Population genomic footprints of selection and associations with climate in natural populations of Arabidopsis halleri from the Alps

Natural genetic variation is essential for the adaptation of organisms to their local environment and to changing environmental conditions. Here, we examine genomewide patterns of nucleotide variation in natural populations of the outcrossing herb Arabidopsis halleri and associations with climatic variation among populations in the Alps. Using a pooled population sequencing (Pool‐Seq) approach, we discovered more than two million SNPs in five natural populations and identified highly differentiated genomic regions and SNPs using F_ST‐based analyses. We tested only the most strongly differentiated SNPs for associations with a nonredundant set of environmental factors using partial Mantel tests to identify topo‐climatic factors that may underlie the observed footprints of selection. Possible functions of genes showing signatures of selection were identified by Gene Ontology analysis. We found 175 genes to be highly associated with one or more of the five tested topo‐climatic factors. Of these, 23.4% had unknown functions. Genetic variation in four candidate genes was strongly associated with site water balance and solar radiation, and functional annotations were congruent with these environmental factors. Our results provide a genomewide perspective on the distribution of adaptive genetic variation in natural plant populations from a highly diverse and heterogeneous alpine environment.     

Signatures of diversifying selection at EST‐SSR loci and association with climate in natural Eucalyptus populations

Understanding the environmental parameters that drive adaptation among populations is important in predicting how species may respond to global climatic changes and how gene pools might be managed to conserve adaptive genetic diversity. Here, we used Bayesian F_ST outlier tests and allele–climate association analyses to reveal two Eucalyptus EST‐SSR loci as strong candidates for diversifying selection in natural populations of a southwestern Australian forest tree, Eucalyptus gomphocephala (Myrtaceae). The Eucalyptus homolog of a CONSTANS‐like gene was an F_ST outlier, and allelic variation showed significant latitudinal clinal associations with annual and winter solar radiation, potential evaporation, summer precipitation and aridity. A second F_ST outlier locus, homologous to quinone oxidoreductase, was significantly associated with measures of temperature range, high summer temperature and summer solar radiation, with important implications for predicting the effect of temperature on natural populations in the context of climate change. We complemented these data with investigations into neutral population genetic structure and diversity throughout the species range. This study provides an investigation into selection signatures at gene‐homologous EST‐SSRs in natural Eucalyptus populations, and contributes to our understanding of the relationship between climate and adaptive genetic variation, informing the conservation of both putatively neutral and adaptive components of genetic diversity.     

High diversity and widespread occurrence of mitotic spore mats in ectomycorrhizal Pezizales

Fungal mitospores may function as dispersal units and/ or spermatia and thus play a role in distribution and/or mating of species that produce them. Mitospore production in ectomycorrhizal (EcM) Pezizales is rarely reported, but here we document mitospore production by a high diversity of EcM Pezizales on three continents, in both hemispheres. We sequenced the internal transcribed spacer (ITS) and partial large subunit (LSU) nuclear rDNA from 292 spore mats (visible mitospore clumps) collected in Argentina, Chile, China, Mexico and the USA between 2009 and 2012. We collated spore mat ITS sequences with 105 fruit body and 47 EcM root sequences to generate operational taxonomic units (OTUs). Phylogenetic inferences were made through analyses of both molecular data sets. A total of 48 OTUs from spore mats represented six independent EcM Pezizales lineages and included truffles and cup fungi. Three clades of seven OTUs have no known meiospore stage. Mitospores failed to germinate on sterile media, or form ectomycorrhizas on Quercus, Pinus and Populus seedlings, consistent with a hypothesized role of spermatia. The broad geographic range, high frequency and phylogenetic diversity of spore mats produced by EcM Pezizales suggests that a mitospore stage is important for many species in this group in terms of mating, reproduction and/or dispersal.     

Experimental elimination of parasites in nature leads to the evolution of increased resistance in hosts

A reduction in the strength of selection is expected to cause the evolution of reduced trait expression. Elimination of a parasite should thus cause the evolution of reduced resistance to that parasite. To test this prediction in nature, we studied the fourth- and eighth-generation descendants of guppies (Poecilia reticulata) introduced into four natural streams following experimental elimination of a common and deleterious parasite (Gyrodactylus spp.). After two generations of laboratory rearing to control for plasticity and maternal effects, we infected individual fish to assess their resistance to the parasite. Contrary to theoretical expectations, the introduced guppy populations had rapidly and repeatably evolved increased resistance to the now-absent parasite. This evolution was not owing to a resistance-tolerance trade-off, nor to differences in productivity among the sites. Instead, a leading candidate hypothesis is that the rapid life-history evolution typical in such introductions pleiotropically increases parasite resistance. Our study adds a new dimension to the growing evidence for contemporary evolution in the wild, and also points to the need for a re-consideration of simple expectations from host–parasite theory. In particular, our results highlight the need for increased consideration of multiple sources of selection and pleiotropy when studying evolution in natural contexts.     

Diurnal fluctuations in seawater pH influence the response of a calcifying macroalga to ocean acidification

Coastal ecosystems that are characterized by kelp forests encounter daily pH fluctuations, driven by photosynthesis and respiration, which are larger than pH changes owing to ocean acidification (OA) projected for surface ocean waters by 2100. We investigated whether mimicry of biologically mediated diurnal shifts in pH—based for the first time on pH time-series measurements within a kelp forest—would offset or amplify the negative effects of OA on calcifiers. In a 40-day laboratory experiment, the calcifying coralline macroalga, Arthrocardia corymbosa, was exposed to two mean pH treatments (8.05 or 7.65). For each mean, two experimental pH manipulations were applied. In one treatment, pH was held constant. In the second treatment, pH was manipulated around the mean (as a step-function), 0.4 pH units higher during daylight and 0.4 units lower during darkness to approximate diurnal fluctuations in a kelp forest. In all cases, growth rates were lower at a reduced mean pH, and fluctuations in pH acted additively to further reduce growth. Photosynthesis, recruitment and elemental composition did not change with pH, but δ¹³C increased at lower mean pH. Including environmental heterogeneity in experimental design will assist with a more accurate assessment of the responses of calcifiers to OA.     

Predictive systems ecology

Human societies, and their well-being, depend to a significant extent on the state of the ecosystems that surround them. These ecosystems are changing rapidly usually in response to anthropogenic changes in the environment. To determine the likely impact of environmental change on ecosystems and the best ways to manage them, it would be desirable to be able to predict their future states. We present a proposal to develop the paradigm of predictive systems ecology, explicitly to understand and predict the properties and behaviour of ecological systems. We discuss the necessary and desirable features of predictive systems ecology models. There are places where predictive systems ecology is already being practised and we summarize a range of terrestrial and marine examples. Significant challenges remain but we suggest that ecology would benefit both as a scientific discipline and increase its impact in society if it were to embrace the need to become more predictive.     

Competitive and demographic leverage points of community shifts under climate warming

Accelerating rates of climate change and a paucity of whole-community studies of climate impacts limit our ability to forecast shifts in ecosystem structure and dynamics, particularly because climate change can lead to idiosyncratic responses via both demographic effects and altered species interactions. We used a multispecies model to predict which processes and species'' responses are likely to drive shifts in the composition of a space-limited benthic marine community. Our model was parametrized from experimental manipulations of the community. Model simulations indicated shifts in species dominance patterns as temperatures increase, with projected shifts in composition primarily owing to the temperature dependence of growth, mortality and competition for three critical species. By contrast, warming impacts on two other species (rendering them weaker competitors for space) and recruitment rates of all species were of lesser importance in determining projected community changes. Our analysis reveals the importance of temperature-dependent competitive interactions for predicting effects of changing climate on such communities. Furthermore, by identifying processes and species that could disproportionately leverage shifts in community composition, our results contribute to a mechanistic understanding of climate change impacts, thereby allowing more insightful predictions of future biodiversity patterns.     

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。     

油松天然群体的种实性状表型多样性研究

为了揭示油松天然种群在不同地理环境条件下表型变异的程度和规律,在油松整个天然分布范围内选择了12个具有代表性的居群作为研究对象,对其球果、种子、种翅等12个种实性状的变异程度及其与环境因子间关系进行了比较分析。结果显示:(1)各个性状在居群内和居群间均存在较大的变异(CV>12%)。其中千山(QS),曾家镇(ZJ)和互助(HZ)3个居群表现出了较高的变异(CV>20%),而球果干重(CDW)和种子长(CL)是所有表型性状中变异幅度最大的(CV分别为31%和21%),但种翅性状与其他性状相比具有较高的稳定性。(2)巢式设计方差分析表明,在居群内表型分化系数(Vst)变化在3.18%~89.86%之间,而群体间的Vst为38.97%;与其他针叶树种相比,油松拥有较高的表型分化系数,且居群内的变异程度远高于居群间的变异,尤其是千山(QS)、曾家镇(ZJ)和互助(HZ)3个居群,这说明油松具有较高的环境异质性适应能力或恶劣环境耐受能力。(3)相关性分析表明,该研究的各形态特征与潜在蒸发量均为负相关,且大部分形态指标间及它们与潜在蒸发量间存在显著相关性,表明潜在蒸发量是油松形态特征变化的最重要环境影响因子,预示油松最适宜生长于温暖潮湿的环境中;并表明因各形态特征间相互紧密关联,所以它们受环境条件影响而共变。