Phylogenetic niche conservatism and the evolutionary basis of ecological speciation

Phylogenetic niche conservatism (PNC) typically refers to the tendency of closely related species to be more similar to each other in terms of niche than they are to more distant relatives. This has been implicated as a potential driving force in speciation and other species‐richness patterns, such as latitudinal gradients. However, PNC has not been very well defined in most previous studies. Is it a pattern or a process? What are the underlying endogenous (e.g. genetic) and exogenous (e.g. ecological) factors that cause niches to be conserved? What degree of similarity is necessary to qualify as PNC? Is it possible for the evolutionary processes causing niches to be conserved to also result in niche divergence in different habitats? Here, we revisit these questions, codifying a theoretical and operational definition of PNC as a mechanistic evolutionary process resulting from several factors. We frame this both from a macroevolutionary and population‐genetic perspective. We discuss how different axes of physical (e.g. geographic) and environmental (e.g. climatic) heterogeneity interact with the fundamental process of PNC to produce different outcomes of ecological speciation. We also review tests for PNC, and suggest ways that these could be improved or better utilized in future studies. Ultimately, PNC as a process has a well‐defined mechanistic basis in organisms, and future studies investigating ecological speciation would be well served to consider this, and frame hypothesis testing in terms of the processes and expected patterns described herein. The process of PNC may lead to patterns where niches are conserved (more similar than expected), constrained (divergent within a limited subset of available niches), or divergent (less similar than expected), based on degree of phylogenetic relatedness between species.     

Predicting the success of an invader: Niche shift versus niche conservatism

Invasive species can encounter environments different from their source populations, which may trigger rapid adaptive changes after introduction (niche shift hypothesis). To test this hypothesis, we investigated whether postintroduction evolution is correlated with contrasting environmental conditions between the European invasive and source ranges in the Asian tiger mosquito Aedes albopictus. The comparison of environmental niches occupied in European and source population ranges revealed more than 96% overlap between invasive and source niches, supporting niche conservatism. However, we found evidence for postintroduction genetic evolution by reanalyzing a published ddRADseq genomic dataset from 90 European invasive populations using genotype–environment association (GEA) methods and generalized dissimilarity modeling (GDM). Three loci, among which a putative heat‐shock protein, exhibited significant allelic turnover along the gradient of winter precipitation that could be associated with ongoing range expansion. Wing morphometric traits weakly correlated with environmental gradients within Europe, but wing size differed between invasive and source populations located in different climatic areas. Niche similarities between source and invasive ranges might have facilitated the establishment of populations. Nonetheless, we found evidence for environmental‐induced adaptive changes after introduction. The ability to rapidly evolve observed in invasive populations (genetic shift) together with a large proportion of unfilled potential suitable areas (80%) pave the way to further spread of Ae. albopictus in Europe.     

Ecological niche conservatism: a time‐structured review of evidence

Aim To evaluate the evolutionary conservatism of coarse‐resolution Grinnellian (or scenopoetic) ecological niches. Location Global. Methods I review a broad swathe of literature relevant to the topic of niche conservatism or differentiation, and illustrate some of the resulting insights with examplar analyses. Results Ecological niche characteristics are highly conserved over short‐to‐moderate time spans (i.e. from individual life spans up to tens or hundreds of thousands of years); little or no ecological niche differentiation is discernible as part of the processes of invasion or speciation. Main conclusions Although niche conservatism is widespread, many methodological complications obscure this point. In particular, niche models are frequently over‐interpreted: too often, they are based on limited occurrence data in high‐dimensional environmental spaces, and cannot be interpreted robustly to indicate niche differentiation.     

Lineage diversification in a widespread species: roles for niche divergence and conservatism in the common kingsnake, Lampropeltis getula

Niche conservatism and niche divergence are both important ecological mechanisms associated with promoting allopatric speciation across geographical barriers. However, the potential for variable responses in widely distributed organisms has not been fully investigated. For allopatric sister lineages, three patterns for the interaction of ecological niche preference and geographical barriers are possible: (i) niche conservatism at a physical barrier; (ii) niche divergence at a physical barrier; and (iii) niche divergence in the absence of a physical barrier. We test for the presence of these patterns in a transcontinentally distributed snake species, the common kingsnake ( Lampropeltis getula ), to determine the relative frequency of niche conservatism or divergence in a single species complex inhabiting multiple distinct ecoregions. We infer the phylogeographic structure of the kingsnake using a range-wide data set sampled for the mitochondrial gene cytochrome b . We use coalescent simulation methods to test for the presence of structured lineage formation vs. fragmentation of a widespread ancestor. Finally, we use statistical techniques for creating and evaluating ecological niche models to test for conservatism of ecological niche preferences. Significant geographical structure is present in the kingsnake, for which coalescent tests indicate structured population division. Surprisingly, we find evidence for all three patterns of conservatism and divergence. This suggests that ecological niche preferences may be labile on recent phylogenetic timescales, and that lineage formation in widespread species can result from an interaction between inertial tendencies of niche conservatism and natural selection on populations in ecologically divergent habitats.     

The geography and ecology of plant speciation: range overlap and niche divergence in sister species

A goal of evolutionary biology is to understand the roles of geography and ecology in speciation. The recent shared ancestry of sister species can leave a major imprint on their geographical and ecological attributes, possibly revealing processes involved in speciation. We examined how ecological similarity, range overlap and range asymmetry are related to time since divergence of 71 sister species pairs in the California Floristic Province (CFP). We found that plants exhibit strikingly different age-range correlation patterns from those found for animals; the latter broadly support allopatric speciation as the primary mode of speciation. By contrast, plant sisters in the CFP were sympatric in 80% of cases and range sizes of sisters differed by a mean of 10-fold. Range overlap and range asymmetry were greatest in younger sisters. These results suggest that speciation mechanisms broadly grouped under ‘budding’ speciation, in which a larger ranged progenitor gives rise to a smaller ranged derivative species, are probably common. The ecological and reproductive similarity of sisters was significantly greater than that of sister–non-sister congeners for every trait assessed. However, shifts in at least one trait were present in 93% of the sister pairs; habitat and soil shifts were especially common. Ecological divergence did not increase with range overlap contrary to expectations under character displacement in sympatry. Our results suggest that vicariant speciation is more ubiquitous in animals than plants, perhaps owing to the sensitivity of plants to fine-scale environmental heterogeneity. Despite high levels of range overlap, ecological shifts in the process of budding speciation may result in low rates of fine-scale spatial co-occurrence. These results have implications for ecological studies of trait evolution and community assembly; despite high levels of sympatry, sister taxa and potentially other close relatives, may be missing from local communities.     

Phylogenetic patterns in zopherine beetles are related to ecological niche width and dispersal limitation

Niche conservatism has been proposed as the mechanism driving speciation in temperate montane clades through range fragmentation during climatic oscillations. Thus, a negative relationship between speciation rates and niche width is expected. Here, we test this prediction using American zopherine beetles. Our phylogenetic analyses recovered two clades in addition to that of the genus Zopherus: the genera Verodes and Phloeodes, which originated most likely in the Eocene, and diversified during the Miocene and the Pliocene. The assessment of clade niche width in relation to clade diversity supported the proposition of narrow niches leading to a higher probability of range fragmentation during climatic oscillations, thus increasing speciation. Additionally, almost all current populations of Phloeodes and Verodes are located within regions that retained favourable climatic conditions across warm and cold Pleistocene periods, suggesting that dispersal limitation is a strong factor controlling clade distribution. In sum, our results suggest that (i) niche width is a major determinant of the probability of speciation in temperate montane clades, by controlling the probability of potential range fragmentation and (ii) dispersal limitation is also a major determinant of the speciation process, by increasing the fragmentation of realized ranges even when potential distributions are cyclically fused during climatic oscillations. When dispersal limitation is extreme, as in zopherine beetles, populations persist just in those areas that have retained suitable conditions during extremes of past climatic oscillations. Paradoxically, this relict condition confers zopherine beetles great resilience for facing future climate change.     

Speciation and ecology revisited: phylogenetic niche conservatism and the origin of species

Evolutionary biologists have often suggested that ecology is important in speciation, in that natural selection may drive adaptive divergence between lineages that inhabit different environments. I suggest that it is the tendency of lineages to maintain their ancestral ecological niche (phylogenetic niche conservatism) and their failure to adapt to new environments which frequently isolates incipient species and begins the process of speciation. Niche conservatism may be an important and widespread component of allopatric speciation but is largely unstudied. The perspective outlined here suggests roles for key microevolutionary processes (i.e., natural selection, adaptation) that are strikingly different from those proposed in previous literature on ecology and speciation. Yet, this perspective is complementary to the traditional view because it focuses on a different temporal stage of the speciation process.     

The importance (or lack thereof) of niche divergence to the maintenance of a northern species complex: the case of the long‐toed salamander (Ambystoma macrodactylum Baird)

The relative importance of ecological vs. nonecological factors for the origin and maintenance of species is an open question in evolutionary biology. Young lineages – such as the distinct genetic groups that make up the ranges of many northern species – represent an opportunity to study the importance of ecological divergence during the early stages of diversification. Yet, few studies have examined the extent of niche divergence between lineages in previously glaciated regions and the role of ecology in maintaining the contact zones between them. In this study, we used tests of niche overlap in combination with ecological niche models to explore the extent of niche divergence between lineages of the long‐toed salamander (Ambystoma macrodactylum Baird) species complex and to determine whether contact zones correspond to (divergent) niche limits. We found limited evidence for niche divergence between the different long‐toed salamander lineages, substantial overlap in the predicted distribution of suitable climatic space for all lineages and range limits that are independent of niche limits. These results raise questions as to the importance of ecological divergence to the development of this widespread species complex and highlight the potential for non‐ecological factors to play a more important role in the maintenance of northern taxa.     

Pliocene–Pleistocene ecological niche evolution shapes the phylogeography of a Mediterranean plant group

Estimating species ability to adapt to environmental changes is crucial to understand their past and future response to climate change. The Mediterranean Basin has experienced remarkable climatic changes since the Miocene, which have greatly influenced the evolution of the Mediterranean flora. Here, we examine the evolutionary history and biogeographic patterns of two sedge sister species (Carex, Cyperaceae) restricted to the western Mediterranean Basin, but with Pliocene fossil record in central Europe. In particular, we estimated the evolution of climatic niches through time and its influence in lineage differentiation. We carried out a dated phylogenetic–phylogeographic study based on seven DNA regions (nDNA and ptDNA) and fingerprinting data (AFLPs), and modelled ecological niches and species distributions for the Pliocene, Pleistocene and present. Phylogenetic and divergence time analyses revealed that both species form a monophyletic lineage originated in the late Pliocene–early Pleistocene. We detected clear genetic differentiation between both species with distinct genetic clusters in disjunct areas, indicating the predominant role of geographic barriers limiting gene flow. We found a remarkable shift in the climatic requirements between Pliocene and extant populations, although the niche seems to have been relatively conserved since the Pleistocene split of both species. This study highlights how an integrative approach combining different data sources and analyses, including fossils, allows solid and robust inferences about the evolutionary history of a plant group since the Pliocene.     

Bridging the gap between community ecology and historical biogeography: niche conservatism and community structure in emydid turtles

Historical (phylogenetic) biogeography and community ecology were once integrated as part of the broader study of organismal diversity, but in recent decades have become largely separate disciplines. This is unfortunate because many patterns studied by community ecologists may originate through processes studied by historical biogeographers and vice versa. In this study, we explore the causes of a geographic pattern of community structure (habitat use) in the emydid turtle assemblages of eastern North America, with more semi-terrestrial species of the subfamily Emydinae in the north and more aquatic species of Deirochelyinae in the south. Specifically, we address the factors that prevent northern emydines from invading southern communities. We test for competitive exclusion by examining patterns of range overlap, and test for the role of niche conservatism using analyses of climatic and physiological data based on a multilocus molecular phylogeny. We find no support for competitive exclusion, whereas several lines of evidence support the idea that niche conservatism has prevented northern emydines from dispersing into southern communities. Our results show how understanding the causes of patterns of historical biogeography may help explain patterns of community structure.     

Realized niche shift associated with Galinsoga quadriradiata (Asteraceae) invasion in China

粗毛牛膝菊在中国的入侵与生态位漂移有关 在外来物种入侵和扩散过程中,生态位的漂移可能起到了重要作用。粗毛牛膝菊(Galinsoga quadriradiata) 在中国已造成了较为严重的入侵,占据了许多与其原产地不同的气候区。为此,本研究力图揭示粗毛牛膝菊入侵过程中的气候生态位漂移,分析其在该物种入 侵中国过程中可能发挥的作用。本研究结合粗毛牛膝菊原 产地和入侵地的分布点与气候数据, 采用Maxent模型预测了其在中国潜在的分布,并采用主成分分析的方法评估 了在入侵中国过程中粗毛牛膝菊气候生态位的漂移。模型结果显示,该物种原产地种群和入侵地种群之间只 有32.7%的生态位重叠,两个种群的生态位相似性较低(Schoener's D = 0.093, P < 0.005),这暗示了在其入侵过程中发生了生态位漂移。相比于其原产地种群,其在中国的入侵种群气候生态位的整体范围和中心都明 显地漂移向了温度更低、降水更少的区域;中国南方大部分区域属于粗毛牛膝菊的稳定适生区,而位于入侵 前沿的北方地区则存在局域适应和潜在拓殖区域。这些研究结果说明,粗毛牛膝菊在中国的入侵种群仍处于准平衡阶段,未来有可能继续向新的适生区扩散入侵,其生态位的变化有力地解释了为什么该物种在中国的入侵性强、危害范围大。     

Physiology in ecological niche modeling: using zebra mussel's upper thermal tolerance to refine model predictions through Bayesian analysis

Climate change and human-mediated dispersal are increasingly influencing species’ geographic distributions. Ecological niche models (ENMs) are widely used in forecasting species’ distributions, but are weak in extrapolation to novel environments because they rely on available distributional data and do not incorporate mechanistic information, such as species’ physiological response to abiotic conditions. To improve accuracy of ENMs, we incorporated physiological knowledge through Bayesian analysis. In a case study of the zebra mussel Dreissena polymorpha, we used native and global occurrences to obtain native and global models representing narrower and broader understanding of zebra mussel’ response to temperature. We also obtained thermal limit and survival information for zebra mussel from peer-reviewed literature and used the two types of information separately and jointly to calibrate native models. We showed that, compared to global models, native models predicted lower relative probability of presence along zebra mussel's upper thermal limit, suggesting the shortcoming of native models in predicting zebra mussel's response to warm temperature. We also found that native models showed improved prediction of relative probability of presence when thermal limit was used alone, and best approximated global models when both thermal limit and survival data were used. Our result suggests that integration of physiological knowledge enhances extrapolation of ENM in novel environments. Our modeling framework can be generalized for other species or other physiological limits and may incorporate evolutionary information (e.g. evolved thermal tolerance), thus has the potential to improve predictions of species’ invasive potential and distributional response to climate change.     

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.     

提高生态位模型转移能力来模拟入侵物种 的潜在分布

生态位模型利用物种分布点所关联的环境变量去推算物种的生态需求, 模拟物种的分布。在模拟入侵物种分布时, 经典生态位模型包括模型构建于物种本土分布地, 然后将其转移并投射至另一地理区域, 来模拟入侵物种的潜在分布。然而在模型运用时, 出现了模型的转移能力较低、模拟的结果与物种的实际分布不相符的情况, 由此得出了生态位漂移等不恰当的结论。提高生态位模型的转移能力, 可以准确地模拟入侵物种的潜在分布, 为入侵种的风险评估提供参考。作者以入侵种茶翅蝽(Halyomorpha halys)和互花米草(Spartina alterniflora)为例, 从模型的构建材料(即物种分布点和环境变量)入手, 全面阐述提高模型转移能力的策略。在构建模型之前, 需要充分了解入侵物种的生物学特性、种群平衡状态、本土地理分布范围及物种的生物历史地理等方面的知识。在模型构建环节上, 物种分布点不仅要充分覆盖物种的地理分布和生态空间的范围, 同时要降低物种采样点偏差; 环境变量的选择要充分考虑其对物种分布的限制作用、各环境变量之间的空间相关性, 以及不同地理种群间生态空间是否一致, 同时要降低环境变量的空间维度; 模型构建区域要真实地反映物种的地理分布范围, 并考虑种群的平衡状态。作者认为, 在生态位保守的前提下, 如果模型是构建在一个合理方案的基础上, 生态位模型的转移能力是可以保证的, 在以模型转移能力较低的现象来阐述生态位分化时需要引起注意。     

Environmental data sets matter in ecological niche modelling: an example with Solenopsis invicta and Solenopsis richteri

Aim  In response to a recent paper suggesting the failure of ecological niche models to predict between native and introduced distributional areas of fire ants ( Solenopsis invicta ), we sought to assess methodological causes of this failure.
Location  Ecological niche models were developed on the species' native distributional area in South America, and projected globally.
Methods  We developed ecological niche models based on six different environmental data sets, and compared their respective abilities to anticipate the North American invasive distributional area of the species.
Results  We show that models based on the 'bioclimatic variables' of the WorldClim data set indeed fail to predict the full invasive potential of the species, but that models based on four other data sets could predict this potential correctly.
Main conclusions  The difference in predictive abilities appears to centre on the complexity of the environmental variables involved. These results emphasize important influences of environmental data sets on the generality and ability of ecological niche models to anticipate novel phenomena, and offer a simpler explanation for the lack of predictive ability among native and invaded distributional areas than that of niche shifts.