Nestedness, niche metrics and temporal dynamics of a metacommunity in a dynamic natural model system

Prediction of extinction and colonization rates for whole species assemblages emerges as an urgent task for ecology. We hypothesized that nestedness of species assemblage reflects differential ability of species to occupy sites and of sites to support species. If correct, a nested ordering of species and sites should condense long‐term dynamics of metacommunities. To test this we characterized the differential ability of species to use habitat (niche position and niche breadth) using eight surveys of invertebrate communities inhabiting 49 tropical rock pools. We examined temporal consistency of the nested rank of species and pools, and related them to species and pool characteristics to infer temporal dynamics of species composition. Invertebrate assemblages in the rock‐pools were significantly nested and species ranks were generally preserved over time. By contrast, pool ranks were usually conserved between adjacent years only but their similarity declined with time separating surveys. The nested species‐by‐pool matrix of the first survey served as a benchmark to assess individual species and local community changed in subsequent years. As hypothesized, benchmark cells with high state occupancy probability had low extinction rates in subsequent years. Moreover, species high in the nested matrix (also with high regional occupancy probability) were better survivors and colonizers relative to species that ranked low. The year‐to‐year dynamics were similar. Species with non‐marginal niche position retained high ranks in the matrix. Yet, niche position predicted only colonization rate of species. Niche breadth and species’ nested ranking, extinction risk, or ability to colonize a pool showed no relationship. Counter to the expectation, pool ranks did not predict species extinction and colonization rates. Apparently, even in dynamic systems, regional nested pattern remains consistent and the underlying extinction and colonization dynamics appear to be largely determined by the hierarchical order among species and much less by that among sites.     

Nested communities,invasive species and Holocene extinctions: evaluating the power of a potential conservation tool

General ecological methods and models that require a minimum amount of information yet are still able to inform conservation planning are particularly valuable. Nested subset analysis has been advocated as such a tool for the prediction of extinction-prone species and populations. However, such advocacy has not been without skepticism and debate, and in the majority of published examples assessing extinction vulnerability, actual extinctions are based on assumptions rather than direct evidence. Here, we empirically test the power of nested subset analysis to predict extinction-prone species, using documented Holocene insular mammal extinctions on three island archipelagos off the west coast of North America. We go on to test whether the introduction of invasive mammals promotes nestedness on islands via extinction. While all three archipelagos were significantly nested before and after the extinction events, nested subset analysis largely failed to predict extinction patterns. We also failed to detect any correlations between the degree of nestedness at the genus-level with area, isolation, or species richness and extinction risk. Biogeography tools, such as nested subset analysis, must be critically evaluated before they are prescribed widely for conservation planning. For these island archipelagos, it appears detailed natural history and taxa-specific ecology may prove critical in predicting patterns of extinction risk.     

Nestedness in insular floras: spatiotemporal variation and underlying mechanisms

Aims Nestedness is a characteristic of insular metacommunity structure. Relatively few studies, however, have attempted to evaluate temporal changes in nestedness, or elucidate the mechanisms underlying nestedness. I evaluated both spatial and temporal patterns of nestedness in the insular floras of four archipelagoes of small islands in the Bahamas and the potential underlying environmental gradients.Methods The NODF (a nestedness metric based on overlap and decreasing fill) and the matrix temperature measure, T, were used to quantify nestedness in insular floras on small islands near Abaco, Andros, Great Exuma and the Exuma Cays, Bahamas. Two different null models were employed for each nestedness measure. Six environmental variables were evaluated in relation to nestedness by ordering islands according to gradients and recalculating NODF scores.Important findings All archipelagoes were significantly nested. Nestedness among sites contributed more to overall nestedness than did nestedness among species. NODF scores varied among archipelagoes, but were surprisingly constant over time. Ordering islands by vegetated area yielded the highest nestedness scores for three archipelagoes; ordering islands by protection from exposure yielded the highest nestedness score for one archipelago. Nestedness scores varied little over time even though species compositions changed, indicating that extinctions occurred in a deterministic manner. The relative importance of area suggests extinction is an important mechanism in producing nestedness. Attempting to determine the relative importance of immigrations or extinctions requires some assumptions, however, and both processes are likely cumulative in most cases.     

Can the biotic nestedness matrix be used predictively?

The biotas of a suite of neighboring patches of remnant vegetation often form a series of nested sub-sets, in which the species present in species-poor patches are non-random sub-sets of those present in richer patches. There has been recent interest in ways in which this knowledge may be used to aid conservation. We focus here on whether nested patterns can be used predictively. If nestedness in a fragmented system increases over time through biotic relaxation, locations where particular species may become extinct or are likely to colonize might be predictable and this could be useful in threatened-species management. We used the Temperature Calculator of Atmar and Patterson (1995) to arrange a matrix of bird species' occurrences in a series of buloke Allocasuarina leuhmannii woodland remnants so that nestedness was maximized. Probability bands generated by the calculator were used to predict possible colonization and extinction events. We then re-surveyed the avifauna of the fragments after a seven-year interval to test these predictions. Although nestedness increased between the two survey periods, there was no linear relationship between the generated probability of extinctions or colonizations and the accuracy of the predictions. The predictions derived from the calculator were no more accurate than a second set of predictions generated by use of a simple non-nested model. Despite the increase in nestedness, the arrangement of sites in each of the two maximally packed matrices was substantially different. For the nestedness matrix to generate accurate predictions, an increase in nestedness must be due to a minimization of unexpected species presences and absences rather than an extensive redistribution of species among remnants, as we found. The potential utility of nested patterns in predicting systematic colonization and extinction events should be further evaluated in other, less dynamic, fragmented systems such as those undergoing biotic relaxation.     

Effects of habitat size and isolation on species immigration–extinction dynamics and community nestedness in a desert river system

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Biogeography of Puerto Rican ants: a non-equilibrium case?

Ants were studied on Puerto Rico and 44 islands surrounding Puerto Rico. Habitat diversity was the best predictor of the number of species per island and the distributions of species followed a nested subset pattern. The number of extinctions per island was low, approximately 1–2 extinctions per island in a period of 18 years, and the rates of colonization seem to be greater than the extinction rates. Ant dynamics on these islands do not seem to support the basic MacArthur and Wilson model of island biogeography. The MacArthur and Wilson equilibrium is based on the notion that species are interchangeable, but some extinctions and colonizations can change the composition and number of species drastically.     

BIODIVERSITY RESEARCH: Nestedness for different reasons: the distributions of birds,lizards and small mammals on islands of an inundated lake

Aim We examined whether the community compositions of birds, lizards and small mammals were nested in a fragmented landscape in the Thousand Island Lake, China. We also assessed whether the mechanisms influencing nestedness differed among these taxonomic groups. Location Thousand Island Lake, China. Methods Presence/absence matrices were compiled for birds (42 islands) and lizards (42 islands) using line‐transect methods, and for small mammals (14 islands) using live‐trapping methods from 2006 to 2009. Nestedness was analysed using BINMATNEST, and statistical significance was assessed using the conservative null model 3. We used Spearman rank correlations and partial Spearman rank correlations to examine associations of nestedness and habitat variables (area, isolation, habitat diversity and plant richness) as well as life‐history traits (body size, habitat specificity, geographical range size and area requirement) related to species extinction and immigration tendencies. Results The community compositions of birds, lizards and small mammals were all significantly nested, but the causal factors underlying nestedness differed among taxonomic groups. For birds, island area, habitat specificity and area requirement were significantly correlated with nestedness after controlling for other independent variables. For lizards, habitat heterogeneity was the single best correlate of nestedness. For small mammals, island area, habitat heterogeneity and habitat specificity were significantly correlated with nestedness. The nested patterns of birds, lizards and small mammals were not attributable to passive sampling or selective colonization. Main conclusions The processes influencing nested patterns differed among taxonomic groups. Nestedness of bird assemblages was driven by selective extinction, and lizard assemblage was caused by habitat nestedness, while nestedness of small mammals resulted from both selective extinction and habitat nestedness. Therefore, we should take taxonomic differences into account when analysing nestedness to develop conservation guidelines and refrain from using single taxa as surrogates for others.     

The influence of colonization in nested species subsets

Biotic communities inhabiting collections of insular habitat patches often exhibit compositional patterns described as nested subsets. In nested biotas, the assemblages of species in relatively depauperate sites comprise successive subsets of species in relatively richer sites. In theory, nestedness may result from selective extinction, selective colonization, or other mechanisms, such as nested habitats. Allopatric speciation is expected to reduce nestedness. Previous studies, based largely on comparisons between land-bridge and oceanic archipelagos, have emphasized the role of selective extinction. However, colonization could also be important in generating strong patterns of nestedness. We apply a recently published index of nestedness to more than 50 island biogeographic data sets, and examine the roles of colonization, extinction, endemism, and, to a limited extent, habitat variability on the degree on nestedness. Most data sets exhibit a significant degree of nestedness, although there is no general tendency for land-bridge biotas to appear more nested than oceanic ones. Endemic species are shown to generally reduce nestedness. Comparisons between groups of non-endemic species differing in overwater or inter-patch dispersal ability indicate that superior dispersers generally exhibit a greater degree of nestedness than poorer dispersers, a result opposite that expected if colonization were a less predictable process than extinction. These results suggest that frequent colonization is likely to enhance nestedness, thereby increasing the compositional overlap among insular biotas. The prevalence of selective extinction in natural communities remains in question. The importance of colonization in generating and maintaining nested subsets suggests that (1) minimum critical areas will be difficult to determine from patterns of species distributions on islands; (2) multiple conservation sites are likely to be required to preserve communities in subdivided landscapes; and (3) management of dispersal processes may be as important to preserving species and communities as is minimizing extinctions.     

Nestedness of desert bat assemblages: species composition patterns in insular and terrestrial landscapes

Nested patterns of community composition exist when species at depauperate sites are subsets of those occurring at sites with more species. Nested subset analysis provides a framework for analyzing species occurrences to determine non-random patterns in community composition and potentially identify mechanisms that may shape faunal assemblages. We examined nested subset structure of desert bat assemblages on 20 islands in the southern Gulf of California and at 27 sites along the Baja California peninsula coast, the presumable source pool for the insular faunas. Nested structure was analyzed using a conservative null model that accounts for expected variation in species richness and species incidence across sites (fixed row and column totals). Associations of nestedness and island traits, such as size and isolation, as well as species traits related to mobility, were assessed to determine the potential role of differential extinction and immigration abilities as mechanisms of nestedness. Bat faunas were significantly nested in both the insular and terrestrial landscape and island size was significantly correlated with nested structure, such that species on smaller islands tended to be subsets of species on larger islands, suggesting that differential extinction vulnerabilities may be important in shaping insular bat faunas. The role of species mobility and immigration abilities is less clearly associated with nestedness in this system. Nestedness in the terrestrial landscape is likely due to stochastic processes related to random placement of individuals and this may also influence nested patterns on islands, but additional data on abundances will be necessary to distinguish among these potential mechanisms.     

Effects of site and species characteristics on nested patterns of species composition in sedge meadows

Biotas of both geographical islands and habitat islands are often nested subsets of the biotas of successively more species-rich islands within the same system. The life history characteristics of a species may determine how that species contributes to the general pattern of species nestedness. Here, I investigate the floras of 56 sedge meadow wetlands in northern Illinois (USA) in order to characterize the degree of nestedness in these communities, determine which individual plant species contribute to the nested pattern, and investigate species characteristics that might be related to nonrandom patterns of distribution in individual plant species. The entire assemblage of species at all sedge meadows was significantly nested. Species richness and area were significantly correlated, and the nested pattern was closely related to site area, suggesting that species drop out of the assemblage in a predictable order as site area decreases. Some individual species exhibited nonrandom distributions across the sites, occurring more often in large, species-rich sites. Large sites were more likely than smaller sites to contain conservative species, i.e., those typical of pristine natural habitat, whereas nonconservative species were distributed more randomly among sites. Nested patterns of distribution of conservative species with respect to site area may result from their high probability of extinction on small sites or from a tendency for required habitats to co-occur on the same large sites. This revised version was published online in June 2006 with corrections to the Cover Date.     

Investigating causality of nestedness of insular communities: selective immigrations or extinctions?

Abstract. Most archipelagos are comprised of a nested set of communities, with species on depauperate islands representing proper subsets of those on richer islands. The causality for this common intra-archipelago pattern, however, remains elusive. Here, I present a Monte Carlo approach for investigating whether nestedness results from selective extinctions, selective immigrations, or both. Results for mammal communities of three nearshore archipelagos and two montane forest archipelagos suggested that nestedness may result from both forces. Nestedness was significantly associated with area (extinctions) for all archipelagos studied, and with isolation (immigrations) for islands of Lake Huron and the American Southwest. The degree of nestedness is influenced by the degree of variations among species and islands. In addition, our ability to assess causality of nestedness is influenced by our ability to calculate biologically relevant measures of isolation, and by the potentially confounding effects of selective immigrations and extinctions on community nestedness.     

Invasive species and land bird diversity on remote South Atlantic islands

Invasive species pose significant threats to biodiversity, especially on islands. They cause extinctions and population declines, yet little is known about their consequences on the emergent, metacommunity-level patterns of native species in island assemblages. We investigated differences in species–area relationships, nestedness, and occupancy of 9 species of native land birds between island assemblages with and without invasive Norway rats (Rattus norvegicus) in the Falkland Archipelago. We found that species–area curves, nestedness, and individual species’ occurrences differed between island assemblages with and without rats. Rat-free islands had, on average, 2.1 more land bird species than rat-infested islands of similar size. Passerine bird communities on islands with and without rats were significantly nested, but nestedness was significantly higher on rat-free islands than on rat-infested islands. The presence of rats was associated with differences in the incidence of many, but not all bird species. On rat free islands the occurrence of all species increased with island area. The occurrence of most, albeit not all, bird species was lower on islands with than on islands without rats. Two species of conservation concern, Troglodytes aedon cobbi and Cinclodes antarcticus, were abundant on rat-free islands, but absent or found at very low frequencies on islands with rats. The occurrence of three species was not associated with the presence of rats. The patterns presented here can be used to evaluate the consequences of ongoing rat eradications for passerine diversity, distribution, and abundance.     

舟山群岛蝶类群落嵌套分布格局及其影响因素

片断化生境中群落的物种组成常呈现嵌套分布格局。2013年7-8月, 我们在浙江舟山群岛采用截线法对28个岛屿上的蝴蝶群落进行了野外调查, 探讨了岛屿物种嵌套分布格局及其影响因素。通过测量采集标本获得蝶类的生活史特征(最小需求面积、翅展和体重), 查阅文献资料获得蝶类的栖息地特征(岛屿面积、距最近大陆距离和距最近大岛距离), 分析了影响蝶类群落嵌套结构的因素。研究结果显示: (1)舟山群岛蝶类群落符合嵌套分布格局; (2)岛屿面积和物种最小需求面积对嵌套格局的形成有显著影响; (3)舟山群岛蝶类群落嵌套格局的形成支持选择性灭绝假说; (4)随机检验零模型结果显示该嵌套分布格局并非采样偏差造成的。因此, 在制定舟山群岛区域蝶类保护措施时, 应优先考虑那些分布在面积较大岛屿的和最小需求面积较大的物种。     

Distributions of forest birds and butterflies in the Andaman islands, Bay of Bengal: nested patterns and processes

The distributional patterns of forest birds and butterflies in the Andaman islands, an oceanic chain located off SE Asia, were tested for nestedness. Both taxa were highly nested. Nestedness could be due to colonization or extinction processes, area or distance effects or nestedness of habitats. Nestedness in forest bird distributions were strongly influenced by area and habitat related factors. Habitats were significantly nested in all three island groups, however most strongly for the North Andamans. However forest bird distributions in the North Andamans, as indicated by row order in the packed matrix, was not correlated with habitat diversity, suggesting that habitat related factors alone cannot account for these patterns. Other causal influences could be passive sampling, where common and abundant species and habitats are more likely to have a widespread distribution than rare species and habitats. The nested subset pattern seen in two unrelated taxa suggests that the Andamans are extinction dominated and that the protection of forests on large islands is critical for the conservation of its biodiversity.     

The measure of order and disorder in the distribution of species in fragmented habitat

Species distribution patterns within naturally fragmented habitat have been found to often exhibit patterns of pronounced nestedness. Highly predictable extinction sequences are implied by these nested species distribution patterns, thus the patterns are important to both the philosophy and practice of conservation biology. A simple thermodynamic measure of the order and disorder apparent in the nested patterns is described. The metric offers (i) a measure of the uncertainty in species extinction order, (ii) a measure of relative populational stabilities, (iii) a means of identifying minimally sustainable population sizes, and (iv) an estimate of the historical coherence of the species assemblage. Four presumptions govern the development of the metric and its theory: (i) the fragmented habitat was once whole and originally populated by a single common source biota, (ii) the islands were initially uniform in their habitat heterogeneity and type mix, and have remained so throughout their post-fragmentation history, (iii) no significant clinal (latitudinal) gradation exists across the archipelago so as to promote species turnover across the archipelago, and (iv) all species of interest are equally isolated on all islands. The violation of these conditions promotes species distributions which are idiosyncratic to the general extinction order expected in fragmentation archipelagos. While some random variation in extinction order is to be expected, idiosyncratic distributional patterns differ from randomness and are readily segregatable from such noise. A method of identifying idiosyncratic species and sites is described.     

Nestedness and niche‐based species loss in moorland plant communities

Communities in isolated habitat patches surrounded by inhospitable matrices often form a nested subset pattern. However, the underlying causal mechanisms and conservation implications of nestedness in regional communities remain controversial. The nested ranks of species in a nested species‐by‐site matrix may reflect a gradient of species vulnerability to extinction or of colonization ability. However, nestedness analysis has rarely been used to explore determinants of species rank; consequently, little is known of underpinning mechanisms. In this study, we examined nestedness in moorland plant communities widely interspersed within the subalpine zone of northern Japan. Moorland sites differed in area (1000–160 000 m²) and were naturally isolated from one another to various extents within an inhospitable forest matrix. We also determined whether site characteristics (physical and morphometric measures) and species characteristics (niche position and breadth, based on species’ traits) are related to nestedness. Moorland plant communities in the study area were significantly nested. The pH and moorland kernel density (proxy for spatial clustering of moorlands around the focal site) were the most important predictors of moorland site nested rank in a nestedness matrix. Niche breadths of species (measured as variation in leaf mass area and height) predicted species’ nested ranks. Selective environmental tolerances imposed by environmental harshness and selective extinction caused by declines in site carrying capacities probably account for the nested subset pattern in moorland plant communities. The nested rank of species in the nestedness matrix can therefore be translated into the potential order of species loss explainable by species niche breadths (based on variation in functional traits). Complementary understanding of the determinants of site ranking and species ranking in the nestedness matrix provides powerful insight into ecological processes underlying nestedness and into the ways by which communities are assembled or disassembled by such processes.     

Nestedness of butterfly assemblages in the Zhoushan Archipelago,China: area effects,life-history traits and conservation implications

The nested subset pattern (nestedness) of faunal assemblages has been a research focus in the fields of island biogeography and conservation biology in recent decades. However, relatively few studies have described nestedness in butterfly assemblages in oceanic archipelago systems. Moreover, previous studies often quantified nestedness using inappropriate nestedness metrics and random fill algorithms with high Type I errors. The aims of this study are to examine the existence of nestedness and underlying causal mechanisms of butterfly assemblages in the Zhoushan Archipelago, China. We used the line-transect method to determine butterfly occupancy and abundance on 42 study islands from July to August 2014. We obtained butterfly life-history traits (wingspan, body weight and minimum area requirement) by field work and island geographical features (area and isolation) from the literature. We used the recently developed metric WNODF to estimate nestedness. Partial Spearman rank correlation was used to evaluate the associations of nestedness and island geographical features as well as butterfly life-history traits related to species extinction risk and colonization ability. The butterfly assemblages were significantly nested. Island area and minimum area requirement of butterflies were significantly correlated with nestedness after controlling for other independent variables. In contrast, the nestedness of butterflies did not appear to result from passive sampling or selective colonization. However, multi-year studies are needed to confirm that target effects are not muddling these results. Our results indicate that selective extinction may be the main driver of nestedness of butterfly assemblages in our study system. From a conservation viewpoint, we should protect both large islands and species with large area requirement to maximize the number of species preserved.     

Mammalian biogeography of the Alexander Archipelago of Alaska: a north temperate nested fauna

Aim A large number of studies have analysed the distribution of mammals within archipelagos, yet few have focused on islands that were heavily glaciated and subsequently colonized following deglaciation. Location We explored the relative effects of island area and isolation on faunal composition based on twenty-three mammalian taxa of twenty-four islands of the Alexander Archipelago, Southeast Alaska. Methods We used regression of log-transformed variables and several indices of nestedness. Results These faunas showed significant nested structure using tests of nestedness and regression models. Unlike most landbridge and mainland archipelagos studied previously, isolation appears to be the primary factor determining patterns of species richness. Main conclusions Colonization ability of particular taxa, rather than extinction, has determined this nested structure. We suggest that other higher latitude archipelagos may show similar historical patterns.     

Nested species subsets of amphibians and reptiles on Neotropical forest islands

Nested species subsets are a common pattern of community assembly characteristic of many types of fragmented landscapes and insular systems. Here we describe nested subset patterns of amphibian and reptile occupancy on 23 forest islands in north-eastern Bolivia. We used observed occupancy patterns to differentiate five distributional guilds: widespread species, rare species, poor colonizers, area-sensitive species and supertramps. Amphibian occurrences were nested along a forest island isolation gradient, and when species from each of the distribution classes were removed from subsequent analyses of nestedness, we found that dispersal-limited poor colonizers were responsible for the association between nestedness and isolation. Amphibians associated with the grassland matrix at the study site showed a nested pattern linked with area, although this pattern did not scale up to all amphibians and could not be unequivocally attributed to any of the distributional guilds we recognized. There were no strong associations between two biological characteristics, body size and relative abundance in the matrix, and the likelihood of occupancy along either forest island area or isolation gradients. The relative importance of isolation in shaping nested patterns of amphibians on these forest islands may be a result of either (1) the greater range in isolation values included in this study compared with many others; (2) the long time since isolation in this landscape, manifesting a footprint of isolation not apparent in more recently fragmented patches; (3) the relatively homogeneous grassland matrix surrounding forest islands that likely provides little refuge for animals moving among forest islands.     

From sampling stations to archipelagos: investigating aspects of the assemblage of insular biota

Aim To investigate the formation of nestedness and species co‐occurrence patterns at the local (sampling station), the intermediate (island group), and the archipelago scale. Location The study used data on the distribution of terrestrial isopods on 20 islands of the central Aegean (Greece). These islands are assigned to two distinct subgroups (Kyklades and Eastern islands). Methods The Nestedness Temperature Calculator was used to obtain nestedness values and maximally nested matrices, the EcoSim7 software and a modified version of Sanderson (2000 ) method were used for the analysis of species co‐occurrences. Idiosyncratic temperatures of species and the order of species placement in the maximally nested matrices were used for further comparisons among spatial scales. The relationships of nestedness values with beta‐diversity, habitat diversity and a number of ecological factors recorded for each sampling station were also investigated. Results Significant nestedness was found at all spatial scales. Levels of nestedness were not related to beta‐diversity or habitat diversity. Nestedness values were similar among spatial scales, but they were affected by matrix size. The species that contributed most to the nested patterns within single islands were not the same as those that produce nestedness at the archipelago scale. There was significant variation in the frequency of species occurrence among islands and among spatial scales. There was no direct effect of ecological factors on the shaping of patterns of nestedness within individual islands, but habitat heterogeneity was crucial for the existence of such patterns. Positive associations among species prevailed at all scales when species per station were considered, while negative associations prevailed in the species per island matrices. All associations resulted from the habitat structure of sampling stations and from particularities of geographical distributions. Conclusions There was no clear‐cut distinction between nestedness patterns among spatial scales, even though different species, and partially different factors, contributed to the formation of these patterns in each case. There was a core of species that contributed to the formation of nested patterns at all spatial scales, while the patterns of species associations suggested that biotic interactions are not an important causal factor. The results of this study suggest that locally rare species cannot be widespread at a higher spatial scale, while locally common species can have a restricted distribution.