Nestedness pattern in stream diatom assemblages of central Western Ghats

Community diversity and the population abundance of a particular group of species are controlled by immediate environment, inter-and intra-species interactions, landscape conditions, historical events and evolutionary processes. Nestedness is a measure of order in an ecological system, referring to the order in which the number of species is related to area or other factors. In this study we have studied the nestedness pattern in stream diatom assemblages in 24 stream sites of central Western Ghats, and report 98 taxa from the streams of central Western Ghats region. The communities show highly significant nested pattern. The Mantel test of matrix revealed a strong relationship between species assemblages and environmental conditions at the sites. A significant relationship between species assemblage and environmental condition was observed. Principal component analysis (PCA) indicated that environmental conditions differed markedly across the sampling sites, with the first three components explaining 78% of variance. Species composition of diatoms is significantly correlated with environmental distance across geographical extent. The current pattern suggests that micro-environment at regional levels influences the species composition of epilithic diatoms in streams. The nestedness shown by the diatom community was highly significant, even though it had a high proportion of idiosyncratic species, characterized with high numbers of cosmopolitan species, whereas the nested species were dominated by endemic species. PCA identifies ionic parameters and nutrients as the major features which determine the characteristics of the sampling sites. Hence the local water quality parameters are the major factors in deciding the diatom species assemblages.

An experimental examination of colonization as a generator of biotic nestedness

Species assemblages of systems of islands and other fragmented habitats frequently show a "nested-subset" structure in which the biotas of sites with low species richness are non-random subsets of the biotas of richer sites. Much literature suggests that extinction is more likely to produce strongly nested patterns than colonization, although very few experiments have been conducted on the generation of nested-subset patterns. Here, we describe an experiment on nestedness of benthic invertebrates occupying rocks in the littoral zone of a lake in western Victoria, Australia. Data collected from previous work indicated that the invertebrate biotas of rocks were nested. We used initially defaunated, different-sized habitat patches (half house-bricks, full house-bricks, double house-bricks) and followed the time-course of occupation to assess whether nested-subset patterns would emerge, and whether extinction or colonization best accounted for the patterns. We predicted that nestedness would increase through time up to the end of the experiment. This was found to be the case with colonization dominating the establishment of a strongly nested system; extinction appeared to be of relatively little importance over the duration of the experiment. These results suggest that at least in some circumstances, differential colonization may be influential in producing nested-subset patterns but experiments conducted over longer times may be needed to more completely understand the respective roles of extinction and colonization in generating nested-subset patterns in this system.

Nestedness in fragmented landscapes: birds of the box-ironbark forests of south-eastern Australia

Nestedness in biota as a function of species richness – biota of depauperate assemblages being non-random subsets of richer biotas – has been widely documented in recent years (see Wright et al. 1998, Oecologia 113: 1–20). Ordering sites by richness maximizes nestedness indices; however, ordering by other criteria such as area or isolation may be more ecologically interpretable. We surveyed birds in true fragments (35 in all), and in "reference areas" in large extant forest blocks (30 locations), of the same range of areas (10, 20, 40, 80 ha). The avifauna was divided into "bush birds"– species dependent on forest and woodland, and "open country" species. We looked at nestedness in four data sets: "bush birds" in fragments and reference areas, and "all birds" in fragments and in reference areas. All data sets were significantly nested. Ordering by area in all cases was not significantly less nested than ordering by richness. Ordering by area in fragments was significantly greater than in reference areas, but the differences in standardized nestedness indices were small (<15%). We identified those birds that had distributions among fragments that conformed strongly with area, those that were more randomly distributed and some species that were more likely to occupy the smallest fragments. Among the latter was a hyperaggressive, invasive, colonial native species (noisy miner Manorina melanocephala). A suite of small, insectivorous birds were more likely to strongly conform with expected distributions in relation to area, which was consistent with observations of their vulnerability to the effects of the noisy miner in smaller fragments.

Patterns in permuted binary matrices

Reorganizing a dataset so that its hidden structure can be observed is useful in any data analysis task. For example, detecting a regularity in a dataset helps us to interpret the data, compress the data, and explain the processes behind the data. We study datasets that come in the form of binary matrices (tables with 0s and 1s). Our goal is to develop automatic methods that bring out certain patterns by permuting the rows and columns. We concentrate on the following patterns in binary matrices: consecutive-ones (C1P), simultaneous consecutive-ones (SC1P), nestedness, k-nestedness, and bandedness. These patterns reflect specific types of interplay and variation between the rows and columns, such as continuity and hierarchies. Furthermore, their combinatorial properties are interlinked, which helps us to develop the theory of binary matrices and efficient algorithms. Indeed, we can detect all these patterns in a binary matrix efficiently, that is, in polynomial time in the size of the matrix. Since real-world datasets often contain noise and errors, we rarely witness perfect patterns. Therefore we also need to assess how far an input matrix is from a pattern: we count the number of flips (from 0s to 1s or vice versa) needed to bring out the perfect pattern in the matrix. Unfortunately, for most patterns it is an NP-complete problem to find the minimum distance to a matrix that has the perfect pattern, which means that the existence of a polynomial-time algorithm is unlikely. To find patterns in datasets with noise, we need methods that are noise-tolerant and work in practical time with large datasets. The theory of binary matrices gives rise to robust heuristics that have good performance with synthetic data and discover easily interpretable structures in real-world datasets: dialectical variation in the spoken Finnish language, division of European locations by the hierarchies found in mammal occurrences, and co-occuring groups in network data. In addition to determining the distance from a dataset to a pattern, we need to determine whether the pattern is significant or a mere occurrence of a random chance. To this end, we use significance testing: we deem a dataset significant if it appears exceptional when compared to datasets generated from a certain null hypothesis. After detecting a significant pattern in a dataset, it is up to domain experts to interpret the results in the terms of the application.

As comunidades de anfíbios e lagartos dos remanescentes de restingas do estado do Espírito Santo: uma análise da ocorrência e distribuição das espécies

Ecologicamente, comunidades são conjuntos de populações convivendo no mesmo espaço e tempo. A forma como as espécies que compõem estas comunidades, como elas se distribuem e como estão estruturadas, depende de inúmeros fatores, entre eles históricos, biogeográficos e evolutivos. Neste estudo, buscamos compreender como as comunidades de anfíbios anuros e de lagartos estão estruturadas e quais fatores ambientais e de degradação são determinantes nesta estruturação. Amostramos cinco remanescentes de restinga no estado do Espírito Santo, utilizando método de procura ativa em transecções lineares nas diferentes fisionomias vegetais destes ecossistemas. Realizamos amostragens nas estações seca e de chuvas em todas as restingas, e somamos um total de 60 horas de esforço amostral para os anfíbios e 75 horas para os lagartos. Registramos um total de 32 espécies de anfíbios anuros conjuntamente nos cinco remanescentes de restinga, sendo duas destas espécies endêmicas deste ecossistema: Scinax agilis e Melanophryniscus setiba. A restinga do Parque Paulo Cesar Vinha foi o remanescente com a maior riqueza de espécies de anuros, enquanto a restinga da Reserva Biológica de Comboios foi, comparativamente, o remanescente com menor riqueza de espécies. Em termos de composição de espécies, as restingas de Praia das Neves e Paulo Cesar Vinha foram as mais similares, enquanto a restinga de Comboios foi a mais distante na análise de agrupamento. Registramos no conjunto de restingas seis modos reprodutivos para as espécies de anuros, sendo 75% deles relacionados aos ambientes aquáticos. A disponibilidade de locais de desova esteve positivamente relacionada à riqueza de espécies. Todos os mesohábitats das restingas, com exceção das fitofisionomias de halófila-psamófila, foram utilizados pelos indivíduos registrados, entretanto, uma porcentagem considerável dos indivíduos foi encontrada nos alagados. Em relação às comunidades de lagartos, adotamos além dos nossos dados, aqueles disponíveis em Dias e Rocha (2014) e aqueles disponíveis em Winck (2012). Registramos um total de 23 espécies de lagartos nos remanescentes de restinga amostrados nos estados do Rio de Janeiro, Espírito Santo e Bahia. Observamos que as comunidades presentes nos remanescentes estudados possuem considerável diferenciação entre elas. A diversidade beta (β) foi elevada enquanto o grau de aninhamento foi intermediário. Registramos ainda a presença do lagarto exótico invasor Hemidactylus mabouia em ambiente natural nos remanescentes de restinga estudados neste Tese. Encontramos 45 indivíduos, distribuídos em três dos cinco remanescentes amostrados. Registramos ainda ovos de H. mabouia (2 deles eclodidos) em dois dos cinco locais estudados, indicando que o recrutamento de indivíduos está ocorrendo com sucesso nas populações invasoras. A presença de H. mabouia esteve relacionada à restingas com maior frequência de degradação ambiental. Consideramos que os dados obtidos nesta tese, fornecem informações de considerável importância para o entendimento da estrutura das comunidades de anfíbios e lagartos nos ecossistemas de restinga ao longo da costa brasileira

Climate drives temporal replacement and nested‐resultant richness patterns of Scottish coastal vegetation

Beta diversity quantifies spatial and/or temporal variation in species composition. It is comprised of two distinct components, species replacement and nestedness, which derive from opposing ecological processes. Using Scotland as a case study and a β-diversity partitioning framework, we investigate temporal replacement and nestedness patterns of coastal grassland species over a 34-yr time period. We aim to 1) understand the influence of two potentially pivotal processes (climate and land-use changes) on landscape-scale (5 × 5 km) temporal replacement and nestedness patterns, and 2) investigate whether patterns from one β-diversity component can mask observable patterns in the other.

We summarised key aspects of climate driven macro-ecological variation as measures of variance, long-term trends, between-year similarity and extremes, for three important climatic predictors (minimum temperature, water-balance and growing degree-days). Shifts in landscape-scale heterogeneity, a proxy of land-use change, was summarised as a spatial multiple-site dissimilarity measure. Together, these climatic and spatial predictors were used in a multi-model inference framework to gauge the relative contribution of each on temporal replacement and nestedness patterns.

Temporal β-diversity patterns were reasonably well explained by climate change but weakly explained by changes in landscape-scale heterogeneity. Climate was shown to have a greater influence on temporal nestedness than replacement patterns over our study period, linking nestedness patterns, as a result of imbalanced gains and losses, to climatic warming and extremes respectively. Important climatic predictors (i.e. growing degree-days) of temporal β-diversity were also identified, and contrasting patterns between the two β-diversity components revealed.

Results suggest climate influences plant species recruitment and establishment processes of Scotland's coastal grasslands, and while species extinctions take time, they are likely to be facilitated by climatic perturbations. Our findings also highlight the importance of distinguishing between different components of β-diversity, disentangling contrasting patterns than can mask one another.

The modularity of seed dispersal: differences in structure and robustness between bat- and bird-fruit networks

In networks of plant-animal mutualisms, different animal groups interact preferentially with different plants, thus forming distinct modules responsible for different parts of the service. However, what we currently know about seed dispersal networks is based only on birds. Therefore, we wished to fill this gap by studying bat-fruit networks and testing how they differ from bird-fruit networks. As dietary overlap of Neotropical bats and birds is low, they should form distinct mutualistic modules within local networks. Furthermore, since frugivory evolved only once among Neotropical bats, but several times independently among Neotropical birds, greater dietary overlap is expected among bats, and thus connectance and nestedness should be higher in bat-fruit networks. If bat-fruit networks have higher nestedness and connectance, they should be more robust to extinctions. We analyzed 1 mixed network of both bats and birds and 20 networks that consisted exclusively of either bats (11) or birds (9). As expected, the structure of the mixed network was both modular (M = 0.45) and nested (NODF = 0.31); one module contained only birds and two only bats. In 20 datasets with only one disperser group, bat-fruit networks (NODF = 0.53 +/- A 0.09, C = 0.30 +/- A 0.11) were more nested and had a higher connectance than bird-fruit networks (NODF = 0.42 +/- A 0.07, C = 0.22 +/- A 0.09). Unexpectedly, robustness to extinction of animal species was higher in bird-fruit networks (R = 0.60 +/- A 0.13) than in bat-fruit networks (R = 0.54 +/- A 0.09), and differences were explained mainly by species richness. These findings suggest that a modular structure also occurs in seed dispersal networks, similar to pollination networks. The higher nestedness and connectance observed in bat-fruit networks compared with bird-fruit networks may be explained by the monophyletic evolution of frugivory in Neotropical bats, among which the diets of specialists seem to have evolved from the pool of fruits consumed by generalists.

Cheaters in mutualism networks

Mutualism-network studies assume that all interacting species are mutualistic partners and consider that all links are of one kind. However, the influence of different types of links, such as cheating links, on network organization remains unexplored. We studied two flower-visitation networks (Malpighiaceae and Bignoniaceae and their flower visitors), and divide the types of link into cheaters (i.e. robbers and thieves of flower rewards) and effective pollinators. We investigated if there were topological differences among networks with and without cheaters, especially with respect to nestedness and modularity. The Malpighiaceae network was nested, but not modular, and it was dominated by pollinators and had much fewer cheater species than Bignoniaceae network (28% versus 75%). The Bignoniaceae network was mainly a plant-cheater network, being modular because of the presence of pollen robbers and showing no nestedness. In the Malpighiaceae network, removal of cheaters had no major consequences for topology. In contrast, removal of cheaters broke down the modularity of the Bignoniaceae network. As cheaters are ubiquitous in all mutualisms, the results presented here show that they have a strong impact upon network topology.

What makes a species central in a cleaning mutualism network?

Mutualisms often form networks of interacting species, characterized by the existence of a central core of species that potentially drive the ecology and the evolution of the whole community. Centrality measures allow quantification of how central or peripheral a species is within a network, thus informing about the role of each species in network organization, dynamics, and stability. In the present study we addressed the question whether the structural position of species in the network (i.e. their topological importance) relates to their ecological traits. We studied interactions between cleaner and client reef fishes to identify central and peripheral species within a mutualistic network, and investigated five ecological correlates. We used three measures to estimate the level of centrality of a species for distinct structural patterns, such as the number of interactions and the structural proximity to other species. Through the use of a principal component analysis (PCA) we observed that the centrality measures were highly correlated (92.5%) in the studied network, which indicates that the same species plays a similar role for the different structural patterns. Three cleaner and ten client species had positive values of centrality, which suggests that these species are modulating ecological and evolutionary dynamics within the network. Higher centralities were related to higher abundances and feeding habits for client fishes, but not for cleaners. The high correlation between centrality measures in the present study is likely related to the nested structure of the cleaning network. The cleaner species` set, by having central species that are not necessarily the most abundant ones, bears potentially more vulnerable points for network cohesiveness. Additionally, the present study generalizes previous findings for plant-animal mutualisms, as it shows that the structure of marine mutualisms is also related to a complex interplay between abundance and niche-related features.

Changes of a mutualistic network over time: reanalysis over a 10-year period

We analyzed the structure of a multispecific network or interacting ants and plants bearing extrafloral nectaries recorded in 1990 and again in 2000 in La Mancha, Veracruz, Mexico. We assessed the replicability of the number of interactions found among species and also whether there had been changes in the network structure associated with appearance of new ant and plant species during. that 10-year period. Our results show that the nested topology of the network was similar between sampling dates, group dissimilarity increased, mean number of interactions for ant species increased, the frequency distribution of standardized degrees reached higher values for plant species, more ant species and fewer plant species constituted the core of the more recent network, and the presence of new ant and plant species increased while their contribution to nestedness remained the same. Generalist species (i.e., those with the most links or interactions) appeared to maintain the stability of the network because the new species incorporated into the communities were linked to this core of generalists. Camponotus planatus was the most extreme generalist ant species (the one with the most links) in both networks, followed by four other ant species; but other species changed either their position along the continuum of generalists relative to specialists or their presence or absence within the network. Even though new species moved into the area during the decade between the surveys, the overall network structure remained unmodified.

Analysis of a hyper-diverse seed dispersal network: modularity and underlying mechanisms

Mutualistic interactions involving pollination and ant-plant mutualistic networks typically feature tightly linked species grouped in modules. However, such modularity is infrequent in seed dispersal networks, presumably because research on those networks predominantly includes a single taxonomic animal group (e.g. birds). Herein, for the first time, we examine the pattern of interaction in a network that includes multiple taxonomic groups of seed dispersers, and the mechanisms underlying modularity. We found that the network was nested and modular, with five distinguishable modules. Our examination of the mechanisms underlying such modularity showed that plant and animal trait values were associated with specific modules but phylogenetic effect was limited. Thus, the pattern of interaction in this network is only partially explained by shared evolutionary history. We conclude that the observed modularity emerged by a combination of phylogenetic history and trait convergence of phylogenetically unrelated species, shaped by interactions with particular types of dispersal agents.

The nested assembly of individual-resource networks

P>1. Much of the current understanding of ecological systems is based on theory that does not explicitly take into account individual variation within natural populations. However, individuals may show substantial variation in resource use. This variation in turn may be translated into topological properties of networks that depict interactions among individuals and the food resources they consume (individual-resource networks). 2. Different models derived from optimal diet theory (ODT) predict highly distinct patterns of trophic interactions at the individual level that should translate into distinct network topologies. As a consequence, individual-resource networks can be useful tools in revealing the incidence of different patterns of resource use by individuals and suggesting their mechanistic basis. 3. In the present study, using data from several dietary studies, we assembled individual-resource networks of 10 vertebrate species, previously reported to show interindividual diet variation, and used a network-based approach to investigate their structure. 4. We found significant nestedness, but no modularity, in all empirical networks, indicating that (i) these populations are composed of both opportunistic and selective individuals and (ii) the diets of the latter are ordered as predictable subsets of the diets of the more opportunistic individuals. 5. Nested patterns are a common feature of species networks, and our results extend its generality to trophic interactions at the individual level. This pattern is consistent with a recently proposed ODT model, in which individuals show similar rank preferences but differ in their acceptance rate for alternative resources. Our findings therefore suggest a common mechanism underlying interindividual variation in resource use in disparate taxa.

Aninhamento em redes bipartidas

We present a nestedness index that measures the nestedness pattern of bipartite networks, a problem that arises in theoretical ecology. Our measure is derived using the sum of distances of the occupied elements in the adjacency matrix of the network. This index quantifies directly the deviation of a given matrix from the nested pattern. In the most simple case the distance of the matrix element ai,j is di,j = i+j, the Manhattan distance. A generic distance is obtained as di,j = (i¬ + j¬)1/¬. The nestedness índex is defined by = 1 − where is the temperature of the matrix. We construct the temperature index using two benchmarks: the distance of the complete nested matrix that corresponds to zero temperature and the distance of the average random matrix that is defined as temperature one. We discuss an important feature of the problem: matrix occupancy. We address this question using a metric index ¬ that adjusts for matrix occupancy

Nested liana-tree network in three distinct neotropical vegetation formations

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Mistletoes Play Different Roles in a Modular Host-Parasite Network

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)