A two-stage probabilistic approach to multiple-community similarity indices

SUMMARY: A traditional approach for assessing similarity among N (N > 2) communities is to use multiple pairwise comparisons. However, pairwise similarity indices do not completely characterize multiple-community similarity because the information shared by at least three communities is ignored. We propose a new and intuitive two-stage probabilistic approach, which leads to a general framework to simultaneously compare multiple communities based on abundance data. The approach is specifically used to extend the commonly used Morisita index and NESS (normalized expected species shared) index to the case of N communities. For comparing N communities, a profile of N- 1 indices is proposed to characterize similarity of species composition across communities. Based on sample abundance data, nearly unbiased estimators of the proposed indices and their variances are obtained. These generalized NESS and Morisita indices are applied to comparison of three size classes of plant data (seedling, saplings, and trees) within old-growth and secondary rain forest plots in Costa Rica.     

Predictably simple: assemblages of caterpillars (Lepidoptera) feeding on rainforest trees in Papua New Guinea

Predictability in the composition of tropical assemblages of insect herbivores was studied using a sample of 35,952 caterpillars (Lepidoptera) from 534 species, feeding on 69 woody species from 45 genera and 23 families in a lowland rainforest in Papua New Guinea. Caterpillar assemblages were strongly dominated by a single species (median 48% of individuals and 49% of biomass). They were spatially and temporally constant (median normalized expected species shared (NESS) similarity between assemblages from the same host was greater than or equal to 0.85 for three sites 8-17 km apart as well as for three four-month periods of the year). Further, the median presence of species was 11 months per year. Assemblages on hosts from different families and genera were virtually disjunct (NESS similarity less than 0.05) as the caterpillars were mostly specialized to a single plant family (77% of species) and, within families, to a single genus (66% of species), while capable of feeding on multiple congeneric hosts (89% of species). The dominance of caterpillar assemblages by a small number of specialized species, which also exhibited low spatial and temporal variability, permitted robust and reliable estimates of assemblage composition and between-assemblage similarity from small samples, typically less than 300 individuals per host plant. By contrast, even considerably larger samples were insufficient for estimates of species richness. A sample of 300 individuals was typically obtained from 1,050 m(2) of foliage sampled during 596 tree inspections (i.e. a particular tree sampled at a particular time) in the course of 19 sampling days (median values from 69 assemblages). These results demonstrate that, contrary to some previous suggestions, insect herbivore assemblages in tropical rainforests have a predictable structure and, as such, are amenable to study.     

Gene exchange between two divergent species of the fungal human pathogen,Coccidioides

The fungal genus Coccidioides is composed of two species, Coccidioides immitis and Coccidioides posadasii. These two species are the causal agents of coccidioidomycosis, a pulmonary disease also known as valley fever. The two species are thought to have shared genetic material due to gene exchange in spite of their long divergence. To quantify the magnitude of shared ancestry between them, we analyzed the genomes of a population sample from each species. Next, we inferred what is the expected size of shared haplotypes that might be inherited from the last common ancestor of the two species and find a cutoff to find what haplotypes have conclusively been exchanged between species. Finally, we precisely identified the breakpoints of the haplotypes that have crossed the species boundary and measure the allele frequency of each introgression in this sample. We find that introgressions are not uniformly distributed across the genome. Most, but not all, of the introgressions segregate at low frequency. Our results show that divergent species can share alleles, that species boundaries can be porous, and highlight the need for a systematic exploration of gene exchange in fungal species.     

Resource partitioning between large herbivores in Hustai National Park, Mongolia

Re-introduced Przewalski horses in Hustai National Park, Mongolia could suffer from food competition with other herbivore species through food resource depletion. Diet composition of the Przewalski horse (Equus ferus przewalskii), red deer (Cervus elaphus) and four livestock species (sheep, goat, cattle and horse) were studied, using micro histological analysis of faecal samples in the summer of 2005 and winter of 2006 – 2007. We expected that herbivores become less selective in food choice in winter regarding to summer, resulting in a larger diet breadth, a larger similarity in diet and a larger dietary overlap in winter, potentially triggering exploitative competition by depletion of shared resources. Vegetation biomass decreased during winter, and the different herbivores species in HNP changed their diet from summer to winter. As expected diet breadth, diet similarity and dietary overlap were significantly larger in winter in comparison to summer. The existence of competition by resource depletion between the different species cannot be ruled out. Vegetation biomass was probably not a limiting factor according to the correlation between annual rainfall and herbivore species biomass, however the forage quality may be limiting, triggering competition.     

Diversity and composition of Arctiidae moth ensembles along a successional gradient in the Ecuadorian Andes

Andean montane rain forests are among the most species‐rich terrestrial habitats. Little is known about their insect communities and how these respond to anthropogenic habitat alteration. We investigated exceptionally speciose ensembles of nocturnal tiger moths (Arctiidae) at 15 anthropogenically disturbed sites, which together depict a gradient of forest recovery and six closed‐forest understorey sites in southern Ecuador. At weak light traps we sampled 9211 arctiids, representing 287 species. Arctiid abundance and diversity were highest at advanced succession sites, where secondary scrub or young forest had re‐established, followed by early succession sites, and were lowest, but still high, in mature forest understorey. The proportion of rare species showed the reverse pattern. We ordinated moth samples by non‐metric multidimensional scaling using the chord‐normalized expected species shared index (CNESS) index at various levels of the sample size parameter m. A distinct segregation of arctiid ensembles at succession sites from those in mature forest consistently emerged only at high m‐values. Segregation between ensembles of early vs. late succession stages was also clear at high m values only, and was rather weak. Rare species were responsible for much of the faunal difference along the succession gradient, whereas many common arctiid species occurred in all sites. Matrix correlation tests as well as exploration of relationships between ordination axes and environmental variables revealed the degree of habitat openness, and to a lesser extent, elevation, as best predictors of faunal dissimilarity. Faunal differences were not related to geographical distances between sampling sites. Our results suggest that many of the more common tiger moths of Neotropical montane forests have a substantial recolonization potential at the small spatial scale of our study and accordingly occur also in landscape mosaics surrounding nature reserves. These species contribute to the unexpectedly high diversity of arctiid ensembles at disturbed sites, whereas the proportion of rare species declines outside mature forest.     

DNA base composition heterogeneity in some agarophytes (Gracilariales,Rhodophyta) from Mexico and the Philippines

Estimates of nuclear DNA base composition by determination of thermal denaturation temperatures (T_m) indicate guanine + cytosine (G + C) levels of 35.4–46.8% for ten species of the Gracilariaceae, representing the generaGracilaria andHydropuntia. T_m values were found to be reproducible with variation among most samples and replicates of less than 1 °C and 2 mol%. Interspecific variation in G + C values was less than 11.4% amongGracilaria species. Calculation of intragenomic base pair composition distribution based on mid-resolution thermal denaturation (A 1 °C/min with 4s interval H and dT logging) indicated an inverse relationship between maximum similarity values and taxonomic rank. Intraspecific (population level) maximum similarity (homology) values were estimated to range from 79–90% inGracilaria tikvahiae (4 isolates). Interspecific values of 46–69% were found in 13 species ofGracilaria. Nucleotide distribution similarity values for the Gracilariaceae are compared with previous information for genome organization and complexity, genome size and karyotype patterns.Author for correspondence     

Commonness,rarity, and oligarchies of woody plants in the tropical dry forests of Mexico

We assessed woody plant communities in two widely separated forests in the tropical dry forest (TDF) biome of Mexico for evidence of similar patterns of species commonness and rarity. We used belt transects laid out along contour lines (i.e., constant elevation) and stratified across elevation gradients at sites in Jalisco and Oaxaca to sample woody plant species diversity, abundance, relative frequency and basal area. We assembled a combined species list and compared species found in both sites (shared) to species found in only one site, assessing whether the most and least common species at a site tended to be shared or unshared. Of the 8242 individuals sampled, 370 species or morpho‐species were identified, with 222 species recorded at the Jalisco site and 270 at the Oaxaca site—122 (33%) species were shared across sites. Abundance, frequency and basal area of shared species were greater on average than for unshared species, and were positively correlated across sites. A subset of 68 shared species (18%) accounted for over half of all individuals encountered at the two sites. Species in the most common quartile were more likely to be shared than expected by chance, while species in the least common quartile were less likely. A genus‐level analysis found similar patterns. Our findings suggest that the TDF of Pacific coast Mexico shows evidence of widespread dominance by a small subset of species. These findings have potentially important implications for predicting species composition, understanding the role of oligarchic species in ecological processes, and conserving rare species.     

Detecting clonemate pairs in multicellular diploid clonal species based on a shared heterozygosity index

Clonal reproduction, the formation of nearly identical individuals via mitosis in the absence of genetic recombination, is a very common reproductive mode across plants, fungi and animals. To detect clonal genetic structure, genetic similarity indices based on shared alleles are widely used, such as the Jaccard index, or identity by state. Here we propose a new pairwise genetic similarity index, the SH index, based on segregating genetic marker loci (typically single nucleotide polymorphisms) that are identically heterozygous for pairs of samples (N_SH). To test our method, we analyse two old seagrass clones (Posidonia australis, estimated to be around 8500 years old; Zostera marina, >750 years old) along with two young Z. marina clones of known age (17 years old). We show that focusing on shared heterozygosity amplifies the power to distinguish sample pairs belonging to different clones compared to methods focusing on all shared alleles. Our proposed workflow can successfully detect clonemates at a location dominated by a single clone. When the collected samples involve two or more clones, the SH index shows a clear gap between clonemate pairs and interclone sample pairs. Ideally N_SH should be on the order of approximately ≥3000, a number easily achievable via restriction-site associated DNA (RAD) sequencing or whole-genome resequencing. Another potential application of the SH index is to detect possible parent–descendant pairs under selfing. Our proposed workflow takes advantage of the availability of the larger number of genetic markers in the genomic era, and improves the ability to distinguish clonemates from nonclonemates in multicellular diploid clonal species.     

High interannual variation in the diet of a tropical forest frugivore (Hylobates lar)

Frugivores must deal with seasonal changes in fruit availability and changes from year to year, as most species of tropical forest fruiting trees have considerable interannual variation in phenology and many are mast fruiters. We quantified seasonal and interannual changes in the fruit diet in a frugivore and important seed disperser, the white‐handed gibbon, Hylobates lar, in Thailand. We used 40‐d following data during April and May replicated in six consecutive years to study interannual variability in the diet and compared it with seasonal changes measured in monthly samples of the same size collected in three successive years. The 40‐d periods of following also allowed us to measure the decline in dietary similarity with time over a finer scale. We measured fruit diet similarity between replicated 5‐d periods using the percentage overlap (Renkonen's) index and Jaccard's similarity index. Seasonally, average dietary overlap between adjacent months was low, and similarity approached zero after four months. Average rate of decline in similarity exceeded 20 percent per 5‐d period. Variation in fruit species in the diet between years was high and was correlated with interannual variation in fruiting phenology. The strongest correlation occurred in the case of Nephelium melliferum, a highly preferred species that dominated the diet in good fruiting years. It is difficult to separate changes in food species preference from changes in availability from year to year. We devised a relative measure of preference that depends on the degree to which the gibbons rely on prior knowledge to find sources.     

Fire and regeneration: the role of seed banks in the dynamics of northern heathlands

Questions: How do species composition and abundance of soil seed bank and standing vegetation vary over the course of a post‐fire succession in northern heathlands? What is the role of seed banks – do they act as a refuge for early successional species or can they simply be seen as a spillover from the extant local vegetation? Location: Coastal Calluna heathlands, Western Norway. Methods: We analysed vegetation and seed bank along a 24‐year post‐fire chronosequence. Patterns in community composition, similarity and abundances were tested using multivariate analyses, Sørensen's index of similarity, vegetation cover (%) and seedling counts. Results: The total diversity of vegetation and seed bank were 60 and 54 vascular plant taxa, respectively, with 39 shared species, resulting in 68% similarity overall. Over 24 years, the heathland community progressed from open newly burned ground via species rich graminoid‐ and herb‐dominated vegetation to mature Calluna heath. Post‐fire succession was not reflected in the seed bank. The 10 most abundant species constituted 98% of the germinated seeds. The most abundant were Calluna vulgaris (49%; 12 018 seeds m^?2) and Erica tetralix (34%; 8 414 seeds m^?2). Calluna showed significantly higher germination the first 2 years following fire. Conclusions: Vegetation species richness, ranging from 23 to 46 species yr^?1, showed a unimodal pattern over the post‐fire succession. In contrast, the seed bank species richness, ranging from 21 to 31 species yr^?1, showed no trend. This suggests that the seed bank act as a refuge; providing a constant source of recruits for species that colonise newly burned areas. The traditional management regime has not depleted or destroyed the seed banks and continued management is needed to ensure sustainability of northern heathlands.     

Estimating similarity of communities: a parametric approach to spatio‐temporal analysis of species diversity

Several stochastic models with environmental noise generate spatio‐temporal Gaussian fields of log densities for the species in a community. Combinations of such models for many species often lead to lognormal species abundance distributions. In spatio‐temporal analysis it is often realistic to assume that the same species are expected to occur at different times and/or locations because extinctions are rare events. Spatial and temporal β‐diversity can then be analyzed by studying pairs of communities at different times or locations defined by a bivariate lognormal species abundance model in which a single correlation occurs. This correlation, which is a measure of similarity between two communities, can be estimated from samples even if the sampling intensities vary and are unknown, using the bivariate Poisson lognormal distribution. The estimators are approximately unbiased, although each specific correlation may be rather uncertain when the sampling effort is low with only a small fraction of the species represented in the samples. An important characteristic of this community correlation is that it relates to the classical Jaccard‐ or the Sørensen‐indices of similarity based on the number of species present or absent in two communities. However, these indices calculated from samples of species in a community do not necessarily reflect similarity of the communities because the observed number of species depends strongly on the sampling intensities. Thus, we propose that our community correlation should be considered as an alternative to these indices when comparing similarity of communities. We illustrate the application of the correlation method by computing the similarity between temperate bird communities.     

Patterns of tooth crown size and shape variation in great apes and humans and species recognition in the hominid fossil record

It has been suggested that patterns of craniodental variation in living hominids (Gorilla, Homo, Pan, and Pongo) may be useful for evaluating variation in fossil hominid assemblages. Using this approach, a fossil sample exhibiting a pattern of variation that deviates from one shared among living taxa would be regarded as taxonomically heterogeneous. Here we examine patterns of tooth crown size and shape variation in great apes and humans to determine 1) if these taxa share a pattern of dental variation, and 2) if such a pattern can reliably discriminate between samples that contain single species and those that contain multiple species. We use parametric and nonparametric correlation methods to establish the degree of pattern similarity among taxa, and randomization tests to assess their statistical significance. The results of this study show that extant hominids do not share a pattern of dental size variation, and thus these taxa cannot be used to generate expectations for patterns of size variation in fossil hominid species. The hominines (Gorilla, Homo, and Pan) do share a pattern of shape variation in the mandibular dentition; however, Pongo is distinct, and thus it is unclear which, if either, pattern should be expected in fossil hominids. Moreover, in this case, most combined-species samples exhibit patterns of shape variation that are similar to those for single hominine species samples. Thus, although a common pattern of shape variation is present in the mandibular dentition, it is not useful for recognizing taxonomically mixed paleontological samples.     

Population systematics of chimpanzees using molar morphometrics

When dental morphological variation within extant species is used as a guideline to partition variation within fossil samples into species, the underlying assumption is that fossil species are equivalent to extant species. This is the case despite the fact that dental morphology, which is commonly used to differentiate fossil species, is rarely used to differentiate extant species. Aspects of external morphology, ecology, behavior, breeding patterns, and molecular structure that are used to delineate living species are generally not available for fossils. In this paper, the utility of dental evidence for sorting fossil samples into species is evaluated by testing whether molar occlusal morphology is capable of sorting populations of Pan into the species and subspecies already well-established by nondental evidence. The dentitions of 341 chimpanzee individuals, sampled from regions throughout equatorial Africa, were sorted into 16 populations using rivers to demarcate the boundaries between populations. Digital-imaging software was used to measure 15 traits on the occlusal surface of each upper molar and 19 on each lower molar. After applying size adjustments, size-transformed and untransformed variables were subjected to discriminant analysis, with separate analyses carried out for each molar type. Results indicate that populations of Pan troglodytes and Pan paniscus are well differentiated at all molar positions. Populations of P. t. verus are distinct from other populations of P. troglodytes. Populations of P. t. troglodytes and P. t. schweinfurthii show close dental similarity. A distinct population is recognized at the Nigeria-Cameroon border, indicating the presence of P. t. vellerosus. The concordance between the patterns of diversity recognized by this study and other molecular and nonmolecular studies indicates that paleontological species that are similar to species of Pan in terms of size and patterns of diversification may be differentiated using molar morphology.     

Partitioning of pollen resources by two stingless bee species in the north Bahia,Brazil

Analysing the pollen stored by stingless bees allows identification of the diversity of flowering plants visited by these bees while collecting resources during a given period. However, few studies have focused on investigating the sharing of resources between species of native bees that coexist in transitional plant formations, which support conservation efforts and increase colony productivity. This study aims to describe the partitioning of pollen resources among colonies of two species of stingless bees in the state of the Bahia (Brazil) through the analysis of stored pollen. The study was conducted in neighbouring vegetation zones of the relevant species Melipona quadrifasciata anthidioides and Melipona scutellaris by collecting monthly pollen samples stored by three colonies of each species over one year. The collected samples were treated using the acetolysis technique, and the partitioning of pollen resources between the two species was investigated through quali-quantitative analysis of the treated pollen. The results show that among the 16 pollen types belonging to a particular species or group identified in the Melipona quadrifasciata anthidioides samples and the 18 identified in the Melipona scutellaris samples, 13 were shared by both species. The two most common pollen types stored by both species were from Mimosa arenosa (Fabaceae, Mimosoidae) and Eucalyptus sp. (Myrtaceae). These results demonstrate the niche similarity of pollen pasture between these two species and suggest that conservation efforts for these bee species should focus on the plant families most visited by bees.     

Heterogeneity ratio: a measure of beta-diversity and its use in community classification

Fifteen previously proposed similarity indices are examined for the effects of sample size and/or group size (the number of samples included in a cluster). The three indices ofCλ,NESS, andC′λ are free from effects, but the former two are unsuitable for arithmetic averaging unless all of the sample sizes are equal. Thus clustering usingC′λ is found to be superior to the combination of any other similarity index and the group-average strategy. Unfortunately none of these measures have the desirable property of measuring the difference in component species among samples independent of the alpha-diversity. A new index of similarity (HR) is developed based on the assumption that community from which samples are taken is described by a logseries distribution. This new index measures the beta-diversity among samples without the influence of sample size and group size, and has the advantage that the significance of fusing samples can statistically be tested. An example clustering withHR is shown and compared with those obtained by other clustering strategies.     

Maximum growth rate,size and commonness in a community of bactivorous ciliates

Summary Adaptions which confer competitive ability or resistance to predation are thought to be evolved with a resultant loss in intrinsic rate of increase (r _m). Therefore species which are opportunistic should retain high values of r _m, whereas competitively superior species which employ a strategy of persistance will have low values of r _m. Whether a ciliate species is slow or fast-growing can be judged by comparison with the empirically derived equation relating growth rate and size given by Fenchel (1968).This hypothesis was tested on a group of eleven species of bactivorous ciliates inhabiting a small pond. Species' measured and predicted r _m'S were compared with their commonness in the field. The prediction that species with high values of would be less common, as measured by the number of samples in which they are found, was satisfied by the data. The implications of the data for the ciliate community studied and the potential of as a predictor of ecological characteristics of species are discussed.     

Sampled‐based estimation of diversity sensu stricto by transforming Hurlbert diversities into effective number of species

A theoretical framework based on Hill numbers has recently been advocated to measure and partition diversity sensu stricto. Hill numbers can be interpreted intuitively as effective number of species (ENS). They conform to the so‐called replication principle allowing a mathematically coherent multiplicative partitioning of diversity. They form a family of ENS defined by the parameter q which controls the weight attributed to rare species. Despite its advantages, this framework was developed without considering its robustness when treating community samples. In this study, we first show that Hurlbert diversity indices (expected number of species among k individuals) can be transformed into ENS that conform asymptotically to the replication principle while controlling the weight given to rare species through parameter k. We investigate the statistical properties of Hill and Hurlbert ENS using simulated communities with contrasted diversity. The properties of multiplicative beta diversity estimators based on ENS are also characterized by simulating communities with different levels of differentiation. We show that Hurlbert ENS provides a better statistical performance than Hill numbers when dealing with small sample sizes. By contrast, Hill numbers and their estimators suffer from substantial bias except when rare species have a low weight (q= 2). An estimator of ENS estimating both Hill numbers for q= 2 and Hurlbert ENS for k= 2 is shown to give the best performance and is recommended for processing real datasets when rare species receive low weight. In order to better take account of rare species, current estimators of Hill numbers are not recommended when sample size is too low while Hurlbert’s ENS performs reliably. In conclusion, while Hill numbers possess some interesting mathematical properties that are not shared by Hurlbert’s ENS, the latter outperforms Hill numbers in terms of statistical properties and is well suited to processing community samples, as illustrated on a real dataset.     

Electrophoretic karyotypes of the elm tree pathogen Ophiostoma ulmi (sensu lato)

Pulsed field gel electrophoresis using OFAGE, TAFE, and CHEF systems has been used to more fully characterize karyotypic variation within the two closely related fungal species of Ophiostoma ulmi sensu lato. Twelve wild-type and laboratory strains, representing the less agressive species O. ulmi and both of the biotypes of the more aggressive species O. novo-ulmi were studied and their karyotypes determined. Depending on the strain, a minimum of four to a minimum of eight chromosomal DNA bands were present that fall into three distinct size classes, with one exception. Strain CESSI6K (O. novo-ulmi, North American aggressive subgroup) contains a unique chromosomal DNA band which comigrated near a Saccharomyces cerevisiae chromosome of 0.95 Mb. This unique band was the smallest O. ulmi s. l. chromosomal DNA observed. Seven of the twelve strains shared a common chromosomal DNA banding pattern, whereas each of the other five had a unique karyotype. There was no correlation between chromosome profile and species, as some O. novo-ulmi and O. ulmi strains shared common electrophoretic karyotypes.     

Genetic and Chemical Diversity of High Mucilaginous Plants of <Emphasis Type="Italic">Sida</Emphasis> Complex by ISSR Markers and Chemical Fingerprinting

A method was developed based on multiple approaches wherein DNA and chemical analysis was carried out toward differentiation of important species of Sida complex that is being used for commercial preparation. Isolated DNA samples were successfully performed through PCR amplification using ISSR markers and degree of genetic diversity among the different species of Sida is compared with that of chemical diversity. For genetic fingerprint investigation, selected 10 ISSR primers generating reproducible banding patterns were used. Among the total of 63 amplicons, 62 were recorded as polymorphic, genetic similarity index deduced from ISSR profiles ranged from 12 to 51%. Based on similarity index, S. acuta and S. rhombifolia found to be most similar (51%). High number of species-specific bands played pivotal role to delineate species at genetic level. Investigation based on HPTLC fingerprints analysis revealed 23 bands representing to characteristic chemicals and similarity index ranged from 73 to 91%. Prominent distinguishable bands were observed only in S. acuta, while S. cordifolia and S. rhombifolia shared most bands making them difficult to identify on chemical fingerprint basis. This report summarizes the genotypic and chemotypic diversity and the use of profiles for authentication of species of Sida complex.