below the recommended criteria, the risk of SGA (aRR=1.64, 95%CI: 1.23-2.19) might increase. Pre-pregnancy overweight/obese could increase the risk of being LGA (aRR=1.86, 95%CI: 1.33-2.60). Maternal gestational weight gain above the recommendation level was associated with higher rates of LGA (aRR=2.03, 95%CI: 1.49-2.78). Results from the interaction analysis showed that there appeared no significant interaction between pre-pregnancy BMI and gestational weight on birthweight. Conclusion: Pre-pregnancy body mass index and gestational weight gain were independently associated with neonatal birthweight while pre-pregnancy BMI and gestational weight gain did not present interaction on birthweight.

[Comparison of results of two immunoassays for detection of hepatitis B surface antigen in pregnant women]

Objective: To evaluate and compare the detection consistency of hepatitis B surface antigen (HBsAg) by two immunoassays: enzyme-linked immunosorbent assay (ELISA) and electrochemiluminescent immunoassay (ECLIA). Methods: A prospective study was conducted among 2 296 pregnant women recruited consecutively from January 1, 2014 to January 31, 2015 in a hospital. Blood samples were collected from them for the detection of HBsAg by using ELISA and ECLIA, Kappa test was performed on the results. Nested polymerase chain reaction and sequencing of HBV S gene were also performed in all samples. Phylogenetic analysis was performed using Mega 6.0 software. Results: The two methods had high detection consistence of HBsAg (Kappa=0.71). There were significant differences in detection result of B genotype and adw2 serotype HBV strains between two methods. Among 123 identified HBV strains, 113 belonged to genotype B and available for further analysis. The difference in detection of substitution rates between two methods or different positive groups were not significant. Compared with ELISA single positive group, the ECLIA single positive group had completely different substitution sites. Conclusion: The two methods had high detection consistence of HBsAg, but there were still 32.4% HBV DNA positive cases in ELISA/ECLIA single positive group, and complete complementary substitution sites between ELISA single positive group and ECLIA single positive group. Our results suggested that more effective detection procedure should be considered for the possible impact of the HBV silent transmission and infection.

[Influence of intrahepatic cholestasis during pregnancy on the incidence of preterm birth]

Objective: Intrahepatic cholestasis during pregnancy (ICP) and its relation to incidence of preterm birth (PTB) were under study. Methods: A prospective cohort study was carried out that including all the hospitalized pregnant women with live singleton births, from January 2014 to March 2015 in Anqing Municipal Hospitals. Informed consent was followed in every pregnant woman with related demographic information collected through questionnaire and hospital electronic medical record system. Both univariate and multi-variate statistical methods were used to analyze the relations between ICP and incidence of PTB. Results: A total of 2 758 pregnant women were included in this study. The incidence proportions of ICP and PTB appeared as 7.25% and 16.28% respectively. Results from the logistic regression analysis showed that ICP increased the risk of both overall PTB (RR=2.33, 95%CI: 1.67-3.25) and medically indicated PTB (RR=8.46, 95%CI: 5.45-13.12), but not the spontaneous PTB (RR=0.94, 95%CI: 0.57-1.54). Conclusion: ICP seemed to have increased the risk on medically indicated PTB but not the spontaneous PTB.

Preponderance of clonality triggers loss of sex in Bulbophyllum bicolor, an obligately outcrossing epiphytic orchid

Vegetative propagation (clonal growth) conveys several evolutionary advantages that positively affect life history fitness and is a widespread phenomenon among angiosperms that also reproduce sexually. However, a bias towards clonality can interfere with sexual reproduction and lead to sexual extinction, although a dearth of effective genetic tools and mathematical models for clonal plants has hampered assessment of these impacts. Using the endangered tropical epiphytic or lithophytic orchid Bulbophyllum bicolor as a model, we integrated an examination of breeding system with 12 microsatellite loci and models valid for clonal species to test for the "loss of sex" and infer likely consequences for long-term reproductive dynamics. Bagging experiments and field observations revealed B. bicolor to be self-incompatible and pollinator-dependent, with an absence of fruit-set over 4 years. Challenging the assumptions that clonal populations can be as genotypically diverse as sexually reproducing ones and that clonality does not greatly influence genetic structure, just 22 multilocus genotypes were confirmed among all 15 extant natural populations, 12 of the populations were found to be monoclonal, and all three multiclonal ones exhibited a distinct phalanx clonal architecture. Our results suggest that all B. bicolor populations depend overwhelmingly on clonal growth for persistence, with a concomitant loss of sex due to an absence of pollinators and a lack of mating opportunities at virtually all sites, both of which are further entrenched by habitat fragmentation. Such cryptic life history impacts, potentially contributing to extinction debt, could be widespread among similarly fragmented, outcrossing tropical epiphytes, demanding urgent conservation attention.

Inhibition of evoked glutamate release by neurosteroid allopregnanolone via inhibition of L-type calcium channels in rat medial prefrontal cortex

Allopregnanolone is one of the most important neurosteroids in the brain. We studied the effect and mechanism of allopregnanolone on spontaneous and evoked glutamate release in the medial prefrontal cortex using electrophysiological and biochemical methods combined with pharmacological approaches. The results showed that allopregnanolone had no effects on the frequency of miniature excitatory postsynaptic current (mEPSCs), but inhibited the depolarizing agent veratridine-evoked increase in the frequency of spontaneous excitatory postsynaptic currents (sEPSCs) and inhibited the first of the two responses evoked by a pair of electrical pulses more effectively than the second, resulting in increased paired-pulse facilitation (PPF) and thus suggesting a presynaptic inhibitory effect on electrical pulse-evoked glutamate release. A similar effect was also obtained for the effect of allopregnanolone on protein kinase A (PKA) activation, an upstream event of presynaptic glutamate release. Interestingly, allopregnanolone had none of these effects in the striatum. In the study of the upstream mechanism of the PKA inhibition by allopregnanolone, we found that allopregnanolone inhibited extracellular calcium influx-evoked PKA activation, but had no effects on intracellular calcium store release-evoked PKA activation; L-type calcium channel antagonists, but not N- and P/Q-type calcium channel antagonist, blocked the effect of allopregnanolone; allopregnanolone inhibited L-type calcium channel agonist-evoked increase in the PKA activity, intrasynaptosomal calcium concentration and frequency of sEPSCs. These results suggest that allopregnanolone inhibits evoked glutamate release via the inhibition of L-type calcium channels in the medial prefrontal cortex, but does not in the striatum.