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Summary: Tolerance of hypoxia is essential for most plants, but the underlying mechanisms are largely unknown. Here we show that adaptation to submergence induced hypoxia in Arabidopsis involves up‐regulation of RAP2.2 through interactive action of WRKY33 and WRKY12.WRKY33‐ or WRKY12‐overexpressing plants showed enhanced resistance to hypoxia. Y2H, BiFC, Co‐IP and pull‐down experiments confirmed the interaction of WRKY33 with WRKY12. Genetic experiments showed that RAP2.2 acts downstream of WRKY33/WRKY12.WRKY33 and WRKY12 can bind to and activate RAP2.2 individually. Genetic and molecular experiments demonstrate that the two WRKYs can synergistically enhance activation towards RAP2.2 to increase hypoxia tolerance. WRKY33 expression is increased in RAP2.2‐overexpressing plants, indicating a feedback regulation by RAP2.2 during submergence process, which was corroborated by EMSA, ChIP, dual‐LUC and genetic experiments.Our results show that a regulatory cascade module involving WRKY33, WRKY12 and RAP2.2 plays a key role in submergence induced hypoxia response of Arabidopsis and illuminate functions of WRKYs in hypoxia tolerance. See also the Editorial on this article by Sasidharan et al., 229: 5–7. [ABSTRACT FROM AUTHOR]

Summary: Phylogenetic analysis is complicated by interspecific gene flow and the presence of shared ancestral polymorphisms, particularly those maintained by balancing selection. In this study, we aimed to examine the prevalence of these factors during the diversification of Populus, a model tree genus in the Northern Hemisphere.We constructed phylogenetic trees of 29 Populus taxa using 80 individuals based on re‐sequenced genomes. Our species tree analyses recovered four main clades in the genus based on consensus nuclear phylogenies, but in conflict with the plastome phylogeny. A few interspecific relationships remained unresolved within the multiple‐species clade because of inconsistent gene trees. Our results indicated that gene flow has been widespread within each clade and also occurred among the four clades during their early divergence.We identified 45 candidate genes with ancient polymorphisms maintained by balancing selection. These genes were mainly associated with mating compatibility, growth and stress resistance.Both gene flow and selection‐mediated ancient polymorphisms are prevalent in the genus Populus. These are potentially important contributors to adaptive variation. Our results provide a framework for the diversification of model tree genus that will facilitate future comparative studies. [ABSTRACT FROM AUTHOR]

Summary: Nonbifurcating divergence caused by introgressive hybridization is continuously reported for groups of closely related species. In this study, we aimed to reconstruct the genome‐scale classification of deep lineages of the conifer genus Picea, establish their phylogenetic relationships and test the bifurcating hypothesis between deeply branching lineages based on genomic data.We sequenced the transcriptomes of 35 individuals of 27 taxa covering all main lineages of the genus. Four major lineages, comprising three to 12 taxa each, largely consistent with morphological evidence, were recovered across the coalescent and integrated nuclear phylogeny. However, many of the individual gene trees recovered contradict one another. Moreover, the well‐supported coalescent tree inferred here differs from previous studies based on various DNA markers, with respect to topology and inter‐lineage relationships.We identified the shared polymorphisms between four major lineages. ABBA–BABA tests confirmed the inter‐lineage gene flow and thus violated the bifurcating divergence model. Gene flow occurred more frequently between lineages distributed in the same continent than those disjunct between continents.Our results indicate that introgression and nonbifurcating diversification apply, even between deeply branching lineages of the conifer genus Picea. [ABSTRACT FROM AUTHOR]

•The effects of Quaternary climatic oscillations on the demography of organisms vary across regions and continents. In taxa distributed in Europe and North America, several paradigms regarding the distribution of refugia have been identified. By contrast, less is known about the processes that shaped the species' spatial genetic structure in areas such as the Himalayas, which is considered a biodiversity hotspot. Here, we investigated the phylogeographic structure and population dynamics of Primula tibetica by combining genomic phylogeography and species distribution models (SDMs). • Genomic data were obtained for 293 samples of P. tibetica using restriction site-associated DNA sequencing (RADseq). Ensemble SDMs were carried out to predict potential present and past distribution ranges. • Four distinct lineages were identified. Approximate Bayesian computation analyses showed that each of them have experienced both expansions and bottlenecks since their divergence, which occurred during or across the Quaternary glacial cycles. The two lineages at both edges of the distribution were found to be more vulnerable and responded in different ways to past climatic changes. • These results illustrate how past climatic changes affected the demographic history of Himalayan organisms. Our findings highlight the significance of combining genomic approaches with environmental data when evaluating the effects of past climatic changes. [ABSTRACT FROM AUTHOR]

• Many plant species comprising the present-day Arctic flora are thought to have originated in the high mountains of North America and Eurasia, migrated northwards as global temperatures fell during the late Tertiary period, and thereafter attained a circumarctic distribution. However, supporting evidence for this hypothesis that provides a temporal framework for the origin, spread and initial attainment of a circumarctic distribution by an arctic plant is currently lacking. • Here we examined the origin and initial formation of a circumarctic distribution of the arctic mountain sorrel (Oxyria digyna) by conducting a phylogeographic analysis of plastid and nuclear gene DNA variation. • We provide evidence for an origin of this species in the Qinghai-Tibet Plateau of southwestern China, followed by migration into Russia c. 11 million yr ago (Ma), eastwards into North America by c. 4 Ma, and westwards into Western Europe by c. 1.96 Ma. Thereafter, the species attained a circumarctic distribution by colonizing Greenland from both sides of the Atlantic Ocean. • Following the arrival of the species in North America and Europe, population sizes appear to have increased and then stabilized there over the last 1 million yr. However, in Greenland a marked reduction followed by an expansion in population size is indicated to have occurred during the Pleistocene. [ABSTRACT FROM AUTHOR]

• Because of heterogeneous topographies, high-mountain areas could harbor a significant pool of cryptic forest refugia (glacial microrefugia unrecognized by palaeodata), which, as a result of poor accessibility, have been largely overlooked. The juniper forests of the southern Tibetan Plateau, with one of the highest tree lines worldwide, are ideal for assessing the potential of high-mountain areas to harbor glacial refugia. • Genetic evidence for Last Glacial Maximum (LGM) endurance of these microrefugia is presented using paternally inherited chloroplast markers. Five-hundred and ninety individuals from 102 populations of the Juniperus tibetica complex were sequenced at three polymorphic chloroplast regions. • Significant interpopulation differentiation and phylogeographic structure were detected ( GST = 0.49, NST = 0.72, NST > GST, P < 0.01), indicating limited among-population gene flow. Of 62 haplotypes recovered, 40 were restricted to single populations. These private haplotypes and overall degrees of diversity were evenly spread among plateau and edge populations, strongly supporting the existence of LGM microrefugia throughout the present distribution range, partly well above 3500 m. • These results mark the highest LGM tree lines known, illustrating the potential significance of high-mountain areas for glacial refugia. Furthermore, as the close vicinity of orographic rear-edge and leading-edge populations potentially allows gene flow, surviving populations could preserve the complete spectrum of rear-edge and leading-edge adaptations. [ABSTRACT FROM AUTHOR]

• The homoploid hybrid species Pinus densata is restricted to alpine habitats that exceed the altitude range of its two parental species, Pinus tabulaeformis and Pinus yunnanensis. Alpine habitats usually generate cold-induced water stress in plants. To understand the ecological differentiation between these three species, we examined their physiological responses to drought stress. • Potted seedlings of three species were subjected to low, mild, moderate and severe water stress in an automatic-controlled glasshouse. Fifteen indicators of fitness were measured for each species in each treatment, and most of these decreased as drought increased. • Pinus densata exhibited higher fitness than both parental species in terms of total dry mass production (TDM) and long-term water use efficiency (WUEL) across all treatments; several other ecophysiological traits were also extreme but not across every treatment, and not always in the highest stress treatment. • These results indicate that extreme characters that have become well fixed in P. densata, confer a faster seedling growth rate and more efficient water use, which in turn should confer increased drought tolerance. These traits of P. densata likely promoted its ecological separation from its parental species and facilitated its successful colonization and establishment in high-altitude habitats. [ABSTRACT FROM AUTHOR]