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Phylogenomic evidence from an increasing number of studies has demonstrated that different data sets and analytical approaches often reconstruct strongly supported but conflicting relationships. In this study, 785 single‐copy nuclear genes and 75 complete plastomes were used to infer the phylogenetic relationships and estimate the historical biogeography of the apple genus Malus sensu lato, an economically important lineage disjunctly distributed in the Northern Hemisphere and involved in known and suspected hybridization and allopolyploidy events. The nuclear phylogeny recovered the monophyly of Malus s.l. (including Docynia); however, the genus was supported to be biphyletic in the plastid phylogeny. An ancient chloroplast capture event in the Eocene in western North America best explains the cytonuclear discordance. Our conflict analysis demonstrated that ILS, hybridization, and allopolyploidy could explain the widespread nuclear gene tree discordance. One deep hybridization event (Malus doumeri) and one recent event (Malus coronaria) were detected in Malus s.l. Furthermore, our historical biogeographic analysis integrating living and fossil data supported a widespread East Asian‐western North American origin of Malus s.l. in the Eocene, followed by several extinction and dispersal events in the Northern Hemisphere. We also propose a general workflow for assessing phylogenomic discordance and biogeographic analysis using deep genome skimming data sets.

IntroductionThis paper presents an epidemiologic study of appendicitis in Taiwan over a twelve-year period. An analysis of the incidence in the low-income population (LIP) is included to explore the effects of lower socioeconomic status on appendicitis.MethodsWe analyzed the epidemiological features of appendicitis in Taiwan using data from the National Health Insurance Research Database (NHIRD) from 2000 to 2011. All cases diagnosed as appendicitis were enrolled.ResultsThe overall incidences of appendicitis, primary appendectomy, and perforated appendicitis were 107.76, 101.58, and 27.20 per 100,000 per year, respectively. The highest incidence of appendicitis was found in persons aged 15 to 29 years; males had higher rates of appendicitis than females at all ages except for 70 years and older. Appendicitis rates were 11.76 % higher in the summer than in the winter months. A multilevel analysis with hierarchical linear modeling (HLM) revealed that male patients, younger patients (aged ≤14 years), and elderly patients (aged ≥60 years) had a higher risk of perforated appendicitis; among adults, the incidence increased with age. Moreover, the risk of perforation was higher in patients with one or more comorbidities. LIP patients comprised 1.25 % of the total number of patients with appendicitis from 2000 to 2011. The overall incidence of appendicitis was 34.99 % higher in the LIP than in the normal population (NP), and the incidence of perforated appendicitis was 40.40 % higher in the LIP than in the NP. After multivariate adjustment, the adjusted hospital costs and length of hospital stay (LOS) for the LIP patients were higher than those for the NP patients.ConclusionsAppendicitis and appendectomy in Taiwan had similar overall incidences, seasonality patterns, and declining trends compared to numerous previous studies. Compared to NP patients, LIP patients had a higher risk of appendicitis, longer LOS and higher hospital costs as a result of appendectomy.

Adaptation to cool climates has occurred several times in different angiosperm groups. Among them, Pooideae, the largest grass subfamily with ∼3,900 species including wheat and barley, have successfully occupied many temperate regions and play a prominent role in temperate ecosystems. To investigate possible factors contributing to Pooideae adaptive evolution to cooling climates, we performed phylogenetic reconstruction using five gene sets (with 1234 nuclear genes and their subsets) from 157 transcriptomes/genomes representing all 15 tribes and 24 of 26 subtribes. Our phylogeny supports the monophyly of all tribes (except Diarrheneae) and all subtribes with at least 2 species, with strongly supported resolution of their relationships. Molecular dating suggests that Pooideae originated in the late Cretaceous, with subsequent divergences under cooling conditions first among many tribes from the early-middle to late Eocene and again among genera in the middle Miocene and later periods. We identified a cluster of gene duplications (CGD5) shared by the core Pooideae (with 80% Pooideae species) near the Eocene-Oligocene transition, coinciding with the transition from closed to open habitat and an upshift of diversification rate. Molecular evolutionary analyses homologs of CBF for cold resistance uncovered tandem duplications during the core Pooideae history, dramatically increasing their copy number and possibly promoting adaptation to cold habitats. Moreover, duplication of AP1/FUL-like genes before the Pooideae origin might have facilitated the regulation of the vernalization pathway under cold environments. These and other results provide new insights into factors that likely have contributed to the successful adaptation of Pooideae members to temperate regions.