Gossypium hirsutum has proven difficult to sequence owing to its complex allotetraploid (AtDt) genome. Here we produce a draft genome using 181-fold paired-end sequences assisted by fivefold BAC-to-BAC sequences and a high-resolution genetic map. In our assembly 88.5% of the 2,173-Mb scaffolds, which cover 89.6%∼96.7% of the AtDt genome, are anchored and oriented to 26 pseudochromosomes. Comparison of this G. hirsutum AtDt genome with the already sequenced diploid Gossypium arboreum (AA) and Gossypium raimondii (DD) genomes revealed conserved gene order. Repeated sequences account for 67.2% of the AtDt genome, and transposable elements (TEs) originating from Dt seem more active than from At. Reduction in the AtDt genome size occurred after allopolyploidization. The A or At genome may have undergone positive selection for fiber traits. Concerted evolution of different regulatory mechanisms for Cellulose synthase (CesA) and 1-Aminocyclopropane-1-carboxylic acid oxidase1 and 3 (ACO1,3) may be important for enhanced fiber production in G. hirsutum.

The study of positive species interactions is a rapidly evolving field in ecology. Despite decades of research, controversy has emerged as to whether positive and negative interactions predictably shift with increasing environmental stress as hypothesised by the stress-gradient hypothesis (SGH). Here, we provide a synthesis of 727 tests of the SGH in plant communities across the globe to examine its generality across a variety of ecological factors. Our results show that plant interactions change with stress through an outright shift to facilitation (survival) or a reduction in competition (growth and reproduction). In a limited number of cases, plant interactions do not respond to stress, but they never shift towards competition with stress. These findings are consistent across stress types, plant growth forms, life histories, origins (invasive vs. native), climates, ecosystems and methodologies, though the magnitude of the shifts towards facilitation with stress is dependent on these factors. We suggest that future studies should employ standardised definitions and protocols to test the SGH, take a multi-factorial approach that considers variables such as plant traits in addition to stress, and apply the SGH to better understand how species and communities will respond to environmental change.

Restoration has been elevated as an important strategy to reverse the decline of coastal wetlands worldwide. Current practice in restoration science emphasizes minimizing competition between outplanted propagules to maximize planting success. This paradigm persists despite the fact that foundational theory in ecology demonstrates that positive species interactions are key to organism success under high physical stress, such as recolonization of bare substrate. As evidence of how entrenched this restoration paradigm is, our survey of 25 restoration organizations in 14 states in the United States revealed that >95% of these agencies assume minimizing negative interactions (i.e., competition) between outplants will maximize propagule growth. Restoration experiments in both Western and Eastern Atlantic salt marshes demonstrate, however, that a simple change in planting configuration (placing propagules next to, rather than at a distance from, each other) results in harnessing facilitation and increased yields by 107% on average. Thus, small adjustments in restoration design may catalyze untapped positive species interactions, resulting in significantly higher restoration success with no added cost. As positive interactions between organisms commonly occur in coastal ecosystems (especially in more physically stressful areas like uncolonized substrate) and conservation resources are limited, transformation of the coastal restoration paradigm to incorporate facilitation theory may enhance conservation efforts, shoreline defense, and provisioning of ecosystem services such as fisheries production.shoreline defense | facilitation | coastal wetlands | wetland restoration D egradation of coastal ecosystems is occurring worldwide (1).Human-generated threats such as overharvesting, eutrophication, climate change, habitat destruction, and pollution have threatened these valuable ecosystems at local, regional and global scales (2-6). As these threats have intensified and combined, substantial declines in overall habitat coverage have occurred in almost all major coastal ecosystems, including those generated by key habitat-forming foundation species. For example, oyster reefs have declined by at least ∼85% (7), coral reefs by ∼19% (8), seagrasses by ∼29% (9), North American salt marshes by ∼42% (10), and mangroves by ∼35% (1). Because these ecosystems generate some of the richest biodiversity hotspots on Earth (11, 12), and provide critical services for human populations, including storm protection (13), fisheries production (2, 14, 15), and carbon storage (16, 17), conservation resources totaling over 1 billion US dollars have been spent globally in an attempt to halt and reverse the decline of foundation species in the coastal realm (18,19).A number of strategies have been used to conserve coastal ecosystems, including threat reduction, marine protected areas, buffer establishment, and international treaties. Habitat restoration, although in existence for many decades, has only recently been elevated as a global strategy for ...

Abstract. Since proposed two decades ago, the stress-gradient hypothesis (SGH), suggesting that species interactions shift from competition to facilitation with stress, has been widely examined. Despite broad support across species and ecosystems, ecologists debate whether the SGH applies to extreme environments, arguing that species interactions switch to competition or collapse under extreme stress. We show that facilitation often expands distributions on species borders. SGH exceptions occur when weak stress gradients or stresses outside of species' niches are examined, multiple stresses co-occur canceling out their effects, temporally dependent effects are involved, or results are improperly analyzed. We suggest that ecologists resolve debates by standardizing key SGH terms, such as fundamental and realized niche, stress gradients vs. environmental gradients, by quantitatively defining extreme stress, and by critically evaluating the functionality of stress gradients. We also suggest that new research examine the breadth and relevance of the SGH. More rigor needs to be applied to SGH tests to identify actual exceptions rather than those due to failures to meet its underlying assumptions, so that the general principles of the SGH and its exceptions can be incorporated into ecological theory, conservation strategies, and environmental change predictions.