Modelling multilocus selection in an individual‐based,spatially‐explicit landscape genetics framework

We implemented multilocus selection in a spatially‐explicit, individual‐based framework that enables multivariate environmental gradients to drive selection in many loci as a new module for the landscape genetics programs, CDPOP and CDMetaPOP. Our module simulates multilocus selection using a linear additive model, providing a flexible platform to evaluate a wide range of genotype‐environment associations. Importantly, the module allows simulation of selection in any number of loci under the influence of any number of environmental variables. We validated the module with individual‐based selection simulations under Wright‐Fisher assumptions. We then evaluated results for simulations under a simple landscape selection model. Next, we simulated individual‐based multilocus selection across a complex selection landscape with three loci linked to three different environmental variables. Finally, we demonstrated how the program can be used to simulate multilocus selection under varying selection strengths across different levels of gene flow in a landscape genetics framework. This new module provides a valuable addition to the study of landscape genetics, allowing for explicit evaluation of the contributions and interactions between gene flow and selection‐driven processes across complex, multivariate environmental and landscape conditions.     

GIS interpolations of witness tree records (1839–1866) for northern Wisconsin at multiple scales

To construct forest landscape of pre‐European settlement periods, we developed a GIS interpolation approach to convert witness tree records of the U.S. General Land Office (GLO) survey from point to polygon data, which better described continuously distributed vegetation. The witness tree records (1839–1866) were processed for a 3‐million ha landscape in northern Wisconsin, U.S.A. at different scales. We provided implications of processing results at each scale. Compared with traditional GLO mapping that has fixed mapping scales and generalized classifications, our approach allows presettlement forest landscapes to be analysed at the individual species level and reconstructed under various classifications. We calculated vegetation indices including relative density, dominance, and importance value for each species, and quantitatively described the possible outcomes when GLO records are analysed at three different scales (resolution). The 1 × 1‐section resolution preserved spatial information but derived the most conservative estimates of species distributions measured in percentage area, which increased at coarser resolutions. Such increases under the 2 × 2‐section resolution were in the order of three to four times for the least common species, two to three times for the medium to most common species, and one to two times for the most common or highly contagious species. We mapped the distributions of hemlock and sugar maple from the pre‐European settlement period based on their witness tree locations and reconstructed presettlement forest landscapes based on species importance values derived for all species. The results provide a unique basis to further study land cover changes occurring after European settlement.     

Non-random distribution of individual genetic diversity along an environmental gradient

Improving our knowledge of the links between ecology and evolution is especially critical in the actual context of global rapid environmental changes. A critical step in that direction is to quantify how variation in ecological factors linked to habitat modifications might shape observed levels of genetic variability in wild populations. Still, little is known on the factors affecting levels and distribution of genetic diversity at the individual level, despite its vital underlying role in evolutionary processes. In this study, we assessed the effects of habitat quality on population structure and individual genetic diversity of tree swallows (Tachycineta bicolor) breeding along a gradient of agricultural intensification in southern Québec, Canada. Using a landscape genetics approach, we found that individual genetic diversity was greater in poorer quality habitats. This counter-intuitive result was partly explained by the settlement patterns of tree swallows across the landscape. Individuals of higher genetic diversity arrived earlier on their breeding grounds and settled in the first available habitats, which correspond to intensive cultures. Our results highlight the importance of investigating the effects of environmental variability on individual genetic diversity, and of integrating information on landscape structure when conducting such studies.     

Can landscape properties predict occurrence of grey-sided voles?

There has been a long-term decline in spring and fall numbers of Clethrionomys rufocanus in boreal Sweden in 1971–2005. Previous studies on permanent sampling plots in the centre of 2.5 × 2.5 km landscapes suggested that habitat fragmentation (sensu destruction) could have contributed to the decline. Therefore, we tested these findings in a field study and compared trapping results on the central sampling plots of landscapes with a low degree of fragmentation (LDF) and of “hot spot” type with trapping results in managed forest landscapes with a high degree of fragmentation (HDF). We predicted that C. rufocanus would be more common on the LDF plots. We used our permanent plots supplemented with a new sample of plots, mainly of the rare LDF type, inside or just outside the long-term study area. Very few voles were trapped on both plot types, and no difference was found. However, a subsequent pilot study with trapping in a national park with large areas of pristine, unfragmented forest yielded more voles than in the managed, more fragmented, areas. Consequently, the initial field study data and some other recent data were also re-analysed from a “local patch quality” perspective. This alternative approach revealed the positive importance of large focal patches of forest >60 years old and their content of old-growth (pine) forest (>100 years). Interestingly, at the landscape level, the frequency distribution of patches of forest >60 years old, old-growth (>100 years), and especially of old-growth pine forest (>100 years), relative to the properties of plots with C. rufocanus, suggested that there are few forest patches left that are suitable for C. rufocanus. Our current results suggest that habitat fragmentation cannot be excluded as a contributing cause to the long-term decline of C. rufocanus in boreal Sweden.     

Effects of resource availability and social parasite invasion on field colonies of Bombus terrestris

Abstract.  1. The survival, growth and fecundity of bumblebee colonies are affected by the availability of food resources and presence of natural enemies. Social parasites (cuckoo bumblebees and other bumblebees) can invade colonies and reduce or halt successful reproduction; however, little is known about the frequency of invasion or what environmental factors determine their success in the field.
2. We used 48 experimental colonies of the bumblebee Bombus terrestris , and manipulated both resource availability at the landscape scale and date of colony founding, to explore invasion rates of social parasites and their effect on the performance of host colonies.
3. Proximity to abundant forage resources (fields of flowering oilseed rape) and early colony founding significantly increased the probability of parasite invasion and thus offset the potential positive effects of these factors on bumblebee colony performance.
4. The study concludes that optimal colony location may be among intermediate levels of resources and supports schemes designed to increase the heterogeneity of forage resources for bumblebees across agricultural landscapes.     

1991-2017年叶尔羌河流域冰川景观格局时空演变

冰川景观变化是全球环境和气候变化的共同"指示器"。随着全球气候变化加剧，干旱和半干旱地区的冰川景观将进一步变化。科学评估冰川景观格局时空演变特征，为应对冰川景观变化及其影响提供科学参考。基于1991-2017年Landsat TM/ETM+/OLI遥感影像，采用监督分类方法获取叶尔羌河流域冰川景观时空格局及变化数据，利用景观格局指数、质心迁移模型、分形维数等方法分析近26年叶尔羌河流域冰川景观格局时空演变特征。结果表明：（1）1991-2017年叶尔羌河流域冰川斑块面积呈消减趋势，但有所减缓，共减少799.50 km²（-13.09%）。冰川斑块面积消减主要集中在海拔5400-5800 m之间，相较之下，海拔4400 m以下的区域冰川斑块面积消减率最高，达63.68%；不同坡度冰川景观消减率存在差异，陡坡冰川斑块面积消减率最高（15.98%），急陡坡消减率最低（2.87%）；阴阳两坡冰川景观均呈消减趋势，阳坡冰川斑块面积消减速率显著高于阴坡。（2）近26年来，叶尔羌河流域冰川斑块数量、最大斑块指数均减小，而平均形状指数、平均周长面积比、分裂指数均增加，表明冰川景观不断消减，破碎化程度增加。（3）研究期间，叶尔羌河流域冰川景观质心发生迁移，整体呈现东北偏移趋势。（4）通过分形理论对叶尔羌河流域冰川景观空间结构特征进行分析表明，该流域冰川景观消减率略微降低，但仍然处于持续消融状态。     

Distribution of plant functional types along gradients of disturbance intensity and resource supply in an agricultural landscape

Abstract. In this study, plant functional types are understood as groups of plants with similar biological traits displaying significant optima or maxima on a gradient plane of resource supply and disturbance intensity. The biological traits refer to expansion, vegetative regeneration, generative reproduction, dispersal and seed bank longevity. 129 vegetation samples were taken in an agricultural landscape in southwestern Germany, covering a wide range of terrestrial vegetation types – but with the exception of forests and wetlands. For each site, also soil data were recorded. Mean daily soil moisture was estimated with a simple model. Soil moisture, balanced nitrogen supply and available phosphorus were combined into a factor ‘resource supply’. In addition, disturbance intensity was estimated for each site. This factor was based on (1) frequency of disturbance, (2) disturbance depth below or above the soil surface, and (3) proportion of the area affected by a discrete disturbance event. 30 plant groups with similar biological characteristics resulted from a cluster analysis, based on a compilation of 19 biological traits for a regional species pool. Logistic regression on a gradient plane of disturbance intensity and resource supply yielded response curves for 28 groups. The dependent variable was defined as the probability of encountering all members of a group in a sample. 17 groups display a significant response curve on the gradient plane. Plants with a potential for long- range dispersal are concentrated on sites with low or high disturbance intensities (e.g. fallow land, fields, lawns). On sites with medium disturbance intensity (e.g. meadows) and low to medium resource supply, small-range dispersal predominates. There are no distinct trends concerning seed bank longevity. The potential for vertical and lateral expansion increases with decreasing disturbance intensity. Only at medium disturbance intensities does vertical expansion correlate positively with resource supply. Rapid detachment of daughter individuals occurs more often on productive sites than on less productive sites. Diversity of groups with similar biological traits is highest on sites with medium disturbance intensities.     

Monitoring an invasive perennial at the landscape scale with remote sensing

Summary   Worldwide, invasive weeds threaten agricultural, natural and urban ecosystems. In Australia's agricultural and grazing regions, invasive species often establish across extensive areas where weed management is hampered by an inability to detect the location and timing of an outbreak. In these vast landscapes, an effective detection and monitoring system is required to delineate the extent of the invasion and identify spatial and temporal factors associated with weed establishment and thickening. In this study, we utilize a time series of remote sensing imagery to detect the spatial and temporal patterns of Prickly Acacia ( Acacia nilotica ) invasion in the Mitchell grass plains of North Queensland. We develop a spectral index from Landsat images which is applied to images from 1989 to 2004, in combination with a classification mask, to identify locations and monitor changes in Prickly Acacia density across 29 000 km² of Mitchell grass plains. The approach identified spectral and temporal signatures consistent with Prickly Acacia infestation on 1.9% of this landscape. Field checking of results confirmed presence of the weed in previously unrecorded locations. The approach may be used to evaluate future spread, or outcomes of management strategies for Prickly Acacia in this landscape and could be employed to detect and monitor invasions in other extensive landscapes.     

The macronutrient composition of wild and cultivated plant foods of West African chimpanzees (Pan troglodytes verus) inhabiting an anthropogenic landscape

Agricultural expansion encroaches on tropical forests and primates in such landscapes frequently incorporate crops into their diet. Understanding the nutritional drivers behind crop-foraging can help inform conservation efforts to improve human-primate coexistence. This study builds on existing knowledge of primate diets in anthropogenic landscapes by estimating the macronutrient content of 24 wild and 11 cultivated foods (90.5% of food intake) consumed by chimpanzees (Pan troglodytes verus) at Bossou, Guinea, West Africa. We also compared the macronutrient composition of Bossou crops to published macronutrient measures of crops from Bulindi, Uganda, East Africa. The composition of wild fruits, leaves, and pith were consistent with previous reports for primate diets. Cultivated fruits were higher in carbohydrates and lower in insoluble fiber than wild fruits, while wild fruits were higher in protein. Macronutrient content of cultivated pith fell within the ranges of consumed wild pith. Oil palm food parts were relatively rich in carbohydrates, protein, lipids, and/or fermentable fiber, adding support for the nutritional importance of the oil palm for West African chimpanzees. We found no differences in the composition of cultivated fruits between Bossou and Bulindi, suggesting that macronutrient content alone does not explain differences in crop selection. Our results build on the current understanding of chimpanzee feeding ecology within forest-agricultural mosaics and provide additional support for the assumption that crops offer primates energetic benefits over wild foods.