Genomic consequences of a recent three‐way admixture in supplemented wild brown trout populations revealed by local ancestry tracts

Understanding the evolutionary consequences of human‐mediated introductions of domesticated strains into the wild and their subsequent admixture with natural populations is of major concern in conservation biology. However, the genomic impacts of stocking from distinct sources (locally derived vs. divergent) on the genetic integrity of wild populations remain poorly understood. We designed an approach based on estimating local ancestry along individual chromosomes to provide a detailed picture of genomic admixture in supplemented populations. We used this approach to document admixture consequences in the brown trout Salmo trutta, for which decades of stocking practices have profoundly impacted the genetic make‐up of wild populations. In southern France, small local Mediterranean populations have been subject to successive introductions of domestic strains derived from the Atlantic and Mediterranean lineages. To address the impact of stocking, we evaluate the extent of admixture from both domestic strains within populations, using 75,684 mapped SNPs obtained from double‐digested restriction site‐associated DNA sequencing. Then, the chromosomal ancestry profiles of admixed individuals reveal a wider diversity of hybrid and introgressed genotypes than estimated using classical methods for inferring ancestry and hybrid pedigrees. In addition, the length distribution of introgressed tracts retained different timings of introgression between the two domestic strains. We finally reveal opposite consequences of admixture on the level of polymorphism of the recipient populations between domestic strains. Our study illustrates the potential of using the information contained in the genomic mosaic of ancestry tracts in combination with classical methods based on allele frequencies for analysing multiple‐way admixture with population genomic data.     

Diversity and ecology of soil fungal communities in rubber plantations

Monoculture rubber cultivation and its intensive associated human activities are known to have a negative impact on the biodiversity, ecology, and biological conservation of the ecosystems in which they occur. These negative impacts include changes to the biodiversity and function of soil fungal communities, which contribute towards nutrient cycling and interact with other organisms in belowground ecosystems, and may be pathogens. Despite the important role of soil fungi in rubber plantations, these communities have been poorly studied. In this paper, we review the existing literature on the diversity and ecology of belowground fungi in rubber plantations. Various groups of soil fungi, including saprobes, symbionts, and pathogens are discussed. Additionally, the role of plantation management is discussed in the context of both pathogenic soil fungi and the promotion of beneficial soil fungi. Management practices include clone selection, tree age and planting density, application of chemicals, and intercropping systems. Our review shows the strong need for further research into the effects of monoculture rubber plantations on soil fungal communities, and how we can best manage these systems in the future, in order to create a more sustainable approach to rubber production.     

Commercial harvest and export of snapping turtles (Chelydra serpentina) in the United States: trends and the efficacy of size limits at reducing harvest

As Asian turtle populations have crashed, China has increasingly turned to international import to meet domestic demand, which has increased pressure on global turtle populations. Snapping turtles (Chelydra serpentina) are being harvested in unprecedented numbers in the United States (US) to meet the needs of this international market. Here we report US snapping turtle live export from 1999 to 2013, and for the first time test the effectiveness of size limits in reducing commercial harvest numbers. Over three million live snapping turtles from farm and wild caught stock were exported from the US to Asia in 2012–14 alone. Increases in the export of wild caught snapping turtles to over 200,000 individuals in 2012 and 2014, compared to under 50,000 in other years, may indicate that farms are becoming unable to keep up with increasing demand. Annual harvest pressure at the state level increased linearly from 1998 to 2013, mirroring trends in federal export over the same time period. Our model estimates that size-limits were effective at reducing harvest by 30–87% in years with high harvest pressure. However, the majority of size limit regulations result in the removal of larger breeding adults, which has been shown to be detrimental to long term population viability. Regulatory approaches dedicated to the long term management of this iconic species will need to balance the short term gains, in the form of reduced harvest rates, with long term population viability.     

Impact of the non-indigenous shrub species Spartium junceum (Fabaceae) on native vegetation in central Spain

Aims The introduction of potentially invasive species through ornamental cultivation or for rehabilitation purposes is a serious environmental problem. They cause damage to biodiversity through loss, increased mortality or ' in situ ' selection phenomena in natural flora. Spartium junceum is a Mediterranean shrub that is not native in most areas of the Iberian Peninsula, although it is extensively grown for the rehabilitation of roadsides. We have investigated the effect on the native vegetation of an old S. junceum (Fabaceae) plantation in a conservation area in the centre of the Iberian Peninsula: the Cuenca Alta del Manzanares nature reserve in Madrid.Methods We compared S. junceum stands with the native nanophanerophytic Cistus ladanifer community at different ecosystem properties: soil properties, temporal soil seed bank contents, standing vegetation and net primary production of annual grasslands growing in these shrublands.Important findings The results highlighted S. junceum 's ability to become established in the new environment (marginal areas of the nature reserve) and ensure its successful growth. This is more apparent in northern and eastern exposures where this formation contacts with the core of the best conserved native vegetation in the nature reserve. Soils under Spartium showed a higher nitrogen content, indicating its capacity—in common with other legumes—to fix N, and conferring an advantage over Cistus, which is N-limited. Other soil nutrients such as phosphorus, magnesium and calcium and water availability are also higher in Spartium soils than in Cistus. Phosphorus is usually a constraint for N-fixers, but in our study, it is the most significant soil variable in both shrub formations and is important to the success of Spartium. Water availability is a key factor for Mediterranean vegetation, and particularly in autumn when soils are recharged. The Spartium formation is able to retain water as its growth produces a closer canopy than Cistus, thereby preventing water evaporation and contributing to the success of this species. Perennials are more frequent in the standing vegetation than in the seed bank, whereas therophytes are similar. The standing vegetation has therophytes and chamaephytes as the predominant growth forms in Spartium sites, and hemicryptophytes and phanerophytes in Cistus. Therophytes are dominant in Spartium and Cistus seed banks, although the first formation has more species. Spartium has a higher number of hemicryptophytes and Cistus is higher in phanerophytes. Northern and eastern aspects show significant differences in richness—with a predominance of annual weed species in Spartium —and in above-ground net primary production, probably as a consequence of the nutrients present in the soils. Ruderal annual species under Spartium (Bromus tectorum, Chenopodium album) have higher germination rates in the greenhouse than in the standing vegetation, suggesting they are at potential risk if environmental conditions change.     

Thicket expansion in a South African savanna under divergent land use: local vs. global drivers?

Woody plant increase in grassy biomes has been widely reported over the last century. Increases have been attributed to local drivers associated with land use change, such as heavy grazing or fire suppression, or, controversially, to global drivers such as increased atmospheric carbon dioxide (CO₂). Here, we report a comparison of woody increase since the 1930s in three neighbouring areas with highly contrasting land use systems to help distinguish between local and global causes of woody increase. Aerial photography was used to measure changes in tree cover for three time intervals (1937, 1960, 2004) for three adjacent 25 km² sites which remained under radically different tenure (conservation, commercial farms, and communal rangeland) over the study period. From previous studies on drivers affecting savanna dynamics, we predicted a decrease in tree cover for the conservation and communal sites and an increase in tree cover at the commercial site. The analyses showed highly significant increases in tree cover at all sites. Total tree cover increased from 14% in 1937 to 58% in 2004 at the conservation site, 3–50% in the commercial ranching area and 6–25% in the communal farming area. Reconstruction of past land use practices showed large differences in stocking rates, herbivore species, burning practices, human population densities and natural resource harvesting between the three sites. These land use differences are reflected in differences in woody cover among the three sites in 2004. However, despite major differences in land use, tree cover also increased significantly in all three areas. This suggests global drivers favouring woody plant increase in grassy vegetation regardless of land use practises. In our study area the most likely candidates are increased CO₂ and/or atmospheric nitrogen deposition.     

农林复合系统固碳潜力研究进展

农林复合系统是解决当前资源枯竭、农林用地紧张和实现环境保护的一种可持续土壤管理模式。自《京都议定书》签订以来, 农林复合系统因其较高的固碳潜力引起了科学家的广泛关注。深入理解农林复合系统的固碳过程及其对气候变化、环境条件的改变和管理措施的响应, 是准确地预测农林复合系统在全球变化情景下固碳潜力的关键。该文综述了农林复合系统的概念和分类, 探讨了农林复合系统相比单一系统的固碳潜力及固碳机理, 分析了农林复合系统固碳潜力的测定方法和当前面临的挑战, 综述了气候因子、环境条件和人为管理措施对农林复合系统固碳潜力的影响。我国农林复合系统的固碳潜力相比全球其他区域还处于较低水平, 为提高我国农林复合系统的固碳潜力, 未来需要加强以下四个方面的工作: 扩大农林复合系统的分布面积、加强农林复合系统的合理配置和管理、选择适宜的物种组合和优化系统的群体结构。     

人类聚居地的古树:分布格局、驱动因素与保护实践

古树是人类聚居地最具标志性的生物体,具有极其重要的社会文化和生态价值。由于人类活动和气候变化的影响,全球范围内的古树正面临衰退。如何保护人类聚居地的古树及其社会文化和生态价值是科学家和林业管理者需要共同思考的问题。尽管目前在世界范围内有一定数量的古树研究论文发表,但仍然缺乏对人类聚居地古树研究现状和观点的总结。我们从古树的社会文化和生态价值、分布格局和驱动因素、保护的文化根源和保护实践,以及古树保护面临的挑战等方面对目前人类聚居地古树的研究现状和观点进行了综述。希望能够对未来古树的研究提供一定的思考和启发,并为古树的可持续保护提供建议和参考。     

Does seed mass drive interspecies variation in the effect of management practices on weed demography?

Optimizing the effect of management practices on weed population dynamics is challenging due to the difficulties in inferring demographic parameters in seed banks and their response to disturbance. Here, we used a long‐term plant survey between 2006 and 2012 in 46 French vineyards and quantified the effects of management practices (tillage, mowing, and herbicide) on colonization, germination, and seed survival of 30 weed species in relation to their seed mass. To do so, we used a recent statistical approach to reliably estimate demographic parameters for plant populations with a seed bank using time series of presence–absence data, which we extended to account for interspecies variation in the effects of management practices on demographic parameters. Our main finding was that when the level of disturbance increased (i.e., in plots with a higher number of herbicides, tillage, or mowing treatments), colonization success and survival in large‐seeded species increased faster than in small‐seeded species. High disturbance through tillage increased survival in the seed bank of species with high seed mass. The application of herbicides increased germination, survival, and colonization probabilities of species with high seed mass. Mowing, representing habitats more competitive for light, increased the survival of species with high seed mass. Overall, the strong relationships between the effects of management practices and seed mass provide an indicator for predicting the dynamics of weed communities under disturbance.