Niche evolution and diversification in a Neotropical radiation of birds (Aves: Furnariidae)

Rapid diversification may be caused by ecological adaptive radiation via niche divergence. In this model, speciation is coupled with niche divergence and lineage diversification is predicted to be correlated with rates of niche evolution. Studies of the role of niche evolution in diversification have generally focused on ecomorphological diversification but climatic‐niche evolution may also be important. We tested these alternatives using a phylogeny of 298 species of ovenbirds (Aves: Furnariidae). We found that within Furnariidae, variation in species richness and diversification rates of subclades were best predicted by rate of climatic‐niche evolution than ecomorphological evolution. Although both are clearly important, univariate regression and multivariate model averaging more consistently supported the climatic‐niche as the best predictor of lineage diversification. Our study adds to the growing body of evidence, suggesting that climatic‐niche divergence may be an important driver of rapid diversification in addition to ecomorphological evolution. However, this pattern may depend on the phylogenetic scale at which rate heterogeneity is examined.     

Phylogenetic relationships and ecological niche conservatism in killifish (Profundulidae) in Mesoamerica

The family Profundulidae is a group of small-sized fish species distributed between southern Mexico and Honduras, where they are frequently the only fish representatives at higher elevations in the basins where they occur. We characterized their ecological niche using different methods and metrics drawn from niche modelling and by re-examining phylogenetic relationships of a recently published molecular phylogeny of this family to gain a better understanding of its biogeographic and evolutionary history. We assessed both lines of evidence from the perspective of niche conservatism to set a foundation for discussing hypotheses about the processes underlying the distribution and evolution of the group. In fish clades where the species composition is not clear, we examined whether niche classification could be informative to discriminate groups geographically and ecologically consistent with any of the different hypotheses of valid species. The characterization of the ecological niche was carried out using the Maxent algorithm under different parameterizations and the projection of the presence on the main components of the most relevant environmental coverage, and the niche comparison was calculated with two indices (D and I), both in environmental space and in that projected geographically. With the molecular data, a species tree was generated using the *BEAST method. The comparison of these data was calculated with an age-overlap correlation test. Based on the molecular phylogeny and on niche overlap analyses, we uncovered strong evidence to support the idea that ecologically similar species are not necessarily sister species. The correlation analysis for genetic distance and niche overlap was not significant (P > 0.05). In clades with taxonomic conflicts, we only identified Profundulus oaxacae as a geographically and ecologically distinct group from P. punctatus. All the evidence considered leads us to propose that Profundulidae do not show evidence of niche conservatism and that there are reasons to consider P. oaxacae as a valid species. Our study suggests that niche divergence is a driving evolutionary force that caused the diversification and speciation processes of the Profundulidae, along with the geological and climatic events that promoted the expansion or contraction of suitable environments.     

Swimming with the giant: coexistence patterns of a new redfin minnow Pseudobarbus skeltoni from a global biodiversity hot spot

Ecological niche theory predicts that coexistence is facilitated by resource partitioning mechanisms that are influenced by abiotic and biotic interactions. Alternative hypotheses suggest that under certain conditions, species may become phenotypically similar and functionally equivalent, which invokes the possibility of other mechanisms, such as habitat filtering processes. To test these hypotheses, we examined the coexistence of the giant redfin Pseudobarbus skeltoni, a newly described freshwater fish, together with its congener Pseudobabus burchelli and an anabantid Sandelia capensis by assessing their scenopoetic and bionomic patterns. We found high habitat and isotope niche overlaps between the two redfins, rendering niche partitioning a less plausible sole mechanism that drives their coexistence. By comparison, environment–trait relationships revealed differences in species–environment relationships, making habitat filtering and functional equivalence less likely alternatives. Based on P. skeltoni's high habitat niche overlap with other species, and its large isotope niche width, we inferred the likelihood of differential resource utilization at trophic level as an alternative mechanism that distinguished it from its congener. In comparison, its congener P. burchelli appeared to have a relatively small trophic niche, suggesting that its trophic niche was more conserved despite being the most abundant species. By contrast, S. capensis was distinguished by occupying a higher trophic position and by having a trophic niche that had a low probability of overlapping onto those of redfins. Therefore, trophic niche partitioning appeared to influence the coexistence between S. capensis and redfins. This study suggests that coexistence of these fishes appears to be promoted by their differences in niche adaptation mechanisms that are probably shaped by historic evolutionary and ecological processes.     

渔山岛岩礁基质潮间带大型底栖动物优势种生态位

2009年3月至2010年1月期间对渔山岛岩礁基质潮间带大型底栖动物进行定量采样调查,并获得大型底栖动物85种,筛选出全年取样获得优势种30种,隶属5门7纲24科。对获得的30个优势种以Shannon—Wiener指数为基础进行了生态位宽度测定,以Pianka重叠指数为基础进行了生态位重叠值分析,结果显示：潮间带大型底栖动物群落中优势种生态位宽度变化范围为0.18~1.94,值较高的有条纹隔贻贝、覆瓦小蛇螺、角偏顶蛤、日本笠藤壶、鳞笠藤壶和马氏毛粒蟹,均大于1.00,它们对环境适应的能力较强;各优势种的生态位重叠程度不均匀,在0~0.97之间,它们对群落环境资源的利用存在着交叉,潜在的种间竞争压力较大。以密度数据四次开方为基础,利用欧氏距离进行群落物种的系统聚类分析和非度量多维标度排序分析,结果均表明30个优势种可以分为三大类,即狭布种、泛化种和特有种。优势种生态位宽度、优势种之间的生态位重叠值与物种的分布与数量密切相关,生境相似程度高的物种聚类和排序距离就小,大型底栖动物主要通过在资源位上的分布、摄食类群和生活型等的差异缓解竞争。     

Towards a trait-based quantification of species niche

Aims Although the niche concept is of prime importance in ecology, the quantification of plant species' niches remains difficult. Here we propose that plant functional traits, as determinants of species performance, may be useful tools for quantifying species niche parameters over environmental gradients.Important findings Under this framework, the mean trait values of a species determine its niche position along gradients, and intraspecific trait variability determines its niche breadth. This trait-based approach can provide an operational assessment of niche for a potentially large number of species, making it possible to understand and predict species niche shifts under environmental changes. We further advocate a promising method that recently appeared in the literature, which partitions trait diversity into among- and within-community components as a way to quantify the species niche in units of traits instead of environmental parameters. This approach allows the switch of the focus from ecological niches to trait niches, facilitating the examination of species coexistence along undefined environmental gradients. Altogether, the trait-based approach provides a promising toolkit for quantifying the species ecological niche and for understanding the evolution of species niche and traits.     

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。     

Five (or so) challenges for species distribution modelling

Species distribution modelling is central to both fundamental and applied research in biogeography. Despite widespread use of models, there are still important conceptual ambiguities as well as biotic and algorithmic uncertainties that need to be investigated in order to increase confidence in model results. We identify and discuss five areas of enquiry that are of high importance for species distribution modelling: (1) clarification of the niche concept; (2) improved designs for sampling data for building models; (3) improved parameterization; (4) improved model selection and predictor contribution; and (5) improved model evaluation. The challenges discussed in this essay do not preclude the need for developments of other areas of research in this field. However, they are critical for allowing the science of species distribution modelling to move forward.     

Testing the role of climate in speciation: New methods and applications to squamate reptiles (lizards and snakes)

Climate may play important roles in speciation, such as causing the range fragmentation that underlies allopatric speciation (through niche conservatism) or driving divergence of parapatric populations along climatic gradients (through niche divergence). Here, we developed new methods to test the frequency of climate niche conservatism and divergence in speciation, and applied it to species pairs of squamate reptiles (lizards and snakes). We used a large‐scale phylogeny to identify 242 sister species pairs for analysis. From these, we selected all terrestrial allopatric pairs with sufficient occurrence records (n = 49 pairs) and inferred whether each originated via climatic niche conservatism or climatic niche divergence. Among the 242 pairs, allopatric pairs were most common (41.3%), rather than parapatric (19.4%), partially sympatric (17.7%), or fully sympatric species pairs (21.5%). Among the 49 selected allopatric pairs, most appeared to have originated via climatic niche divergence (61–76%, depending on the details of the methods). Surprisingly, we found greater climatic niche divergence between allopatric sister species than between parapatric pairs, even after correcting for geographic distance. We also found that niche divergence did not increase with time, further implicating niche divergence in driving lineage splitting. Overall, our results suggest that climatic niche divergence may often play an important role in allopatric speciation, and the methodology developed here can be used to address the generality of these findings in other organisms.     

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.     

Niche-tracking migrants and niche-switching residents: evolution of climatic niches in New World warblers (Parulidae)

Differences in life-history traits between tropical and temperate lineages are often attributed to differences in their climatic niche dynamics. For example, the more frequent appearance of migratory behaviour in temperate-breeding species than in species originally breeding in the tropics is believed to have resulted partly from tropical climatic stability and niche conservatism constraining tropical species from shifting their ranges. However, little is known about the patterns and processes underlying climatic niche evolution in migrant and resident animals. We evaluated the evolution of overlap in climatic niches between seasons and its relationship to migratory behaviour in the Parulidae, a family of New World passerine birds. We used ordination methods to measure seasonal niche overlap and niche breadth of 54 resident and 49 migrant species and used phylogenetic comparative methods to assess patterns of climatic niche evolution. We found that despite travelling thousands of kilometres, migrants tracked climatic conditions across the year to a greater extent than tropical residents. Migrant species had wider niches than resident species, although residents as a group occupied a wider climatic space and niches of migrants and residents overlapped extensively. Neither breeding latitude nor migratory distance explained variation among species in climatic niche overlap between seasons. Our findings support the notion that tropical species have narrower niches than temperate-breeders, but does not necessarily constrain their ability to shift or expand their geographical ranges and become migratory. Overall, the tropics may have been historically less likely to experience the suite of components that generate strong selection pressures for the evolution of migratory behaviour.     

Climatic‐niche evolution with key morphological innovations across clades within Scutiger boulengeri (Anura: Megophryidae)

The studies of climatic‐niche shifts over evolutionary time accompanied by key morphological innovations have attracted the interest of many researchers recently. We applied ecological niche models (ENMs), ordination method (environment principal component analyses; PCA‐env), combined phylogenetic comparative methods (PCMs), and phylogenetic generalized least squares (PGLS) regression methods to analyze the realized niche dynamics and correspondingly key morphological innovations across clades within Scutiger boulengeri throughout their distributions in Qinghai–Tibet Plateau (QTP) margins of China. Our results show there are six clades in S. boulengeri and obvious niche divergences caused by niche expansion in three clades. Moreover, in our system, niche expansion is more popular than niche unfilling into novel environmental conditions. Annual mean temperature, annual precipitation, and precipitation of driest month may contribute to such a shift. In addition, we identified several key climatic factors and morphological traits that tend to be associated with niche expansion in S. boulengeri clades correspondingly. We found phenotypic plasticity [i.e., length of lower arm and hand (LAHL), hind‐limb length (HLL), and foot length (FL)] and evolutionary changes [i.e., snout–vent length (SVL)] may together contribute to niche expansion toward adapting novel niche, which provides us a potential pattern of how a colonizing toad might seed a novel habitat to begin the process of speciation and finally adaptive radiation. For these reasons, persistent phylogeographic divisions and accompanying divergences in niche occupancy and morphological adaption suggest that for future studies, distinct genetic structure and morphological changes corresponding to each genetic clade should be included in modeling niche evolution dynamics, but not just constructed at the species level.     

Genetic admixture in multidimensional environmental space: asymmetrical niche similarity promotes gene flow in armadillos (Dasypus novemcinctus)

We unite genetic data with a robust test of niche divergence to test the hypothesis that patterns of gene flow between two lineages of the nine-banded armadillo are influenced by their climatic niches. We collected Geographical Information System (GIS) data on climate using locality information from 111 individuals from two lineages that had associated genetic material. We tested whether niches of these lineages were more conserved or divergent than the background environments of their geographic ranges and found evidence for niche conservatism on two axes and no evidence for divergence on any axis. To address the role of niche similarity in gene flow, we genotyped the 111 individuals at five microsatellite loci and tested whether admixed individuals tended to be located in parts of multidimensional environmental space (E-space) shared between the two lineages. We observed an asymmetrical pattern of overlap, in which the West lineage's E-space was almost completely included inside East lineage's E-space. Genetic admixture levels were significantly higher in the West lineage and, for both lineages, in shared portions of E-space. This suggests that niche similarity can facilitate gene flow among disjunct groups with moderate-to-good dispersal capabilities, contrasting with the prevailing view of niche conservatism as a diversifying force.     

灵昆岛潮间带大型底栖动物群落结构与生态位分析

2003年11月至2004年8月,在温州湾的灵昆岛东滩进行了大型底栖动物采样调查。共发现大型底栖动物33种,隶属7门8纲21科。主要为软体动物、节肢动物和环节动物多毛类,其中高潮带25种,中潮带30种,低潮带14种。通过对不同季节不同潮带的大型底栖动物密度数据进行成对t检验分析,结果认为各潮带的大型底栖动物密度分布有明显差异,而大型底栖动物密度的季节变化不明显。对定量取样中获得的21个物种以Shannon-W iener指数为基础进行了生态位宽度测定,以P ianka重叠指数为基础进行了生态位重叠值分析,结果表明日本沙蚕(N ereis jap on ica)、纽虫和线虫的生态位较宽,均为2.80以上,它们之间的生态重叠值也较高,均为0.90以上。以密度数据四次开方为基础,利用欧氏距离进行群落物种的系统聚类分析,结果表明21个物种可以分为三大类,即潮间带广布种、中高潮带常见种、狭布种和偶见种,通过非度量多维标度排序分析也支持以上结果。3类物种的生态位重叠值均有不同的表现,与物种的分布与数量相关。研究表明,物种生态宽度、物种之间的生态位重叠值与物种的分布与数量密切相关,反映了大型底栖动物群落中各物种对生境资源的利用能力的强弱。     

The species chromatogram,a new graphical method to represent,characterize, and compare the ecological niches of different species

The ecological niche sensu Hutchinson is defined as the set of environmental conditions allowing a species to grow, maintain, and reproduce. This conception of the niche, which is assimilated to a p‐dimensional hypervolume, with p representing all environmental variables, has been widely applied in ecology. However, displaying the niche hypervolume has proved challenging when more than three environmental dimensions are considered simultaneously. We propose a simple method (implemented in the specieschrom R package) that displays the full multidimensionality of the ecological niche of a species into a two‐dimensional space by means of a graphic we call species chromatogram. This method gives a graphical summary of the niche by representing together abundance gradients with respect to all environmental variables. A chromatogram enables niche optimums and breaths to be rapidly quantified, and when several chromatograms are examined (one per species), rapid comparisons can be made. From our chromatograms, we proposed a procedure that quantifies niche optimum and breadth as well as niche overlapping (index D) and the identification of the most discriminant combination of environmental variables. We apply these analyses on eight planktonic species collected by the Continuous Plankton Recorder (CPR) survey in the North Atlantic Ocean using 10 environmental variables. We display their full multidimensional niches and quantify their niche optimums and breadths along each dimension. We also compare our index D with other indices by means of hypervolume and dynRB R packages. By catching the full complexity of the niche, species chromatograms allow many different niche properties to be rapidly assessed and compared among species from niche optimums and breadths to the identification of the most relevant environmental parameters and the degree of niche overlapping among species. Species chromatograms may be seen as species’ fingerprint and may also allow a better identification of the mechanisms involved in species assembly.     

Genetic diversity and ecological niche modelling of the restricted Recordia reitzii (Verbenaceae) from southern Brazilian Atlantic forest

Genetic diversity analyses, coupled with ecological niche modelling (ENM) of species with a restricted distribution, may provide valuable information for understanding diversification patterns in endangered areas. We analyzed the genetic diversity of Recordia reitzii, a tree restricted to the threatened and highly fragmented Brazilian Atlantic forest, using three intergenic cpDNA spacers and ten microsatellite (SSR) loci. To assess the historical processes that may have influenced the distribution of extant R. reitzii populations, the current potential distributions of R. reitzii and Recordia boliviana, a closely related species, were modelled and projected onto the Last Glacial Maximum (LGM) and Last Interglacial (LIG) periods. Niche divergence was quantified between these two. The cpDNA and SSR data showed a north–south pattern of the diversity distribution and structured populations, suggesting that gene flow is probably limited. According to our data, R. reitzii exhibits low genetic diversity, which may be a result of a founder or distribution‐reduction effect, narrow distribution or small population size. The ecological niche models showed a wider palaeodistribution during the LIG and a retraction during the LGM for both species. Tests of niche divergence and conservatism indicated that bioclimatic factors might have influenced the diversification of these Recordia species. © 2014 The Linnean Society of London, Botanical Journal of the Linnean Society, 2014, 176 , 332–348.     

Host range determination in a novel outbreak pest of sugarcane,Cacosceles newmannii (Coleoptera: Cerambycidae,Prioninae), inferred from stable isotopes

1. An outbreak of Cacosceles newmannii (Coleoptera: Cerambycidae) was detected for the first time on sugarcane (Saccharum spp.) in 2015 in KwaZulu-Natal, South Africa. Although primary host plants of this native species remain unknown, these are central to testing hypotheses concerning the outbreak.
2. We hypothesized that this species has undergone a host plant shift (i.e. a feeding association with a novel host plant).
3. We compared δ¹³C and δ¹⁵N ratios of adult beetles retrieved from South African museum collections, collected between 1891 and 2016 (n = 23; ‘pre-outbreak’), with samples from infested fields in 2017 (n = 9, ‘post-outbreak’) and in 2019 (n = 23, ‘post-outbreak’), as well as diverse, plausible host plants (n = 42 samples across 10 species) from infested fields and surrounding patches of indigenous and commercial forest vegetation. We used Bayesian isotope mixing models to infer the relative contribution of the different plants to the diet of C. newmannii.
4. Pre-outbreak, C₃ plants contributed strongly to the larval diet, whereas post-outbreak, C₄ plants were the largest component of their diet. There was some indication of C₄ plants contributing to their diet pre-outbreak.
5. Our results suggest that the outbreak of this polyphagous beetle was not a dramatic host shift but rather a rapid increase in the proportion of C₄ plants already in their diet.
6. We concluded that plants from the families Fabaceae and Poaceae are the most likely host plants of this species. Nevertheless, the drivers of this rapid outbreak on sugarcane remain poorly determined and should be the focus of future research.

     

Morphological variation of Pinus flexilis (Pinaceae), a bird-dispersed pine, across a range of elevations

Limber pine (Pinus flexilis James) grows across a wider range of elevations than any other tree species in the central Rockies, from ～1600 m at Pawnee Buttes to >3300 m at Rollins Pass. In this study we investigated two possible explanations for limber pine's success across a broad range of elevations: (1) the sites on which it is found, although separated by >1000 m elevation, may not be very different with respect to environmental factors that affect tree growth, and (2) limber pine growth is insensitive to environmental factors that change with elevation. We compared site characteristics of 12 limber pine stands at elevations ranging from 1630 to 3328 m as well as the growth and morphology of trees in each of these stands. Mean daily air temperature in July decreased linearly with the elevation of the site from 22.8° to 12.6°C. The growth and morphology of limber pine leaves, shoots, and trees were, in general, not related to the elevation or July mean air temperature of the sites. There was, however, a significant decrease in stomatal density with increasing elevation, which may be an acclimational response to restrict water loss at high elevations. Our data suggest that the fundamental and realized niche of limber pine is broad with respect to air temperature. In light of the high gene flow and only slight genetic differentiation among populations of species with bird-dispersed seeds, such as limber pine, it is especially unusual to see similar growth throughout an environmental gradient. Physiological and anatomical plasticity or wide physiological tolerance ranges may enable limber pine to uncouple its growth from its environment.     

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.     

Complex patterns of environmental niche evolution in Iberian columbines (genus Aquilegia,Ranunculaceae)

Aims This study explores the patterns of niche differentiation in a group of seven closely related columbines (genus Aquilegia, Ranunculaceae) from the Iberian Peninsula. Populations of these columbines are subject to complex patterns of divergent selection across environments, which partly explain the taxonomic structure of the group. This suggests the hypothesis that niche divergence must have occurred along the process of diversification of the group.Methods We used MaxEnt to build environmental niche models of seven subspecies belonging to the three species of Aquilegia present in the Iberian Peninsula. From these models, we compared the environmental niches through two different approaches: ENMtools and multivariate methods.Important findings MaxEnt distributions conformed closely to the actual distribution of the study taxa. ENMtools methods failed to uncover any clear patterns of niche differentiation or conservatism in Iberian columbines. Multivariate analyses indicate the existence of differentiation along altitudinal gradients and along a gradient of climatic conditions determined by the summer precipitation and temperatures. However, climatic conditions related to winter temperature and precipitation, as well as soil properties, were equally likely to show conservatism or divergence. The complex patterns of niche evolution we found suggest that Iberian Columbines have not been significantly constrained by forces of niche conservatism, so they could respond adaptively to the fast and profound climate changes in the Iberian Peninsula through the glacial cycles of the Pleistocene.