Background Bread wheat is one of the most important and broadly studied crops. However, due to the complexity of its genome and incomplete genome collection of wild populations, the bread wheat genome landscape and domestication history remain elusive. Results By investigating the whole-genome resequencing data of 93 accessions from worldwide populations of bread wheat and its diploid and tetraploid progenitors, together with 90 published exome-capture data, we find that the B subgenome has more variations than A and D subgenomes, including SNPs and deletions. Population genetics analyses support a monophyletic origin of domesticated wheat from wild emmer in northern Levant, with substantial introgressed genomic fragments from southern Levant. Southern Levant contributes more than 676 Mb in AB subgenomes and enriched in the pericentromeric regions. The AB subgenome introgression happens at the early stage of wheat speciation and partially contributes to their greater genetic diversity. Furthermore, we detect massive alien introgressions that originated from distant species through natural and artificial hybridizations, resulting in the reintroduction of ~ 709 Mb and ~ 1577 Mb sequences into bread wheat landraces and varieties, respectively. A large fraction of these intra- and inter-introgression fragments are associated with quantitative trait loci of important traits, and selection events are also identified. Conclusion We reveal the significance of multiple introgressions from distant wild populations and alien species in shaping the genetic components of bread wheat, and provide important resources and new perspectives for future wheat breeding. Electronic supplementary material The online version of this article (10.1186/s13059-019-1744-x) contains supplementary material, which is available to authorized users.

BackgroundComparative neonatal outcomes with respect to singleton births from blastocyst transfers or cleavage-state embryo transfers are controversial with respect to which method is superior. Many studies have yielded contradictory results. We performed a systematic review and meta-analysis for the purpose of comparing neonatal outcomes in single births following IVF/ICSI.MethodsWe searched the Medline, Embase and Cochrane Central Register of Clinical Trials (CCTR) databases until October 2016. Studies and trials that contained neonatal outcomes for singleton births were included. Data were extracted in 2 × 2 tables. The analysis was performed using Rev Man 5.1 software. Risk ratios (RRs) and risk differences, with 95% confidence intervals, were calculated to assess the results of each outcome. Subgroups were applied in all outcomes. Newcastle-Ottawa scale (NOS) checklists were used to assess the quality of the referenced studies.ResultsTwelve studies met the criteria in this meta-analysis. There was a high risk of preterm birth after blastocyst embryo transfer versus the risk after cleavage-stage transfer (RR: 1.11, 95% CI: 1.01–1.22). For the “only fresh” subgroup, the outcome was coincident (RR: 1.16, 95% CI: 1.06–1.27). For the “fresh and frozen” and “only frozen” subgroups, there were no differences. Patients who received fresh blastocyst embryo transfers had a high risk of very preterm births (RR: 1.16, 95% CI: 1.02–1.31). Finally, cleavage-stage embryo transfers were associated with a high risk of infants who were small for gestational age (0.83, 95% CI: 0.76–0.92) and a low risk of those who were large for gestation age (1.14, 95% CI: 1.04–1.25).ConclusionsThe risks of preterm and very preterm births increased after fresh blastocyst transfers versus the risks after fresh cleavage-stage embryo transfers. However, in frozen embryo transfers, there were no differences. Blastocyst embryo transfers resulted in high risks of infants who were large for gestational age, and cleavage-stage embryo transfers resulted in high risks of infants who were small for gestational age.

Oceanic internal waves can be decomposed into an infinite set of modes, and the dominant internal mode 1 waves have been extensively investigated. Although mode 2 waves have been observed, they have not received comparable attention, especially the generation mechanisms. In this work, we examine the generation of mode 2 internal waves by the interaction of mode 1 waves with topography. We use a coupled linear long-wave theory with mode coupling through topography, combined with evolution using a Korteweg–de Vries model, to predict the mode 2 wave amplitude, in an ideal three-layer fluid model, in a smooth density stratification and in two realistic oceanic settings. We find that the mode 2 wave amplitude is usually much smaller than the incident mode 1 wave amplitude and is quite sensitive to the pycnocline thickness, topographic slope and background stratification.

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