The niche, biogeography and species interactions

In this paper, I review the relevance of the niche to biogeography, and what biogeography may tell us about the niche. The niche is defined as the combination of abiotic and biotic conditions where a species can persist. I argue that most biogeographic patterns are created by niche differences over space, and that even ‘geographic barriers’ must have an ecological basis. However, we know little about specific ecological factors underlying most biogeographic patterns. Some evidence supports the importance of abiotic factors, whereas few examples exist of large-scale patterns created by biotic interactions. I also show how incorporating biogeography may offer new perspectives on resource-related niches and species interactions. Several examples demonstrate that even after a major evolutionary radiation within a region, the region can still be invaded by ecologically similar species from another clade, countering the long-standing idea that communities and regions are generally ‘saturated’ with species. I also describe the somewhat paradoxical situation where competition seems to limit trait evolution in a group, but does not prevent co-occurrence of species with similar values for that trait (called here the ‘competition–divergence–co-occurrence conundrum’). In general, the interface of biogeography and ecology could be a major area for research in both fields.     

利用GARP生态位模型预测桔小实蝇(Bactrocera dorsalis)在中国的适生区域

桔小实蝇Bactrocera dorsalis(Hendel)是一种多食性害虫,明确其可能适生的区域对该虫的科学监测及防治意义重大。利用桔小实蝇在我国的已知分布点数据和亚洲地区的14个环境地理变量图层,运用GARP生态位模型结合GIS空间分析模块预测了该虫在亚洲的地理分布。结果表明桔小实蝇可分布在中国、日本、菲律宾、马来西亚、泰国北部、越南、柬埔寨、老挝、缅甸、尼泊尔、巴基斯坦、孟加拉国和斯里兰卡,这与EPPO报道的分布区域一致。将拟合过程中获得的生态位运算法则投影到我国,并考虑模型间的一致性,预测桔小实蝇在我国各省及市县范围的分布:云南大部、四川南部和东部、贵州大部、重庆大部、广西、广东、台湾、香港、澳门、海南、福建、江西、浙江大部、湖南大部、湖北大部、上海、江苏南部、河南局部及安徽部分地区为桔小实蝇的适生区。次适生区沿适生区周围分布,为四川、贵州、重庆、湖北北部、河南南部和江苏南部的一些零星地区。适生区和次适生区大多有较高密度的寄主果树,为桔小实蝇的生存提供了条件。预测结果经独立验证数据的适合性测验表明,选择的最优模型具有显著的统计学意义,显示了很好的预测能力。GARP生态位模型可以解决生态学、生物地理学和环境保护方面的一系列问题,具有广泛的应用前景,为物种已知基础分布点资料的综合分析以及有害生物的适生性分析、监测和防治提供了技术平台。     

An exhaustive analysis of heuristic methods for variable selection in ecological niche modeling and species distribution modeling

Ecological niche models and species distribution models are used in many fields of science. Despite their popularity, only recently have important aspects of the modeling process like model selection been developed. Choosing environmental variables with which to create these models is another critical part of the process, but methods currently in use are not consistent in their results and no comprehensive approach exists by which to perform this step. Here, we compared seven heuristic methods of variable selection against a novel approach that proposes to select best sets of variables by evaluating performance of models created with all combinations of variables and distinct parameter settings of the algorithm in concert. Our results were that—except for the jackknife method for one of the 12 species and fluctuation index for two of the 12 species—none of the heuristic methods for variable selection coincided with the exhaustive one. Performance decreased in models created using variables selected with heuristic methods and both underfitting and overfitting were detected when comparing their geographic projections with the ones of models created with variables selected with the exhaustive method. Using the exhaustive approach could be time consuming, so a two-step exercise may be necessary. However, using this method identifies adequate variable sets and parameter settings in concert that are associated with increased model performance.     

From shallow to deep water: an ecological study of the Hirnantia brachiopod Fauna (Late Ordovician) and its global implications

A large brachiopod fauna collected through the upper Wanyaoshu Formation (middle Hirnantian), West Yunnan, China displays, for the first time, a vertical transition within the Hirnantia fauna. The inner to mid-shelf Fardenia–Hirnantia association segues into the deeper water Aegiromena–Anisopleurella association during the Metabolograptus persculptus marine transgression. This transition parallels the pattern apparent in onshore–offshore gradients within the Hirnantian, imitating Walther’s Law for facies, instead predicting the seaward transitions between community types within a single transgressive sequence. In addition, large-sized brachiopods such as Hirnantia and Eostropheodonta become rarer and small-sized brachiopods, for example, Aegiromena and Anisopleurella more common. It is a rare opportunity to view transformations in community composition and structure within the Hirnantia fauna together with changes in both the size of individuals and populations (from large to small) during the transgression.     

利用GARP生态位模型预测桔小实蝇（Bactrocera dorsalis）在中国的适生区域

桔小实蝇Bactrocera dorsalis (Hendel)是一种多食性害虫,明确其可能适生的区域对该虫的科学监测及防治意义重大。利用桔小实蝇在我国的已知分布点数据和亚洲地区的14个环境地理变量图层,运用GARP生态位模型结合GIS空间分析模块预测了该虫在亚洲的地理分布。结果表明桔小实蝇可分布在中国、日本、菲律宾、马来西亚、泰国北部、越南、柬埔寨、老挝、缅甸、尼泊尔、巴基斯坦、孟加拉国和斯里兰卡,这与EPPO报道的分布区域一致。将拟合过程中获得的生态位运算法则投影到我国,并考虑模型间的一致性,预测桔小实蝇在我国各省及市县范围的分布：云南大部、四川南部和东部、贵州大部、重庆大部、广西、广东、台湾、香港、澳门、海南、福建、江西、浙江大部、湖南大部、湖北大部、上海、江苏南部、河南局部及安徽部分地区为桔小实蝇的适生区。次适生区沿适生区周围分布,为四川、贵州、重庆、湖北北部、河南南部和江苏南部的一些零星地区。适生区和次适生区大多有较高密度的寄主果树,为桔小实蝇的生存提供了条件。预测结果经独立验证数据的适合性测验表明,选择的最优模型具有显著的统计学意义,显示了很好的预测能力。GARP生态位模型可以解决生态学、生物地理学和环境保护方面的一系列问题,具有广泛的应用前景,为物种已知基础分布点资料的综合分析以及有害生物的适生性分析、监测和防治提供了技术平台。     

Investigating niche and lineage diversification in widely distributed taxa: phylogeography and ecological niche modeling of the Peromyscus maniculatus species group

The relationship between lineage formation and variation in the ecological niche is a fundamental evolutionary question. Two prevailing hypotheses reflect this relationship: niche conservatism and niche divergence. Niche conservatism predicts a pattern where sister taxa will occupy similar niche spaces; whereas niche divergence predicts that sister taxa will occupy different niche spaces. Widely distributed species often show distinct phylogeographic structure, but little research has been conducted on how the environment may be related to these phylogenetic patterns. We investigated the relationship between lineage divergence and environmental space for the closely related species Peromyscus maniculatus and P. polionotus utilizing phylogenetic techniques and ecological niche modeling (ENM). We estimated the phylogenetic relationship among individuals based on complete cytochrome b sequences that represent individuals from a majority of the species ranges. Niche spaces that lineages occupy were estimated by using 12 environmental layers. Differences in niche space were tested using multivariate statistics based on location data, and ENMs were employed using maximum entropy algorithms. Two similarity indices estimated significant divergence in environmental space based on the ENM. Six geographically structured lineages were identified within P. maniculatus. Nested within P. maniculatus we found that P. polionotus recently diverged from a clade occupying central and western United States. We estimated that the majority of the genetic lineages occupy distinct environmental niches, which supports a pattern of niche divergence. Two sister taxa showed niche divergence and represent different ecomorphs, suggesting morphological, genetic and ecological divergence between the two lineages. Two other sister taxa were observed in the same environmental space based on multivariate statistics, suggesting niche conservatism. Overall our results indicate that a widely distributed species may exhibit both niche conservatism and niche divergence, and that most lineages seem to occupy distinct environmental niches.     

Combining phylogenetic and ecological niche modeling approaches to determine distribution and historical biogeography of Black Hills mountain snails (Oreohelicidae)

We aim to show how a combination of molecular systematics and ecological niche modelling approaches can be used to test historical biogeographical hypotheses for species of conservation concern. We focus on the land snail genus Oreohelix (Oreohelicidae), a group found throughout the Rocky Mountains. In addition to its larger distribution, a group of Oreohelix is also found in the Black Hills of Wyoming and South Dakota, an isolated, easternmost extension of the Rocky Mountains. We determine the number, distribution, and relationships of Black Hills Oreohelicids, which are a current conservation concern due to their fragmented distribution. We compared Black Hills groups to those in the main part of the Rockies to test historical biogeographical patterns that explain current diversity. We collected mtDNA data (COI and 12S sequences) from multiple populations of Oreohelix throughout the Black Hills and in adjacent populations in the Rocky Mountains to construct phylogenetic hypotheses. To determine whether favourable environmental conditions currently exist between the Black Hills and the north-eastern Rocky Mountains, we used DesktopGARP to generate an ecological niche model for distinct lineages discovered in the molecular phylogenetic analysis. Results show that all Black Hills populations are likely Oreohelix cooperi and that little genetic differentiation exists within this clade. In addition, Black Hills groups are genetically similar or identical to populations found in the Judith Mountains and Bighorn Mountains (north-eastern Rockies). Ecological niche models show that suitable environmental conditions may exist between eastern Rockies and Black Hills O. cooperi samples. Taken together, the phylogenetic and niche model data, along with the low vagility of the snails, support passive long-distance dispersal as a likely explanation for current arrangement of biodiversity.     

Using ecological niche modelling to evaluate niche stability in deep time

Aim To investigate relative niche stability in species responses to various types of environmental pressure (biotic and abiotic) on geological time‐scales using the fossil record. Location The case study focuses on Late Ordovician articulate brachiopods of the Cincinnati Arch in eastern North America. Methods Species niches were modelled for a suite of fossil brachiopod species based on five environmental variables inferred from sedimentary parameters using GARP and Maxent . Niche stability was assessed by comparison of (1) the degree of overlap of species distribution models developed for a time‐slice and those generated by projecting niche models of the previous time‐slice onto environmental layers of a second time‐slice using GARP and Maxent , (2) Schoener’s D statistic, and (3) the similarity of the contribution of each environmental parameter within Maxent niche models between adjacent time‐slices. Results Late Ordovician brachiopod species conserved their niches with high fidelity during intervals of gradual environmental change but responded to inter‐basinal species invasions through niche evolution. Both native and invasive species exhibited similar levels of niche evolution in the invasion and post‐invasion intervals. Niche evolution was related mostly to decreased variance within the former ecological niche parameters rather than to shifts to new ecospace. Main conclusions Although the species examined exhibited morphological stasis during the study interval, high levels of niche conservatism were observed only during intervals of gradual environmental change. Rapid environmental change, notably inter‐basinal species invasions, resulted in high levels of niche evolution among the focal taxa. Both native and invasive species responded with similar levels of niche evolution during the invasion interval and subsequent environmental reorganization. The assumption of complete niche conservatism frequently employed in ecological niche modelling (ENM) analyses to forecast or hindcast species geographical distributions is more likely to be accurate for climate change studies than for invasive species analyses over geological time‐scales.     

Collinearity in ecological niche modeling: Confusions and challenges

Ecological niche models are widely used in ecology and biogeography. Maxent is one of the most frequently used niche modeling tools, and many studies have aimed to optimize its performance. However, scholars have conflicting views on the treatment of predictor collinearity in Maxent modeling. Despite this lack of consensus, quantitative examinations of the effects of collinearity on Maxent modeling, especially in model transfer scenarios, are lacking. To address this knowledge gap, here we quantify the effects of collinearity under different scenarios of Maxent model training and projection. We separately examine the effects of predictor collinearity, collinearity shifts between training and testing data, and environmental novelty on model performance. We demonstrate that excluding highly correlated predictor variables does not significantly influence model performance. However, we find that collinearity shift and environmental novelty have significant negative effects on the performance of model transfer. We thus conclude that (a) Maxent is robust to predictor collinearity in model training; (b) the strategy of excluding highly correlated variables has little impact because Maxent accounts for redundant variables; and (c) collinearity shift and environmental novelty can negatively affect Maxent model transferability. We therefore recommend to quantify and report collinearity shift and environmental novelty to better infer model accuracy when models are spatially and/or temporally transferred.     

Integrating coalescent and ecological niche modeling in comparative phylogeography

Understanding the factors that contribute to the formation of population genetic structure is a central goal of phylogeographic research, but achieving this goal can be complicated by the stochastic variance inherent to genetic processes. Statistical approaches to testing phylogeographic hypotheses accommodate this stochasticity by evaluating competing models of putative historical population structure, often by simulating null distributions of the expected variance. The effectiveness of these tests depends on the biological realism of the models. Information from the fossil record can aid in reconstructing the historical distributions of some taxa. However, for the majority of taxa, which lack sufficient fossils, paleodistributional modeling can provide valuable spatial-geographic data concerning ancestral distributions. Paleodistributional models are generated by projecting ecological niche models, which predict the current distribution of each species, onto a model of past climatic conditions. Here, we generate paleodistributional models describing the suitable habitat during the last glacial maximum for lineages from the mesic forests of the Pacific Northwest of North America, and use these models to generate alternative phylogeographic hypotheses. Coalescent simulations are then used to test these hypotheses to improve our understanding of the historical events that promoted the formation of population genetic structure in this ecosystem. Results from Pacific Northwest mesic forest organisms demonstrate the utility of these combined approaches. Paleodistribution models and population genetic structure are congruent across three amphibian lineages, suggesting that they have responded in a concerted manner to environmental change. Two other species, a willow and a water vole, despite being currently codistributed and having similar population genetic structure, were predicted by the paleodistributional model to have had markedly different distributions during the last glacial maximum. This suggests that congruent phylogeographic patterns can arise from incongruent ancestral distributions. Paleodistributional models introduce a much-needed spatial-geographic perspective to statistical phylogeography. In conjunction with coalescent models of population genetic structure, they have the potential to improve our understanding of the factors that promote population divergence and ultimately produce regional patterns of biodiversity.     

基于MaxEnt的西藏飞蝗在中国的适生区预测

西藏飞蝗是青藏高原本地特有物种,为青稞和牧草的重要害虫,近年来危害范围有扩大蔓延趋势。研究并明确西藏飞蝗在中国的适生区域,对制定该虫的早期监测、预警及控制措施意义重大。近年来最大熵理论在物种适生研究领域得到广泛应用,基于西藏飞蝗的分布信息和环境变量,采用MaxEnt生态位模型和ArcGIS对其在中国的潜在分布区进行预测,用ROC曲线检测模型精度、刀切法(jackknife test)筛选主导环境变量及其适宜值。两次模拟的AUC值分别为0.996和0.993,预测结果与实际拟合度很高。西藏飞蝗在中国的高适生区主要位于四川的甘孜州,西藏的昌都地区、林芝地区、山南地区及拉萨市,中适生区则以高适生区为中心向外扩散,集中在青藏高原东部地区。海拔、8月份平均雨量、1月份平均雨量、等温性、12-2月份的平均温度是影响西藏飞蝗潜在分布的主要环境变量。     

Ordovician biogeography and continental drift

The changeable biogeography of the Ordovician is reviewed, quantitatively analysed and used to assess possible positions and relative movements of the continental plates. Plate boundaries are defined as precisely as possible using geological and palaeontological data. The trilobites, corals, brachiopods, cephalopods, echinoderms, graptolites and ostracods are found to be useful in defining plate boundaries and relative plate movements. Oceanic barriers are considered to be the simplest explanation for the maintenance of faunal provincialisms. The faunal barriers between South America and Africa and between Australia and Gondwanaland may have been climatic and land barriers. The present Asian continent is divided into Kazakhstan, the Siberian Platform, South Asian, Northern China, India and the Jano-Kolymian block. These areas had different faunal histories and are considered to have had different drift histories. The North China and South Asian plates were separated by the Tsinling Ocean, the Northern European plate from the North American plate by Wilson's Proto-Atlantic and the Siberian Platform plate from the Northern European by the Uralian Ocean. Southern and Central Europe are shown to have been joined to Africa and separated from the Northern European plate by a Mid-European Ocean. If Australia is considered as part of an Ordovician Gondwanaland then the best explanation for the faunal histories of most plates is provided by an anticlockwise rotation of Gondwanaland about the South palaeo-pole.     

The relation of Late Ordovician glaciation to the Ordovician-Silurian changeover in North American brachiopod faunas

Sheehan, P. M.: The relation of Late Ordovician glaciation to the Ordovician-Silurian changeover in North American brachiopod faunas.
The Ordovician-Silurian changeover of brachiopod faunas in North American epicontinental seas involved the abrupt extinction of endemic Late Ordovician stocks and subsequent repopulation of North American seas by Old World taxa. The Late Ordovician Gondwanaland glaciation may have lowered sea levels sufficiently to place severe stress on the widespread shallow marine faunas in North America, resulting in their eventual extinction. The Late Ordovician depositional history in North America is not well enough known to establish the presence of a latest Ordovician regression, but the earliest Silurian was an interval of off-lap in North America. Therefore, the glacial lowering of sea level is considered to be the most likely cause of the faunal changeover.     

Korarchaeota diversity, biogeography, and abundance in Yellowstone and Great Basin hot springs and ecological niche modeling based on machine learning

Over 100 hot spring sediment samples were collected from 28 sites in 12 areas/regions, while recording as many coincident geochemical properties as feasible (>60 analytes). PCR was used to screen samples for Korarchaeota 16S rRNA genes. Over 500 Korarchaeota 16S rRNA genes were screened by RFLP analysis and 90 were sequenced, resulting in identification of novel Korarchaeota phylotypes and exclusive geographical variants. Korarchaeota diversity was low, as in other terrestrial geothermal systems, suggesting a marine origin for Korarchaeota with subsequent niche-invasion into terrestrial systems. Korarchaeota endemism is consistent with endemism of other terrestrial thermophiles and supports the existence of dispersal barriers. Korarchaeota were found predominantly in >55°C springs at pH 4.7-8.5 at concentrations up to 6.6×10(6) 16S rRNA gene copies g(-1) wet sediment. In Yellowstone National Park (YNP), Korarchaeota were most abundant in springs with a pH range of 5.7 to 7.0. High sulfate concentrations suggest these fluids are influenced by contributions from hydrothermal vapors that may be neutralized to some extent by mixing with water from deep geothermal sources or meteoric water. In the Great Basin (GB), Korarchaeota were most abundant at spring sources of pH<7.2 with high particulate C content and high alkalinity, which are likely to be buffered by the carbonic acid system. It is therefore likely that at least two different geological mechanisms in YNP and GB springs create the neutral to mildly acidic pH that is optimal for Korarchaeota. A classification support vector machine (C-SVM) trained on single analytes, two analyte combinations, or vectors from non-metric multidimensional scaling models was able to predict springs as Korarchaeota-optimal or sub-optimal habitats with accuracies up to 95%. To our knowledge, this is the most extensive analysis of the geochemical habitat of any high-level microbial taxon and the first application of a C-SVM to microbial ecology.     

Applications of ecological niche modeling for species delimitation: a review and empirical evaluation using day geckos (Phelsuma) from Madagascar

Although the systematic utility of ecological niche modeling is generally well known (e.g., concerning the recognition and discovery of areas of endemism for biogeographic analyses), there has been little discussion of applications concerning species delimitation, and to date, no empirical evaluation has been conducted. However, ecological niche modeling can provide compelling evidence for allopatry between populations, and can also detect divergent ecological niches between candidate species. Here we present results for two taxonomically problematic groups of Phelsuma day geckos from Madagascar, where we integrate ecological niche modeling with mitochondrial DNA and morphological data to evaluate species limits. Despite relatively modest levels of genetic and morphological divergence, for both species groups we find divergent ecological niches between closely related species and parapatric ecological niche models. Niche models based on the new species limits provide a better fit to the known distribution than models based upon the combined (lumped) species limits. Based on these results, we elevate three subspecies of Phelsuma madagascariensis to species rank and describe a new species of Phelsuma from the P. dubia species group. Our phylogeny continues to support a major endemic radiation of Phelsuma in Madagascar, with dispersals to Pemba Island and the Mascarene Islands. We conclude that ecological niche modeling offers great potential for species delimitation, especially for taxonomic groups exhibiting low vagility and localized endemism and for groups with more poorly known distributions. In particular, niche modeling should be especially sensitive for detecting recent parapatric speciation driven by ecological divergence, when the environmental gradients driving speciation are represented within the ecological niche models.     

Global ecological niche conservatism and evolution in Olea species

Background and AimsClimate is an important parameter in delimiting coarse-grained aspects of fundamental ecological niches of species; evolution of these niches has been considered a key component in biological diversification. We assessed phylogenetic niche conservatism and evolution in 24 species of the family Oleaceae in relation to temperature and precipitation variables. We studied niches of 17 Olea species and 7 species from other genera of Oleaceae globally.MethodsWe used nuclear ribosomal and plastid DNA to reconstruct an evolutionary tree for the family. We used an approach designed specifically to incorporate uncertainty and incomplete knowledge of species’ ecological niche limits. We performed parsimony- and likelihood-based reconstructions of ancestral states on two independent phylogenetic hypotheses for the family. After detailed analysis, species’ niches were classified into warm and cold niches, wet and dry niches, and broad and narrow niches.Key ResultsGiven that full estimates of fundamental niches are difficult, we explore the alternative approach of explicit incorporation of knowledge of gaps in the information available, which allows avoidance of overestimation of amounts of evolutionary change. The result is a first synthetic view of evolutionary dynamics of ecological niches and distributional potential in a widespread plant family. Temperate regions of the Earth were occupied only by lineages that could derive with cold and dry niches; Southeast Asia held species with warm and wet niches; and parts of Africa held only species with dry niches.ConclusionsHigh temperature in Lutetian (Oligocene) and low temperature in Rupelian (Eocene) with major desertification events play important role for niche retraction and expansion in the history for Oleaceae clades. Associations between environmental niche characteristics and phylogeny reconstruction play an important role in understanding ecological niche conservatism, the overall picture was relatively slow or conservative niche evolution in this group.     

Integrating coalescent-based species delimitation with ecological niche modeling delimited two species within the Stewartia sinensis complex (Theaceae)

Accurate species delimitation is the key to precise estimation of species diversity and is fundamental to most branches of biology. Unclear species boundaries within species complexes could lead to the underestimation of species diversity. However, species delimitation of species complexes remains challenging due to the continuum of phenotypic variations. To robustly examine species boundaries within a species complex, integrative approaches in phylogeny, ecology, and morphology were applied to the Stewartia sinensis complex (Theaceae) endemic to China. Multispecies coalescent-based species delimitation using 572 nuclear ortholog sequences (anchored enrichment) supported reciprocal phylogenetic monophyly of the northern lineage (NL) and southern lineage (SL), which were not sister clades. Niche equivalency and similarity tests demonstrated significant climatic niche differentiation between NL and SL with observed Warren et al.'s I = 0.0073 and Schoener's D = 0.0021. Species distribution modeling also separated their potential distribution. Morphometric analyses suggested significant interlineage differentiation of multiple traits including the ratio of length and width, leaf width, and pedicel length, although overall similarity did not differ. Based on the integrative species concept, two distinct species were proposed with legitimate names of Stewartia gemmata for SL and S. sinensis for NL. Our empirical study of the S. sinensis complex highlights the importance of applying multiple species criteria, in particular the underappreciated niche differentiation, to species delimitation in species complexes pervasive in plants.     

Predicting the geography of species' invasions via ecological niche modeling

Species' invasions have long been regarded as enormously complex processes, so complex as to defy predictivity. Phases of this process, however, are emerging as highly predictable: the potential geographic course of an invasion can be anticipated with high precision based on the ecological niche characteristics of a species in its native geographic distributional area. This predictivity depends on the premise that ecological niches constitute long-term stable constraints on the potential geographic distributions of species, for which a sizeable body of evidence is accumulating. Hence, although the entire invasion process is indeed complex, the geographic course that invasions are able to take can be anticipated with considerable confidence.