Presence-absence Matrix Research Articles

The pairwise approach to analysing species co‐occurrence

AbstractThe analysis of species co‐occurrence patterns continues to be a main pursuit of ecologists, primarily because the coexistence of species is fundamentally important in evaluating various theories, principles and concepts. Examples include community assembly, equilibrium versus non‐equilibrium organization of communities, resource partitioning and ecological character displacement, the local–regional species diversity relationship, and the metacommunity concept. Traditionally, co‐occurrence has been measured and tested at the level of an entire species presence–absence matrix wherein various algorithms are used to randomize matrices and produce statistical null distributions of metrics that quantify structure in the matrix. This approach implicitly recognizes a presence–absence matrix as having some real ecological identity (e.g. a set of species exhibiting nestedness among a set of islands) in addition to being a unit of statistical analysis. An emerging alternative is to test for non‐random co‐occurrence between paired species. The pairwise approach does not analyse matrix‐level structure and thus views a species pair as the fundamental unit of co‐occurrence. Inferring process from pattern is very difficult in analyses of co‐occurrence; however, the pairwise approach may make this task easier by simplifying the analysis and resulting inferences to associations between paired species.

Using endemic-plant distribution, geology and geomorphology in biogeography: the case of Sardinia (Mediterranean Basin)

The importance of robust systems for classifying biogeographical patterns has been emphasized for its usefulness in designing conservation strategies. For such purposes, the distribution patterns of the endemic flora have often been used. Several studies have identified phytogeographical units within Sardinia (western Mediterranean); however, the main part of the island remains unstudied. Thus, the aim of this study is to lay out a comprehensive biogeographical scheme for Sardinia based on endemic vascular plant distributions, together with geological and geomorphological units. We georeferenced, in a 1-km2 grid cell, the presence of 290 vascular endemic taxa from the literature, herbarium specimens and field investigators’ research. Sardinia was subdivided into 31 homogeneous units through the integration of geological and geomorphological maps and, subsequently, a presence–absence matrix of endemic taxa in each unit was built. Hierarchical cluster analysis was performed to define two levels of biogeographical units (i.e. sectors and subsectors). For each unit the exclusive and differential endemic taxa were identified. For sectors, indicator species were explored by the Indicator Value (Ind Val) analysis and relationships were analysed by quantitative interaction web. A total of six sectors and 22 subsectors were identified. The highest endemic plant richness was found in the Campidanese-Turritano, Sulcitano-Iglesiente and Supramontano sectors, and in the Gennargenteo, Barbaricino, Iglesiente and Sulcitano subsectors. All sectors were characterized by the presence of exclusive, differential and indicator taxa. The interaction analysis showed the highest uniqueness in endemic flora in the Supramontano and Sulcitano-Iglesiente sectors, which hosted a high number of exclusive endemic species. Mostly mountainous sectors/subsectors had higher endemic-species richness compared with lowland ones. The study showed the relevance of geology and geomorphology, together with accurate data on endemic distribution, to define consistent phytogeographical units. Furthermore, the biogeographical scheme presented here helps to define area-based conservation strategies in Sardinia.

Regionalización biogeográfica de la mastofauna de los bosques tropicales perennifolios de Mesoamérica

Mesoamerica is a biologically complex zone that expands from Southern Mexico to extreme Northern Colombia. The biogeographical patterns and relationships of the mammalian fauna associated to the Mesoamerican Tropical Evergreen Forest (MTEF) are poorly understood, in spite of the wide distribution of this kind of habitat in the region. We compiled a complete georeferenced database of mammalian species distributed in the MTEF of specimens from museum collections and scientific literature. This database was used to create potential distribution maps through the use of environmental niche models (ENMs) by using the Genetic Algorithm for Rule-Set Production (GARP) using 22 climatic and topographic layers. Each map was used as a representation of the geographic distribution of the species and all available maps were summed to obtain general patterns of species richness in the region. Also, the maps were used to construct a presence-absence matrix in a grid of squares of 0.5 degrees of side, that was analyzed in a Parsimony Analysis of Endemicity (PAE), which resulted in a hypothesis of the biogeographic scheme in the region. We compiled a total of 41 527 records of 233 species of mammals associated to the MTEF. The maximum concentration of species richness (104-138 species) is located in the areas around the Isthmus of Tehuantepec, Northeastern Chiapas-Western Guatemala, Western Honduras, Central Nicaragua to Northwestern Costa Rica and Western Panama. The proposed regionalization indicates that mammalian faunas associated to these forests are composed of two main groups that are divided by the Isthmus of Tehuantepec in Oaxaca in: a) a Northern group that includes Sierra Madre of Chiapas-Guatemala and Yucatan Peninsula; and b) an austral group, that contains the Pacific slope of Chiapas towards the South including Central America. Some individual phylogenetic studies of mammal species in the region support the relationships between the areas of endemism proposed, which suggest a common biogeographical history. In spite that Mesoamerica is considered one of the most important hotspots for biological conservation, the poor knowledge of the biogeographic patterns, the scarcity of protected areas, and the high rate of habitat transformation due to human activities, make prioritary the development of conservation strategies that include patterns of species richness, endemism, and mammalian associations.

Recluster: an unbiased clustering procedure for beta‐diversity turnover

When dissimilarity matrices of faunistic and phylogenetic beta‐diversity turnover indices are projected in dendrograms, a high frequency of ties and zero values produces trees whose topology and bootstrap support are affected by the order of areas in the original presence–absence matrix. We tested the magnitude of this bias and developed R functions to obtain consensus trees after shuffling of matrix row order and applied this algorithm to a multiscale bootstrap procedure. Our functions not only solve the bias of row order but, owing to varying support for different bootstrap scales, reveal fundamental characteristics about the structure of species assemblages.

Past climate and species ecology drive nested species richness patterns along an east‐west axis in the Himalaya

AbstractAimAlthough global species richness patterns appear consistent across taxa and continents, patterns are elusive at smaller spatial scales. At regional/subcontinental scales, climatic, environmental and taxon‐specific contingencies are likely to interact to modify general richness patterns. We develop a biogeographical paradigm for the Himalayan range as representative of regions at similar spatial scales, and where historical climate fluctuations might interact with species ecology to drive species richness patterns.LocationHimalayan range, AsiaMethodsWe obtained a cell × species presence–absence matrix for babblers and murid rodents in 1° latitude × 1° longitude cells in the Himalayan range. We investigated nestedness in species richness patterns in these taxa along a distance gradient from the species‐rich eastern towards the relatively depauperate west. We also investigated the relationship between species autecology and westward extent along the Himalaya. Climate data were obtained from published sources.ResultsHimalayan babbler and murid assemblages are nested along an east–west axis, with assemblages in westward cells tending to be subsets of assemblages immediately to the east. Distance westward from the eastern Himalaya was related positively to altitudinal mobility of babbler assemblages, while body size increased with distance westward for murid assemblages.Main conclusionsThe eastern Himalaya, which was not glaciated over during glacial maxima, was a potential refugium for babbler and murid species. Following glacial retreat, species could have recolonized the Himalaya westwards to different extents based on ecological traits (size, altitudinal migration) determining ability to deal with the more seasonal west. This produces both (1) a nested species richness pattern, and (2) correlations between ‘filtering’ autecological traits and distance. Such patterns should be replicated in other regions with historical climatic refugia; investigating nestedness along distance gradients from refugia would be a powerful tool in mapping biogeographical history, especially in separating historical effects from currently proposed energy‐productivity relationships.

Intertidal Seaweeds and their Multi-life Forms

Intertidal areas exhibit wide ranges in their extent and environmental conditions and these potentially can result in complex distributional pattern and life styles for many species including seaweeds. A study on seaweeds diversity and life forms was conducted at two intertidal sites in Negeri Sembilan i.e., (1) Teluk Kemang, a rocky outcrops area extending up to 50 m seaward during low tide, with gradual slope with live and dead corals interspersed with sand and (2) Teluk Pelanduk, a stretch of up to 150 m flat beach with mostly mud, sand and little rocks in between. A total of 36 species (16 Chlorophyta, 10 Phaeophyta and 10 Rhodophyta) and 26 species (11 Chlorophyta, 6 Phaeophyta and 9 Rhodophyta) of seaweeds were identified at Teluk Kemang and Teluk Pelanduk, respectively. Jaccard similarity coefficient of 0.442 based on a presence-absence matrix suggests the seaweed composition and diversity varied between the two sites. Both sites possessed their own many specialist species. Variability in environmental conditions e.g., diverse natural substrates or abandoned drift objects (fishing nets and lines, ropes and tyres) introduced by human had caused variation in seaweed composition, diversity and life forms categories. Epilithic (45.71%) seaweed is the most abundant category at Teluk Kemang followed by, epizoic (24.29%), epipelic (12.86%), epiphytic (8.57%) and drift seaweed (8.57%). Seaweed life forms at Teluk Pelanduk are epilithic (38.46%), epipelic (21.15%), epiphytic (17.31%), drift seaweed (13.46%) and epizoic (9.62%). Seaweed species distribution irrespective of sites reflected those that adapt or have adapted to the environmental conditions, particularly in utilizing the availability of the diverse existing natural hard and soft substrates and abandoned drift objects.

Optimizing protection efforts for amphibian conservation in Mediterranean landscapes

Amphibians epitomize the modern biodiversity crisis, and attract great attention from the scientific community since a complex puzzle of factors has influence on their disappearance. However, these factors are multiple and spatially variable, and declining in each locality is due to a particular combination of causes. This study shows a suitable statistical procedure to determine threats to amphibian species in medium size administrative areas. For our study case, ten biological and ecological variables feasible to affect the survival of 15 amphibian species were categorized and reduced through Principal Component Analysis. The principal components extracted were related to ecological plasticity, reproductive potential, and specificity of breeding habitats. Finally, the factor scores of species were joined in a presence-absence matrix that gives us information to identify where and why conservation management are requires. In summary, this methodology provides the necessary information to maximize benefits of conservation measures in small areas by identifying which ecological factors need management efforts and where should we focus them on.

Molecular characterization and a multiplex allele-specific PCR method for detection of thiabendazole resistance in Penicillium expansum from apple

Thiabendazole (TBZ) is commonly used as a postharvest treatment for control of blue mold in apples caused by Penicillium expansum. Different point mutations in the β-tubulin gene conferring benzimidazole resistance have been reported in plant pathogens, but molecular mechanisms of TBZ resistance in P. expansum from apple in Washington State are unknown. Determination of TBZ resistance level showed that all 102 TBZ-resistant (TBZ-R) isolates were highly resistant. Sequencing of the majority of the β-tubulin gene showed that 76 TBZ-R isolates harboured the E198V mutation and 26 harboured the F167Y mutation, and all the sensitive isolates did not possess any of the mutations, indicating that these two point mutations in the β-tubulin gene were correlated with TBZ resistance in P. expansum from apple in Washington State. There was no association between levels of TBZ resistance and types of point mutations (E198V or F167Y) in the β-tubulin gene. A multiplex allele-specific PCR assay was developed to detect these two mutations simultaneously. Microsatellite-primed PCR derived presence-absence matrix used to assess the genetic relationship among 56 isolates suggested that the resistance mutations originated several times independently and that there was no correlation between the types of point mutation and the genetic background of the isolates.

Patterns of Distribution of the Helminth Parasites of Freshwater Fishes of Mexico

In order to draw patterns in helminth parasite composition and species richness in Mexican freshwater fishes we analyse a presence-absence matrix representing every species of adult helminth parasites of freshwater fishes from 23 Mexican hydrological basins. We examine the distributional patterns of the helminth parasites with regard to the main hydrological basins of the country, and in doing so we identify areas of high diversity and point out the biotic similarities and differences among drainage basins. Our dataset allows us to evaluate the relationships among drainage basins in terms of helminth diversity. This paper shows that the helminth fauna of freshwater fishes of Mexico can characterise hydrological basins the same way as fish families do, and that the basins of south-eastern Mexico are home to a rich, predominantly Neotropical, helminth fauna whereas the basins of the Mexican Highland Plateau and the Nearctic area of Mexico harbour a less diverse Nearctic fauna, following the same pattern of distribution of their fish host families. The composition of the helminth fauna of each particular basin depends on the structure of the fish community rather than on the limnological characteristics and geographical position of the basin itself. This work shows distance decay of similarity and a clear linkage between host and parasite distributions.

Taxonomic composition and endemism of the helminth fauna of freshwater fishes of Mexico

We examine the taxonomic composition and endemism of adult helminth parasites of freshwater fishes of Mexico, with regard to the main hydrological basins of the country. A presence-absence matrix, including every species of adult helminth parasites of freshwater fishes from 23 Mexican hydrological basins was compiled and examined in this paper. The helminth fauna of freshwater fishes of Mexico consists of a large group of Central American Neotropical species (S = 119) and another set, less rich of Nearctic species (S = 48), which are distributed along with the families of its fish hosts; insufficient data preclude the assignation of three species. This fauna is composed predominantly by nematodes, trematodes, and monogeneans, which together contributed 86% of the total species recorded; cestodes and acanthocephalans being the taxa with the least species recorded. Current data suggests a 22% (37/170) endemism amongst helminths of freshwater fishes of Mexico. Data suggests that the isolation of bodies of water in the Mexican territory, mostly in the Neotropical areas of southeastern Mexico and in the central Altiplano Mexicano (Mexican Highland Plateau), with well delimited basins separated by orographic features, provided peculiar conditions that have been conducive to the diversification of a unique helminth fauna.

Range–diversity plots for conservation assessments: Using richness and rarity in priority setting

Current claims of biodiversity crisis call for immediate conservation actions. These require the identification of priority sites for conservation based on an assessment of biodiversity patterns. Patterns of species richness are crucial in such endeavor. Also rarity, measured by the size of species’ geographical ranges, is often used as a single or complementary criterion. For instance, hotspots for conservation have been defined using either one or the other criterion. We apply a novel tool, range–diversity plots, which simultaneously analyze species richness and range size from a presence–absence matrix to identify sites and species with potential conservation value. We applied this tool to the Mexican avifauna and show how it can be readily used to conduct broad-scale conservation assessments. Mexican birds showed congruent patterns between richness and rarity, richer sites harbor small-ranged species. Also, we identified Mexican ecoregions harboring richness–rarity sites and compared our assessment with an exhaustive prioritization procedure. A range–diversity approach can be useful when fine-scale information is lacking, such as in poorly studied regions. We demonstrate that spatial congruence between richness and rarity can be easily identified and interpreted using range–diversity plots based solely on a presence–absence matrix, providing a transparent, robust and explicit application for conservation assessments.

Identifying compartments in presence–absence matrices and bipartite networks: insights into modularity measures

AbstractAimThe identification of compartments (i.e. clusters of overlapping species ranges across an environmental gradient) is an important methodological challenge for biogeographical studies. Recent developments in network theory offer promising perspectives on this issue using the measurement of modularity. A presence–absence matrix is modular if particular subgroups of species are mainly linked to particular subgroups of sites. Modularity is still rarely considered in biogeographical studies. Here, I compare different modularity indices to investigate which is the most appropriate for studying presence–absence matrices and similar types of networks, such as bipartite networks.LocationEvaluation was based on 279 data sets from around the world.MethodsI consider the three most commonly used modularity indices. One was developed for unipartite networks and the other two for bipartite networks. The performance of these indices (detection of a modular pattern, quality of compartment identification) is evaluated on test matrices of known compartmentalization levels with varying sizes and fills. Modularity patterns are then evaluated for 279 presence–absence matrices.ResultsThe three modularity measures differ mainly in the identification of the compartments, and less in the statistical significance of the observed modularity. The modularity measure Q3 tends to perform best, whereas Q2 usually performs less well, especially for highly diverse and highly connected networks that include a few extremely well‐connected nodes. These modularity indices all reveal the presence of modular patterns in presence–absence matrices.Main conclusionsThe choice of an appropriate modularity index is particularly important when we are interested in the composition of the different compartments. This analysis suggests that compartmentalized structures can be widespread in presence–absence matrices (about 40% of the matrices considered here). Modularity should thus offer interesting perspectives on the understanding of biogeographical patterns.

A probabilistic model for analysing species co‐occurrence

AbstractAimTo develop a new probabilistic model that can be used to test for statistically significant pair‐wise patterns of species co‐occurrence. The model gives the probability that two species would co‐occur at a frequency less than (or greater than) the observed frequency if the two species were distributed independently of one another among a set of sites. The model can be used to classify species associations as negative, positive or random.InnovationHistorically, the analysis of species co‐occurrence has involved the use of data randomization. An observed species presence–absence matrix is compared with randomized matrices to determine if the observed matrix has structure, either an excess or deficit of species positively or negatively associated with each other. The computer algorithms used to randomize matrices can sometimes produce Type I and Type II errors (when the randomization algorithm produces a biased set of all possible matrices) due to the randomization process itself. The probabilistic model does not rely on any data randomization, hence it has a very low Type I error rate and is powerful having a low Type II error rate.Main conclusionsWhen applied to 10 different data sets the probabilistic model revealed significant positive and negative species associations in most of the data sets. Compared with previous analyses the model tended to find fewer significant associations; this may indicate a generally low rate of Type I error in the model. The model is easy to implement and requires no special software. The model could potentially transform the way that ecologists test for species co‐occurrence in a wide range of ecological studies.

On the application of network theory to arbuscular mycorrhizal fungi–plant interactions: the importance of basic assumptions

On the application of network theory to arbuscular mycorrhizal fungi–plant interactions: the importance of basic assumptions

Use of null models to explain crustacean zooplankton assemblages in waterbodies of Alerce Andino National Park (41°S, Chile)

The zooplankton assemblages in deep, mostly oligotrophic northern Patagonian lakes are characterized by low species numbers and a marked dominance of calanoid copepods. In the present study, data collected in field work on six water bodies located in Alerce Andino National Park (41°S) were analysed using the Jaccard Index of community similarity and a co-occurrence of null models, and such with the aim of determining potential regulating factors for the observed crustacean assemblages, using a presence-absence matrix. A significant correlation between species number and surface area was found. The null model used species co-occurrence, and the basis of this model is that the species associations observed are random. The results revealed the absence of regulating factors and indicate that the sites are relatively homogeneous, with low species numbers and similar plankton assemblages at all studied sites. This finding is in accordance with similar descriptions for zooplankton assemblages in other Chilean Patagonian lakes.

The presence–absence matrix reloaded: the use and interpretation of range–diversity plots

ABSTRACTAim A great deal of information on distribution and diversity can be extracted from presence–absence matrices (PAMs), the basic analytical tool of many biogeographic studies. This paper presents numerical procedures that allow the analysis of such information by taking advantage of mathematical relationships within PAMs. In particular, we show how range–diversity (RD) plots summarize much of the information contained in the matrices by the simultaneous depiction of data on distribution and diversity.Innovation We use matrix algebra to extract and process data from PAMs. Information on the distribution of species and on species richness of sites is computed using the traditional R (by rows) and Q (by columns) procedures, as well as the new Rq (by rows, considering the structure of columns) and Qr (by columns, considering the structure by rows) methods. Matrix notation is particularly suitable for summarizing complex calculations using PAMs, and the associated algebra allows the implementation of efficient computational programs. We show how information on distribution and species richness can be depicted simultaneously in RD plots, allowing a direct examination of the relationship between those two aspects of diversity. We explore the properties of RD plots with a simple example, and use null models to show that while parameters of central tendency are not affected by randomization, the dispersion of points in RD plots does change, showing the significance of patterns of co‐occurrence of species and of similarity among sites.Main conclusion Species richness and range size are both valid measures of diversity that can be analysed simultaneously with RD plots. A full analysis of a system requires measures of central tendency and dispersion for both distribution and species richness.

Binary matrices and checkerboard distributions of birds in the Bismarck Archipelago

Aim We examine a presence–absence matrix of the avifauna of the Bismarck Archipelago, for which the concept of competitively driven community assembly rules was formulated, to determine whether data support widespread competitive determination of geographical distributions. Location Bismarck Archipelago. Methods We obtained occurrences of 154 land and freshwater bird species on 31 islands. We calculated the observed number of checkerboards for all species pairs, for congeneric species pairs and for pairs of species within guilds, and employed randomization techniques to detect unusual co-occurrence patterns. Results Compared with random expectations, there are excesses of checkerboard pairs within both genera and defined guilds, but a detailed examination shows that competition is a cogent possible explanation in few instances. For many checkerboard pairs, species are not widely interspersed but are regionally allopatric, which probably reflects historical biogeography and dispersal limitation. Most congeneric and intraguild checkerboards include a species classified as a supertramp; when supertramps are omitted, there are 11 congeneric checkerboards and four intraguild but heterogeneric checkerboards. Main conclusions In isolation, presence–absence matrices provide limited insight into the role of competition in structuring bird communities of the Bismarcks. A major problem is disentangling historical geography and colonization history of the archipelago from the present-day ecology of the species. Examination of observed checkerboards from a geographically explicit perspective and with knowledge of colonization routes suggests that many checkerboards are likely to result, at least in part, from historical biogeography and supertramps. Although species may be forced into supertramp status by competition, other factors (e.g. habitat preference) may be causal, and biogeographical distributions alone cannot distinguish between causes.

Taxonomic Implications of a Field Study of Morphotypes of Hanuman Langurs (Semnopithecus entellus) in Peninsular India

The Hanuman langur is one of the most widely distributed and morphologically variable non-human primates in South Asia. Even though it has been extensively studied, the taxonomic status of this species remains unresolved due to incongruence between various classification schemes. This incongruence, we believe, is largely due to the use of plastic morphological characters such as coat color in classification. Additionally these classification schemes were largely based on reanalysis of the same set of museum specimens. To bring greater resolution in Hanuman langur taxonomy we undertook a field survey to study variation in external morphological characters among Hanuman langurs. The primary objective of this study is to ascertain the number of morphologically recognizable units (morphotypes) of Hanuman langur in peninsular India and to compare our field observations with published classification schemes. We typed five color-independent characters for multiple adults from various populations in South India. We used the presence-absence matrix of these characters to derive the pair-wise distance between individuals and used this to construct a neighbor-joining (NJ) tree. The resulting NJ tree retrieved six distinct clusters, which we assigned to different morphotypes. These morphotypes can be identified in the field by using a combination of five diagnostic characters. We determined the approximate distributions of these morphotypes by plotting the sampling locations of each morphotype on a map using GIS software. Our field observations are largely concordant with some of the earliest classification schemes, but are incongruent with recent classification schemes. Based on these results we recommend Hill (Ceylon Journal of Science, Colombo 21:277-305, 1939) and Pocock (Primates and carnivora (in part) (pp. 97–163). London: Taylor and Francis, 1939) classification schemes for future studies on Hanuman langurs.

Use of Null Models to Explain Crustacean Zooplankton Assemblages in Northern Patagonian Lakes (Chile) with and Without Mixotrophic Ciliates

AbstractThe zooplankton assemblages in deep, mostly oligotrophic northern Patagonian lakes are characterized by a low species number and a marked dominance of calanoid copepods, as well as often by the presence of large mixotrophic ciliates (Stentor). In the present study, data collected in field work on four northern Patagonian lakes were analysed using co-occurrence of null models, with the aim to determine potential regulating factors for the observed crustacean and mixotrophic ciliate assemblages, using a presence-absence matrix. The null model uses species co-occurrence, and the basis of this model is that the species associations observed are random. The results revealed the absence of regulating factors and indicate that the sites are relatively homogeneous, with low species numbers, and similar plankton assemblages at all study sites. This finding coincides with similar descriptions for zooplankton assemblages in other Chilean Patagonian lakes.

Class-based stratification matrix for physical leaf traits in phenetic relations of Withania somnifera (L.) Dunal accessions

Withania somnifera (L.) Dunal is a promising herb with many pharmaceutical and therapeutic uses ranging from immunomodulation to anticarcinogenicity. It is commonly known as Indian ginseng, as it is comparable to Panax ginseng, which is a widely studied and utilized herb. There are limited studies on the genetic diversity of W. somnifera from the northeastern region of the Indian Subcontinent. This paper describes the characterization of wild accessions collected from Tamil Nadu State. A total of 15 accessions collected from wild populations were studied for their physical leaf traits such as leaf fresh weight (g), dry weight (mg), leaf dry matter content (mg g−1), specific leaf area (mm2 mg−1), leaf size (mm2), total carbon and nitrogen, and total withaferin-A content in leaves. An attempt was made to correlate physical leaf traits with withaferin-A content. The molecular traits, which were treated in a presence–absence matrix, failed to group the hyper-withaferin-A accessions. The quantified physical leaf traits were converted into a presence–absence matrix using a novel method of class-based stratification. The phenetic relations inferred from the Fitch–Margoliash algorithm applied to physical leaf trait data resulted in grouping of accessions with high withaferin-A content. These traits were used in the selection of promising accessions which can be further used for breeding programmes.