International principles and standards for native seeds in ecological restoration

The growing demand for native seeds in ecological restoration and rehabilitation, whether for mining, forest, or ecosystem restoration, has resulted in a major global industry in the sourcing, supply, and sale of native seeds. However, there are no international guidance documents for ensuring that native seeds have the same standards of quality assurance that are regular practice in the crop and horticultural industries. Using the International Principles and Standards for the Practice of Ecological Restoration as a foundation document, we provide for the first time a synthesis of general practices in the native seed supply chain to derive the Principles and Standards for Native Seeds in Ecological Restoration (“Standards”). These practices and the underpinning science provide the basis for developing quality measures and guidance statements that are adaptable at the local, biome, or national scale. Importantly, these Standards define what is considered native seed in ecological restoration and highlight the differences between native seeds versus seeds of improved genetics. Seed testing approaches are provided within a logical framework that outline the many different dormancy states in native seed that can confound restoration outcomes. A “pro‐forma” template for a production label is included as a practical tool that can be customized for local needs and to standardize reporting to end‐users on the level of seed quality and germinability to be expected in a native seed batch. These Standards are not intended to be mandatory; however, the guidance statements provide the foundation upon which regulatory approaches can be developed by constituencies and jurisdictions.     

A comprehensive landscape genomics approach for seed sourcing strategies in landscapes under varying degrees of habitat disturbance

As most ecosystems around the world are threatened by anthropogenic degradation and climate change, there is an increasing urgency to implement restoration strategies aiming at ensuring ecosystem self‐sustainability and resilience. An initial step towards that goal relies on selecting the most suitable seed sources for a successful revegetation, which can be extremely challenging in highly degraded landscapes. The most common seed sourcing strategy is to select local seeds because it is assumed that plants experience strong adaptations to their natal sites. An alternative strategy is the selection of climate‐adapted genotypes to future conditions. While considering future climatic projections is important to account for spatial shifts in climate to inform assisted gene flow and translocations, to restore highly degraded landscapes we need a comprehensive approach that first accounts for species adaptations to current at‐site environmental conditions. In this issue of Molecular Ecology Resources, Carvalho et al. present a novel landscape genomics framework to identify the most appropriate seed sourcing strategy for moderately and highly degraded sites by integrating genotype, phenotype and environmental data in a spatially explicit context for two native plant species with potential to help restore iron‐rich Amazonian savannas. This framework is amenable to be applicable and adapted to a broad range of restoration initiatives, as the dichotomy between focusing on the current or future climatic conditions should depend on the goals and environmental circumstances of each restoration site.     

Dendrochronological analysis of an English chest: Contributing to knowledge about wood supply and chest production in 16th century England

Historic furniture has a great ethnographic and historical value, as styles and designs responded to specific uses, fashion trends and the social status of the buyer or the commissioner. Placing it in an exact chronological and geographical production context increases our knowledge about preferences for materials, designs, and woodworking practices for household commodities. Here we present the results of dendrochronological research carried out on an English chest from a private collection. The chest is of a hybrid construction, with boarded sides and back, and a joined front with four carved linenfold panels. It had been described as made of Baltic oak and dating to the mid-16th century, a crucial transition period for which only a few early chests have been analysed. Our results demonstrate, however, that the wood from the lid, side boards and back originates from the south of England. Heartwood/sapwood border in the left side board has allowed an estimated felling date for the tree of between 1520 and 1552. Terminus post quem dates of the rest of the elements pre-dating this interval indicate that the chest was likely made in the second quarter of the 16th century, as initially described. Three linenfold panels show typical features of Baltic wood, whereas the fourth one has different characteristics and could have been made with English oak, but the lack of access to the tree-ring patterns hampers verifying this hypothesis. Mixture of provenances suggests a production workshop in London, although other town in the south with a major timber market cannot be discarded. The construction features are described, and two distinct marks found in the chest are discussed in the regional context of its production. To allow the compilation and inventory of such marks, the ‘Marks on Wood’ community has been created in Zenodo and is presented here.     

A genetic assessment of a successful seagrass meadow (Posidonia australis) restoration trial

Seagrass meadows are in decline globally. Although numerous experimental methods have been implemented to restore meadows, few have been successful in the long term. Poor decisions on the sourcing of transplants from donor sites, including poor genetic integration and/or low genetic diversity, may impact on restoration success. However, despite evidence to suggest a positive association between genetic diversity and ecological resilience, there is usually little or no input from genetic data to inform on the genetic management of ecological restoration. Cockburn Sound has seen a 77% decline in seagrass cover since 1967. A transplant trial was conducted between 2004 and 2008 with sprigs of Posidonia australis being planted into a bare sand area. Survival was monitored annually, and in 2012, we compared genetic diversity in this transplant area with the original donor site. Genetic diversity in the restored meadow was very high and comparable to the donor site, with no genetic differentiation detected. The high level of genetic diversity and choice of site may have played an important role in the success of this restoration trial. The observed natural recruits around the site after establishment of transplants suggest that local restoration efforts may improve seafloor habitat and facilitate natural expansion of the meadow.     

Modeling mate-finding behavior of the swarming polychaete,Nereis succinea,with TangoInSilico,a scientific orkflow-based simulation system for sexual searching

Summary

Pheromones can be used as attractants for the opposite sex in many environments; however, little is known about the search strategies employed in responding to pheromones in the marine environment. The spawning behavior of males of the polychaete Nereis succinea is known to be triggered at close range by a high concentration (>～10^?7 M) of pheromone, cysteine glutathione disulfide (CSSG), released by females. Since CSSG also causes acceleration of swimming and increased turning, in addition to eliciting ejaculation, we proposed the hypothesis that these behaviors elicited by low concentrations of pheromone can be used by males to find females. The current study develops a computer simulation model of male and female N. succinea behavior for testing whether male responses to low concentrations of CSSG can facilitate finding females. Video recording of female swimming behavior in the field showed spontaneous loops, spirals, and circles that have been incorporated into the model. The scientific workflow paradigm within which the computer model has been developed also incorporates a data provenance system to enable systematic replay and testing of responses to individual parameters. Output of the model shows complex turning behavior leading to successful mating encounters at concentrations as low as 3×10^?9 M CSSG. Behavior resembling the output of the model was recorded in field observations. Application of the model in the future will be used to determine what pheromone concentrations produce significant increases in the probability of mating encounters.     

兴安落叶松针叶解剖结构变化及其光合能力对气候变化的适应性

叶片易受环境因子影响,其形态解剖结构特征不但与叶片的生理功能密切相关,而且反映树木对环境变化的响应和适应。叶片结构的改变势必会改变树木的生理功能。同一树种长期生长在异质环境条件下,经过自然选择和适应,会在形态和生理特性等方面产生变异,形成特定的地理种群。另外,母体所经受的环境胁迫也会影响到其子代的生长、发育和生理等特征。因此,了解植物叶片形态结构对环境变化的响应与适应是探索植物对环境变化的响应适应机制的基础。兴安落叶松(Larix gmelinii Rupr.)是我国北方森林的优势树种,主要分布在我国东北地区,但日益加剧的气候变化可能会改变其现有的分布区。为了区分叶片对气候变化的可塑性和适应性,本研究采用同质园法比较测定了6个不同气候条件下的兴安落叶松种源的32年生树木的针叶解剖结构和光合生理相关因子,利用石蜡切片方法分析了针叶的解剖结构特征、光合能力（Pmax-a）、水分利用效率（WUE）之间的关系及其对气候变化的适应性。结果表明：表皮细胞厚度、叶肉细胞厚度、传输组织厚度、维管束厚度、内皮层厚度以及叶片总厚度均存在显著的种源间差异（P < 0.05）。叶肉细胞厚度与Pmax-a、气孔导度和WUE之间均存在显著的正相关关系（P < 0.05）。叶肉细胞厚度、表皮细胞厚度、叶片总厚度以及叶肉细胞厚度和表皮细胞厚度在叶片总厚度中所占比例均与种源地的干燥度指数（即年蒸发量与年降水量之比）呈正线性关系。这些结果说明：不同种源兴安落叶松针叶解剖结构因对种源原地气候条件的长期适应而产生显著的差异,从而引起其针叶光合作用、水分利用等生理功能发生相应的变化,从而有利于该树种在气候变化的情景下得以生存和繁衍。     

Using provenance to manage knowledge of in silico experiments

This article offers a briefing in one of the knowledge management issues of in silico experimentation in bioinformatics. Recording of the provenance of an experiment-what was done; where, how and why, etc. is an important aspect of scientific best practice that should be extended to in silico experimentation. We will do this in the context of eScience which has been part of the move of bioinformatics towards an industrial setting. Despite the computational nature of bioinformatics, these analyses are scientific and thus necessitate their own versions of typical scientific rigour. Just as recording who, what, why, when, where and how of an experiment is central to the scientific process in laboratory science, so it should be in silico science. The generation and recording of these aspects, or provenance, of an experiment are necessary knowledge management goals if we are to introduce scientific rigour into routine bioinformatics. In Silico experimental protocols should themselves be a form of managing the knowledge of how to perform bioinformatics analyses. Several systems now exist that offer support for the generation and collection of provenance information about how a particular in silico experiment was run, what results were generated, how they were generated, etc. In reviewing provenance support, we will review one of the important knowledge management issues in bioinformatics.     

短枝木麻黄种群苗期表型多样性评价

以来源于大洋洲原生种源区、亚洲原生种源区、亚洲引种次生区以及非洲引种次生区4个区域的20个种源短枝木麻黄种子和当年生幼苗为材料,通过种子千粒重以及幼苗苗高、地径、一级侧枝粗度、一级侧枝长度等7个性状对短枝木麻黄表型多样性进行了研究,以探讨种群苗期表型遗传差异,为短枝木麻黄早期遗传选择和遗传改良提供基本资料。结果表明:(1)短枝木麻黄种子千粒重在区域间和区域内种源间差异极显著,且千粒重具有显著的地理变异模式,随经度的增大而降低。(2)当年生幼苗苗高、地径在不同区域间及区域内种源间均存在极显著差异,其中泰国干东港种源幼苗生长最好(苗高76.6cm,地径4.64mm),而种源汤加的幼苗生长最差(苗高28.3cm,地径2.58mm)。(3)当年生幼苗一级侧枝粗度、一级侧枝长度、二级侧枝长度、每小枝节数和齿叶数在不同区域间及区域内种源间均存在极显著差异,其中齿叶数在区域间的变异系数最大(82.15%)。(4)通径分析表明,一级侧枝长度对苗高具有显著的正向影响作用,而一级侧枝粗度和二级侧枝长度对地径具有显著正向影响作用,它们可作为短枝木麻黄优良新品种筛选的参考因子。     

Genetic variation in productivity of foundation riparian species at the edge of their distribution: implications for restoration and assisted migration in a warming climate

We examined the hypothesis that genotypic variation among populations of commonly co‐occurring phreatophytic trees (Populus fremontii, Salix gooddingii) and the shrub (Salix exigua) regulates aboveground net primary productivity (ANPP) at a hot site at the edge of the species’ distribution. We used a provenance trial in which replicated genotypes from populations varying in mean annual temperature were transplanted to a common garden adjacent to the Lower Colorado River in southeastern California. The garden environment represented an extreme maximum temperature for the study species. Four major findings emerged: (1) Genotypic variation in ANPP was significant for all species with broad‐sense heritability (H²) across populations of 0.11, 0.13, and 0.10 for P. fremontii, S. gooddingii, and S. exigua, respectively, and within‐population H² ranging from 0.00 to 0.25, 0.00 to 0.44, and 0.02 to 0.21, respectively. (2) Population ANPP decreased linearly as mean annual maximum temperature (MAMT) transfer distance increased for both P. fremontii (r² = 0.64) and S. gooddingii (r² = 0.37), whereas it did not change for S. exigua; (3) Populations with similar MAMT to that of the common garden were 1.5 and 1.2 times more productive than populations with 5.0 °C MAMT transfer distances for P. fremontii and S. gooddingii, respectively; and (4) Variation in regression slopes among species for the relationship between ANPP and MAMT indicate species‐specific responses to temperature. As these plant species characterize a threatened habitat type and support a diverse community that includes endangered species, ecosystem restoration programs should consider using both local genotypes and productive genotypes from warmer environments to maximize productivity of riparian ecosystems in the face of global climate change.