Modeling the Potential Geographic Distribution of Black Pepper (Piper nigrum) in Asia Using GIS Tools

Known as the "king of spices", black pepper (Piper nigrum), a perennial crop of the tropics, is economically the most important and the most widely used spice crop in the world. To understand its suitable bioclimatic distribution, maximum entropy based on ecological niche modeling was used to model the bioclimatic niches of the species in its Asian range. Based on known occurrences, bioclimatic areas with higher probabilities are mainly located in the eastern and western coasts of the Indian Peninsula, the east of Sumatra Island, some areas in the Malay Archipelago, and the southeast coastal areas of China. Some undocumented places were also predicted as suitable areas. According to the jackknife procedure, the minimum temperature of the coldest month, the mean monthly temperature range, and the precipitation of the wettest month were identified as highly effective factors in the distribution of black pepper and could possibly account for the crop's distribution pattern. Such climatic requirements inhibited this species from dispersing and gaining a larger geographical range.

Using ecological niche models to support tree species selection for forest restoration planning in largely deforested regions

Species selection for forest restoration is often supported by expert knowledge on local distribution patterns of native tree species. This approach is not applicable to largely deforested regions unless enough data on pre-human tree species distribution is available. In such regions, ecological niche models may provide essential information to support species selection in the framework of forest restoration planning. In this study we used ecological niche models to predict habitat suitability for native tree species in "Tierra de Campos" region, an almost totally deforested area of the Duero Basin (Spain). Previously available models provide habitat suitability predictions for dominant native tree species, but including non-dominant tree species in the forest restoration planning may be desirable to promote biodiversity, specially in largely deforested areas were near seed sources are not expected. We used the Forest Map of Spain as species occurrence data source to maximize the number of modeled tree species. Penalized logistic regression was used to train models using climate and lithological predictors. Using model predictions a set of tools were developed to support species selection in forest restoration planning. Model predictions were used to build ordered lists of suitable species for each cell of the study area. The suitable species lists were summarized drawing maps that showed the two most suitable species for each cell. Additionally, potential distribution maps of the suitable species for the study area were drawn. For a scenario with two dominant species, the models predicted a mixed forest (Quercus ilex and a coniferous tree species) for almost one half of the study area. According to the models, 22 non-dominant native tree species are suitable for the study area, with up to six suitable species per cell. The model predictions pointed to Crataegus monogyna, Juniperus communis, J.oxycedrus and J.phoenicea as the most suitable non-dominant native tree species in the study area. Our results encourage further use of ecological niche models for forest restoration planning in largely deforested regions.

Ecological-economic modeling for biodiversity management: Potential, pitfalls, and prospects

Ecologists and economists both use models to help develop strategies for biodiversity management. The practical use of disciplinary models, however, can be limited because ecological models tend not to address the socioeconomic dimension of biodiversity management, whereas economic models tend to neglect the ecological dimension. Given these shortcomings of disciplinary models, there is a necessity to combine ecological and economic knowledge into ecological-economic models. It is insufficient if scientists work separately in their own disciplines and combine their knowledge only when it comes to formulating management recommendations. Such an approach does not capture feedback loops between the ecological and the socioeconomic systems. Furthermore, each discipline poses the management problem in its own way and comes up with its own most appropriate solution. These disciplinary solutions, however are likely to be so different that a combined solution considering aspects of both disciplines cannot be found. Preconditions for a successful model-based integration of ecology and economics include (1) an in-depth knowledge of the two disciplines, (2) the adequate identification and framing of the problem to be investigated, and (3) a common understanding between economists and ecologists of modeling and scale. To further advance ecological-economic modeling the development of common benchmarks, quality controls, and refereeing standards for ecological-economic models is desirable.

Projecting the fate of fish populations using ecological-economic modeling

Four marine fish species are among the most important on the world market: cod, salmon, tuna, and sea bass. While the supply of North American and European markets for two of these species - Atlantic salmon and European sea bass - mainly comes from fish farming, Atlantic cod and tunas are mainly caught from wild stocks. We address the question what will be the status of these wild stocks in the midterm future, in the year 2048, to be specific. Whereas the effects of climate change and ecological driving forces on fish stocks have already gained much attention, our prime interest is in studying the effects of changing economic drivers, as well as the impact of variable management effectiveness. Using a process-based ecological-economic multispecies optimization model, we assess the future stock status under different scenarios of change. We simulate (i) technological progress in fishing, (ii) increasing demand for fish, and (iii) increasing supply of farmed fish, as well as the interplay of these driving forces under different sce- narios of (limited) fishery management effectiveness. We find that economic change has a substantial effect on fish populations. Increasing aquaculture production can dampen the fishing pressure on wild stocks, but this effect is likely to be overwhelmed by increasing demand and technological progress, both increasing fishing pressure. The only solution to avoid collapse of the majority of stocks is institutional change to improve management effectiveness significantly above the current state. We conclude that full recognition of economic drivers of change will be needed to successfully develop an integrated ecosystem management and to sustain the wild fish stocks until 2048 and beyond.

Landscape metrics as indicators of coastal morphology and its use in ecological niche modelling of seagrass species

Dependence of some species on landscape structure has been proved in numerous studies. So far, however, little progress has been made in the integration of landscape metrics in the prediction of species associated with coastal features. Specific landscape metrics were tested as predictors of coastal shape using three coastal features of the Iberian Peninsula (beaches, capes and gulfs) at different scales. We used the landscape metrics in combination with environmental variables to model the niche and find suitable habitats for a seagrass species (Cymodocea nodosa) throughout its entire range of distribution. Landscape metrics able to capture variation in the coastline enhanced significantly the accuracy of the models, despite the limitations caused by the scale of the study. We provided the first global model of the factors that can be shaping the environmental niche and distribution of C. nodosa throughout its range. Sea surface temperature and salinity were the most relevant variables. We identified areas that seem unsuitable for C. nodosa as well as those suitable habitats not occupied by the species. We also present some preliminary results of testing historical biogeographical hypotheses derived from distribution predictions under Last Glacial Maximum conditions and genetic diversity data.

Concordance in phylogeography and ecological niche modelling identify dispersal corridors for reptiles in arid Australia

Aim: Using the rock-specialist agamid Ctenophorus caudicinctus as a model, we test hypothesized biogeographical dispersal corridors for lizards in the Australian arid zone (across the western sand deserts), and assess how these dispersal routes have shaped phylogeographical structuring. Location: Arid and semi-arid Australia. Methods: We sequenced a c. 1400 bp fragment of mtDNA (ND2) for 134 individuals of C. caudicinctus as well as a subset of each of the mtDNA clades for five nuclear loci (BDNF, BACH1, GAPD, NTF3, and PRLR). We used phylogenetic methods to assess biogeographical patterns within C. caudicinctus, including relaxed molecular clock analyses to estimate divergence times. Ecological niche modelling (Maxent) was employed to estimate the current distribution of suitable climatic envelopes for each lineage. Results: Phylogenetic analyses identified two deeply divergent mtDNA clades within C. caudicinctus - an eastern and western clade - separated by the Western Australian sand deserts. However, divergences pre-date the Pleistocene sand deserts. Phylogenetic analyses of the nuclear DNA data sets generally support major mtDNA clades, suggesting past connections between the western C. c. caudicinctus populations in far eastern Pilbara (EP) and the lineages to the east of the sand deserts. Ecological niche modelling supports the continued suitability of climatic conditions between the Central Ranges and the far EP for C. c. graafi. Main conclusions: Estimates of lineage ages provide evidence of divergence between eastern and western clades during the Miocene with subsequent secondary contact during the Pliocene. Our results suggest that this secondary contact occurred via dispersal between the Central Ranges and the far EP, rather than the more southerly Giles Corridor. These events precede the origins of the western sand deserts and divergence patterns instead appear associated with Miocene and Pliocene climate change.

The role of environmental factors in the spatial distribution of Japanese encephalitis in mainland China

Japanese encephalitis (JE) is the most common cause of viral encephalitis and an important public health concern in the Asia-Pacific region, particularly in China where 50% of global cases are notified. To explore the association between environmental factors and human JE cases and identify the high risk areas for JE transmission in China, we used annual notified data on JE cases at the center of administrative township and environmental variables with a pixel resolution of 1 km×1 km from 2005 to 2011 to construct models using ecological niche modeling (ENM) approaches based on maximum entropy. These models were then validated by overlaying reported human JE case localities from 2006 to 2012 onto each prediction map. ENMs had good discriminatory ability with the area under the curve (AUC) of the receiver operating curve (ROC) of 0.82-0.91, and low extrinsic omission rate of 5.44-7.42%. Resulting maps showed JE being presented extensively throughout southwestern and central China, with local spatial variations in probability influenced by minimum temperatures, human population density, mean temperatures, and elevation, with contribution of 17.94%-38.37%, 15.47%-21.82%, 3.86%-21.22%, and 12.05%-16.02%, respectively. Approximately 60% of JE cases occurred in predicted high risk areas, which covered less than 6% of areas in mainland China. Our findings will help inform optimal geographical allocation of the limited resources available for JE prevention and control in China, find hidden high-risk areas, and increase the effectiveness of public health interventions against JE transmission.

白豆杉的地理分布格局及潜在分布区估计

　　根据物种的分布信息结合环境因子估计物种的分布区对珍稀濒危物种的保护有着重要的意义。白豆杉Pseudotaxus chienii为第三纪孑遗植物，我国东南部地区特有，分布区狭窄。本文通过对白豆杉的标本记录研究它的地理分布，找出影响其分布的关键因子并对其潜在分布区进行估计，并解释其分布区形成的原因。全球升温将对物种分布造成重要影响，通过温度升高情况下2100年的气候数据模拟白豆杉未来的潜在分布区，估计温度升高对白豆杉的影响，将对白豆杉的保护有着重要的意义。 　　根据白豆杉的标本信息结合Diva-Gis软件对白豆杉的地理分布进行研究。以海拔图层和植被图层为底图对白豆杉的分布格局进行研究，并对白豆杉种群的多度进行统计分析。用Diva-Gis软件的气候数据提取功能提取白豆杉分布点的气候信息，并运用主成分分析对影响白豆杉分布的气候因子进行分析，找出影响白豆杉分布的主要环境因子。根据白豆杉的分布信息和气候数据，运用Diva-Gis内嵌的BIOCLIM模型和DOMAIN模型对白豆杉在不同气候条件下的潜在分布区进行估计，评价温度升高对白豆杉分布区的影响。 　　白豆杉分布格局研究结果表明，白豆杉分布在我国东南部地区中低海拔山区，白豆杉的分布和植被类型及海拔有着密切的关系。白豆杉的分布与海拔的关系表现为，由东到西，分布的最低海拔升高，海拔范围缩小。白豆杉分布地的植被类型为常绿灌木林，常绿阔叶林及针、阔叶混交林。白豆杉由东向西的海拔变化趋势与植被类型的由东向西的海拔变化趋势相一致。PCA分析结果表明白豆杉的分布与温度相关因子有着密切的关系。 　　现在气候对潜在分布区的估计表明,白豆杉的潜在分布区散布于浙、闽、粤、赣、湘，桂及黔几省各自交界之处即从浙江南部山区沿武夷山山系至南岭山系（向北到沿湘赣交界的罗宵山系）至大瑶山山系（向北沿雪峰山）。潜在分布区南部有三处分布的热点地区，即浙江南部、湖南南部和广西北部地区。三个主要分布区之间仅有有星散的潜在分布区存在，或没有潜在分布区出现，处在一种高度的隔离状态。造成这种潜在分布格局形成的原因可能有二，一是第四纪冰期的到来使白豆杉的分布区向南迁移，局部性气候的变化和地质变化可能导致了部分白豆杉的生境的消失，从而使得原来连续的分布区破碎化，形成了现在的星散分布；二是白豆杉的潜在分布区预测结果与中国东南部地区的山脉走势非常一致，山脉地带小生境多样化能够为白豆杉在垂直地带上的迁移提供更大的可能性。 　　未来气候数据对白都杉的潜在分布区估计表明，温度升高后白豆杉最适生分布区显著缩小。白豆杉的潜在分布区的地理分布格局发生了明显的变化，原来在南部的适生区明显缩小，星散程度更高。除已知的分布地外，在江西西南部武夷山、南岭山脉的湖南、广西、广东三省交界的地方都是白豆杉的适生区。江西和湖南交界的罗宵山山脉北部到井冈山都有白豆杉分布可能性较大，可以作为野外调查的重点地区。气候变化会使白豆杉在浙江、湖南南部的最适生境破碎化从而影响白豆杉的分布。生境保护对白豆杉的保护起着关键作用。

外来入侵种紫茎泽兰竞争策略与扩散动态

紫茎泽兰（Eupatorium adenophorum Spreng.）作为重要的外来入侵种之一，已严重破坏了入侵地生态系统的结构与功能，同时使当地农林业生产蒙受巨大的损失。因此，明确紫茎泽兰的竞争策略与扩散潜力，对制定合理的控制措施具有重要意义。 土壤氮素增加常常有助于外来种的入侵，那么降氮能否抵制入侵呢？向土壤中添加碳素，增强微生物对氮素的吸收，从而降低土壤中可被植物吸收的氮素是目前常用的降氮方法。为检验这一假说对入侵种紫茎泽兰的适用性，选取入侵种紫茎泽兰和本地种禾本科雀麦（Bromus japonicus）、菊科鱼眼草（Dichrocephala integrifolia），分别单栽或与紫茎泽兰混栽，向各植物组合中添加碳素（按1650克有机质/平方米计）或氮素（按30克氮素/平方米计），并设立对照进行盆栽实验。在碳素添加条件下，紫茎泽兰地上与地下生物量分别比对照降低了71.9% 和 74.9%，而本地种的生物量却没有受到显著影响。同时，碳素添加导致紫茎泽兰对本地种的竞争强度（RII）明显下降。氮素添加则减弱或逆转了上述碳素的作用。因此，向土壤中添加碳素有助于抵抗氮沉降对外来种入侵的促进作用，特别对抵御那些与氮素有亲和力的入侵种更为有效。在不同氮素条件下，紫茎泽兰对本地种竞争中，资源竞争强度均明显大于化感作用。尽管在紫茎泽兰发育早期化感作用较小，但是，碳素添加使紫茎泽兰可利用氮素减少，激发了化感作用在竞争中占有更大的比例，说明资源竞争与化感是相互结合、共同发挥作用的。 去叶作为模拟采食方法之一，至少可以通过两种方式影响植物竞争。一是去叶对目标种生长产生负面影响，二是邻种去叶有利于目标种生长，进而改变种间竞争关系。基于以上假定，对紫茎泽兰与相邻本地种分别单栽、同种合栽和异种混栽，进行去叶处理。结果恰与假定相悖：在整个生长季内，去叶增加目标株生物量的1.0 – 198.9%。对于入侵种而言，当邻居本地种去叶时，紫茎泽兰能完全弥补竞争产生的负面效应，即它与未去叶的单栽紫茎泽兰生长无显著差异;而紫茎泽兰去叶降低了相邻本地种的生长，加剧了原本由于竞争给对本地种带来的负面影响。因此，去叶效应与邻种的存在与否及邻种的类型均有关。在应用生物控制对目标株采食时，特别是在没有造成严重伤害或致死情况下，可以使本来具有竞争优势的入侵种变得更具强势。竞争与去叶之间存在复杂的相互作用，采食带来的间接效应可能比预想的更为复杂。因此，在生物控制措施实施之前，充分地估计生物控制的间接作用至关重要。 为检验反应—扩散模型（reaction–diffusion model）能否正确模拟紫茎泽兰小尺度扩散速率，本研究调查了四川攀枝花山区5个不同的生境的紫茎泽兰群落。对各样地内紫茎泽兰定位和年龄确定，基于克里金插值法做出其入侵格局的等年线图，通过等年线之间的垂直距离即可得到紫茎泽兰扩散速率的经验值。同时，计算内禀增长率和扩散系数，根据模型计算得到扩散速率的预测值。结果表明：紫茎泽兰扩散速率经验值明显小于模型预测值。因此，尽管反应—扩散模型已在大尺度扩散预测方面得到广泛的应用和验证，但在小尺度上，由于没有借助于复杂的生活史模型和分层模型，单凭反应—扩散模型不足以得到准确的预测。另外，在没有遭受干扰的生境中，可以发现紫茎泽兰扩散早期存在明显的时滞期。倘若这种时滞效应在入侵扩散中是频繁发生的，那么在判定物种是否具有入侵性时，很可能由于物种处于时滞期而被误认为非入侵种。 基于紫茎泽兰入侵至中国60年来所收集到的441已知分布记录和23个环境变量，采用GARP模型对其潜在分布范围做出了预测，并通过Kappa和ROC（receiver–operator characteristic）对预测结果进行检验。结果表明紫茎泽兰目前分布以云贵高原为主体，逐渐向四川盆地东部、山东半岛、东南沿海、台湾沿海以及海南岛等地扩散。冷季降水量、年极端低温和年均最高温对分布影响较大。RDA（Redundancy Analysis）分析结果显示温度和降水是限制紫茎泽兰扩散的重要因素。在过去的20年里，紫茎泽兰已经从温度较高、天气波动较小的亚热带气候逐渐向气候温凉、降水减少的高海拔地区扩散。紫茎泽兰可以适应相对较宽的温度和降水梯度，年均温度在10—22 ˚C，年降水量在800—2000 mm区间均有分布。本研究结果为发展早期预警工作、防止紫茎泽兰在中国进一步入侵提供了科学依据。

Shifting ranges and conservation challenges for lemurs in the face of climate change.

Geospatial modeling is one of the most powerful tools available to conservation biologists for estimating current species ranges of Earth's biodiversity. Now, with the advantage of predictive climate models, these methods can be deployed for understanding future impacts on threatened biota. Here, we employ predictive modeling under a conservative estimate of future climate change to examine impacts on the future abundance and geographic distributions of Malagasy lemurs. Using distribution data from the primary literature, we employed ensemble species distribution models and geospatial analyses to predict future changes in species distributions. Current species distribution models (SDMs) were created within the BIOMOD2 framework that capitalizes on ten widely used modeling techniques. Future and current SDMs were then subtracted from each other, and areas of contraction, expansion, and stability were calculated. Model overprediction is a common issue associated Malagasy taxa. Accordingly, we introduce novel methods for incorporating biological data on dispersal potential to better inform the selection of pseudo-absence points. This study predicts that 60% of the 57 species examined will experience a considerable range of reductions in the next seventy years entirely due to future climate change. Of these species, range sizes are predicted to decrease by an average of 59.6%. Nine lemur species (16%) are predicted to expand their ranges, and 13 species (22.8%) distribution sizes were predicted to be stable through time. Species ranges will experience severe shifts, typically contractions, and for the majority of lemur species, geographic distributions will be considerably altered. We identify three areas in dire need of protection, concluding that strategically managed forest corridors must be a key component of lemur and other biodiversity conservation strategies. This recommendation is all the more urgent given that the results presented here do not take into account patterns of ongoing habitat destruction relating to human activities.

Taxonomia e biogeografia da espécie politípica Herpsilochmus rufimarginatus (TEMMINCK, 1822) (Aves: THAMNOPHILIDAE)

The genus Herpsilochmus is composed mainly of cryptic species, among them is Herpsilochmus rufimarginatus, which is currently represented by four subspecies: H. r. rufimarginatus, H. r. frater, H. r. scapularis and H. r. exiguus. Differences in plumage and vocalization suggest that there are more than one species involved in this complex. Thus this and other subspecific taxa need urgent revision, the disjunct distribution of this species also allows us to infer the relationship between birds that occur in this biome and / or different centers of endemism. This study aims to make a taxonomic revision of the taxa included in the complex time Herpsilochmus rufimarginatus based on morphological, morphometric, vocals and geographical distribution of this bird. Besides creating distribution models current potential and make the reconstruction of the distribution bygone using ecological niche modeling, and testing the niche conservatism and divergence between different subspecies. Consultations for examination of the skins of specimens of the museums: Museum of Zoology, University of São Paulo (MZUSP), National Museum of Rio de Janeiro (MN) and Emilio Goeldi Museum of Pará (MPEG), and the skins deposited at the collection of Ornithological Federal University of Rio Grande do Norte (COUFRN). We studied the following measures length of specimens: exposed culmen, culmen and total culmen nostril, tarsus, wing and tail flattened. The voice analysis was performed with vocalizations banks and / or digital banks people where 17 voice parameters were measured. This information and more available in the literature were used to assemble a bunch of data under the limit distribution of taxa and generate ecological niche models. This analyzes carried out in the program Maxent, having as model selection criterion the AUC, and the models were greater than 0.80 are considered good models. Environmental data for the realization of the modeling were downloaded on the website of Worldclim. The morphometric information, vocals and geographic distribution point for the separation of these taxa to be considering various uni and multivariate analyzes. The potential distribution models performed well (AUC> 0.80), and its distribution associated with environmental characteristics of the Amazon forest and Atlantic forest (forests of south and southeast, northeast and forest). The reconstruction of the distribution indicates a possible contact between the southern part of the Atlantic forest in the northern part of the Amazon. The analysis of niche overlap showed a low overlap between taxa and comparisons between the null model and the generated overlay link probably occurring niche conservatism. The data suggest that the taxa that occur in the Amazon and Atlantic forest represent three distinct species