Distinguishing the importance between habitat specialization and dispersal limitation on species turnover

Understanding what governs community assembly and the maintenance of biodiversity is a central issue in ecology, but has been a continuing debate. A key question is the relative importance of habitat specialization (niche assembly) and dispersal limitation (dispersal assembly). In the middle of the Loess Plateau, northwestern China, we examined how species turnover in Liaodong oak (Quercus wutaishanica) forests differed between observed and randomized assemblies, and how this difference was affected by habitat specialization and dispersal limitation using variation partitioning. Results showed that expected species turnover based on individual randomization was significantly lower than the observed value (P < 0.01). The turnover deviation significantly depended on the environmental and geographical distances (P < 0.05). Environmental and spatial variables significantly explained approximately 40% of the species composition variation at all the three layers (P < 0.05). However, their contributions varied among forest layers; the herb and shrub layers were dominated by environmental factors, whereas the canopy layer was dominated by spatial factors. Our results underscore the importance of synthetic models that integrate effects of both dispersal and niche assembly for understanding the community assembly. However, habitat specialization (niche assembly) may not always be the dominant process in community assembly, even under harsh environments. Community assembly may be in a trait‐dependent manner (e.g., forest layers in this study). Thus, taking more species traits into account would strengthen our confidence in the inferred assembly mechanisms.     

Distinguishing species of European sturgeons Acipenser spp. using microsatellite allele sequences

Five microsatellite markers were analysed and their alleles were sequenced for the three sturgeon species that lived in western Europe: the European sturgeon Acipenser sturio, the Atlantic sturgeon Acipenser oxyrinchus and the Adriatic sturgeon Acipenser naccarii. A total of 94 different allele sequences were obtained. Fixed mutations in the flanking regions or in the core repeat of microsatellites provided a clear distinction between the different species. Comparison of allele sequences also provided some insights into microsatellites and the evolution of Acipenser species. These nuclear markers can be used to solve species determination problems, and combined with mitochondrial markers, will be useful to identify introgression and hybridization among the three species. Moreover, because they are short and with a limited allele size range, they are particularly suited for analysis of museum specimens or archaeological remains.     

Distinguishing area and habitat heterogeneity effects on species richness: Birds in Victorian buloke remnants

Abstract Resolving whether area per se or habitat heterogeneity has the greater influence in controlling species richness remains a controversial yet important question. Here we show that avian species richness of same-sized transects (1 ha) is independent of the remnant area (of buloke woodland) within which a transect is positioned. We also show that avi-faunal similarity of pairs of transects randomly placed within the largest remnants (≥ 48 ha) is not consistently related to either proximity (i. e. being within the same remnant) nor to physiognomic characteristics of the transects. We believe that much of the controversy over area/habitat heterogeneity effects is probably related to scalar issues and propose a protocol by which some resolution of the question might be reached. The protocol involves ‘zoom’ sampling in which successively larger transect sizes are used, and measures of faunal richness and habitat heterogeneity are made at these different grains of resolution. One of our intentions is to stimulate discussion on how heterogeneity might be measured when grains increase from typical transect sizes (ca 1 ha) up to much larger grains (ca 128 ha).     

Distinguishing rice (Oryza sativa poaceae) from wildOryza species through phytolith analysis, II Finalized method

Asian rice is an important grain, not only in its homeland but in many areas of the world. Preliminary studies suggested that phytolith analysis, the identification of opaline silica bodies, provided a reliable way of identifying rice, especially in situations where preservation of charred botanical remains was poor. Results of this follow-up study, which incorporates all Asian wild Oryza species and a diverse array of traditional Oryza sativa cultivars, confirm that rice can be identified with a high level of certainty by the size and qualitative features of a distincitve phytolith, the double-peaked glume cell.     

Distinguishing between two sympatric Acanthopagrus species from Dapeng Bay, Taiwan, using morphometric and genetic characters

Morphometric and genetic data were used to compare two sympatric and morphologically similar species, Acanthopagrus berda and Acanthopagrus taiwanensis , in Dapeng Bay, South-western Taiwan. A principle component analysis of morphological data indicated a distinction between the two species, with pectoral fin length and eye diameter accounting for 32·27% of the variation. Interspecific sequence divergence, based on mtDNA cytochrome b (0·118 ± 0·01), was larger than intraspecific divergences between haplotypes (0·007 for A. taiwanensis and 0·003 for A. berda ). Individuals of the two species clustered into different groups in three phylogenetic trees with 100% bootstrap support. The mean observed heterozygosity for eight microsatellite loci was 0·471 ± 0·202 for A. taiwanensis and 0·637 ± 0·145 for A. berda . Nei's unbiased measure of interspecific genetic distance ( D _S) was 1·334. F _ST (0·134) and R _ST (0·404) values indicated significant differentiation between species. An unrooted neighbour-joining tree was constructed by allele-sharing distances and the factorial correspondence analysis split all specimens into two distinct clusters. The results of morphometric, mtDNA and microsatellite analyses indicated the presence of two species, A. taiwanensis and A. berda .     

Distinguishing Family from Friends

Kinship and friendship are key human relationships. Increasingly, data suggest that people are not less altruistic toward friends than close kin. Some accounts suggest that psychologically we do not distinguish between them; countering this is evidence that kinship provides a unique explanatory factor. Using the Implicit Association Test, we examined how people implicitly think about close friends versus close kin in three contexts. In Experiment 1, we examined generic attitudinal dispositions toward friends and family. In Experiment 2, attitude similarity as a marker of family and friends was examined, and in Experiments 3 and 4, strength of in-group membership for family and friends was examined. Findings show that differences exist in implicit cognitive associations toward family and friends. There is some evidence that people hold more positive general dispositions toward friends, associate attitude similarity more with friends, consider family as more representative of the in-group than friends, but see friends as more in-group than distant kin.     

Distinguishing rice (Oryza sativa Poaceae) from wild Oryza species through Phytolith analysis: Results of preliminary research

Asian rice is an important grain, not only in its homeland but in many areas of the world. Identifying rice in the archaeological record is a challenge, especially in the moist tropics, where organic materials preserve only when charred. Phytolith analysis, the identification of opaline silica bodies, provides an alternative method for identifying this important crop. Results of our research suggest thatOryza contributes phytoliths that are genus-specific, that bulliform characteristics alone do not permit separation of wild and domesticatedOryza in regions where species overlap, and that a number of phytolith types, especially silicified glumes, show promise for separating wild from domesticated forms. With further research it should be possible to identify rice through its phytolith assemblage in archaeological soils in the heartland of its domestication and use.     

Distinguishing local from global climate influences in the variation of carbon status with altitude in a tree line species

Aim Two alternative hypotheses attempt to explain the upper elevation limit of tree lines world‐wide, the carbon‐limitation hypothesis (CLH) and the growth‐limitation hypothesis (GLH); the altitudinal decrease of temperature is considered the driver constraining either carbon gain or growth. Using a widely distributed tree line species (Nothofagus pumilio) we tested whether tree line altitude is explained by the CLH or the GLH, distinguishing local from global effects. We elaborated expectations based on most probable trends of carbon charging with altitude according to both hypotheses, considering the alternative effects of drought. Location Two climatically contrasting tree line ecotones in the southern Andes of Chile: Mediterranean (36°54′ S) and Patagonia (46°04′ S). Methods At both locations, 35–50 trees of different ages were selected at each of four altitudes (including tree line), and stem and root sapwood tissues were collected to determine non‐structural carbohydrate (NSC) concentrations. NSC accumulates whenever growth is more limited than photosynthesis. An altitudinal increase in NSCs means support for the GLH, while the opposite trend supports the CLH. We also determined stable carbon isotope ratios (δ¹³C) to examine drought constraints on carbon gain. Results NSC concentrations were positively correlated with altitude for stem tissue at the Mediterranean and root sapwood tissue at the Patagonia site. No depletion of NSC was found at either site in either tissue type. For both tissues, mean NSC concentrations were higher for the Patagonia site than for the Mediterranean site. Mean root sapwood NSC concentration values were five times higher than those of the corresponding stem sapwood at all altitudes. Values for δ¹³C were positively correlated with altitude in the Mediterranean site only. Main conclusions We found support for the GLH at the site without drought effects (Patagonia) and no support for the CLH at either site. It is suggested that drought moderated the effects of low temperature by masking the expected trend of the GLH at the Mediterranean site.     

Distinguishing ulcerative colitis from autoimmunity

Lymphoid hyperplasia, autoimmunity, and compromised intestinal intraepithelial lymphocyte development in colitis-free gnotobiotic IL-2-deficient miceContractor, N.V. et al. (1998)J. Immunol. 160, 385–394     

Distinguishing Ichthyoses by Protein Profiling

To explore the usefulness of protein profiling for characterization of ichthyoses, we here determined the profile of human epidermal stratum corneum by shotgun proteomics. Samples were analyzed after collection on tape circles from six anatomic sites (forearm, palm, lower leg, forehead, abdomen, upper back), demonstrating site-specific differences in profiles. Additional samples were collected from the forearms of subjects with ichthyosis vulgaris (filaggrin (FLG) deficiency), recessive X-linked ichthyosis (steroid sulfatase (STS) deficiency) and autosomal recessive congenital ichthyosis type lamellar ichthyosis (transglutaminase 1 (TGM1) deficiency). The ichthyosis protein expression patterns were readily distinguishable from each other and from phenotypically normal epidermis. In general, the degree of departure from normal was lower from ichthyosis vulgaris than from lamellar ichthyosis, parallel to the severity of the phenotype. Analysis of samples from families with ichthyosis vulgaris and concomitant modifying gene mutations (STS deficiency, GJB2 deficiency) permitted correlation of alterations in protein profile with more complex genetic constellations.     

Distinguishing Anuran species by high‐resolution melting analysis of the COI barcode (COI‐HRM)

Taxonomic identification can be difficult when two or more species appear morphologically similar. DNA barcoding based on the sequence of the mitochondrial cytochrome c oxidase 1 gene (COI) is now widely used in identifying animal species. High‐resolution melting analysis (HRM) provides an alternative method for detecting sequence variations among amplicons without having to perform DNA sequencing. The purpose of this study was to determine whether HRM of the COI barcode can be used to distinguish animal species. Using anurans as a model, we found distinct COI melting profiles among three congeners of both Lithobates spp. and Hyla spp. Sequence variations within species shifted the melting temperature of one or more melting domains slightly but do not affect the distinctness of the melting profiles for each species. An NMDS ordination plot comparing melting peak profiles among eight Anuran species showed overlapping profiles for Lithobates sphenocephala and Gastrophryne carolinensis. The COI amplicon for both species contained two melting domains with melting temperatures that were similar between the two species. The two species belong to two different families, highlighting the fact that COI melting profiles do not reveal phylogenetic relationships but simply reflect DNA sequence differences among stretches of DNA within amplicons. This study suggests that high‐resolution melting analysis of COI barcodes (COI‐HRM) may be useful as a simple and rapid method to distinguish animal species that appear morphologically similar.     

Distinguishing molecular features and clinical characteristics of a putative new rhinovirus species, human rhinovirus C (HRV C)

Background

Human rhinoviruses (HRVs) are the most frequently detected pathogens in acute respiratory tract infections (ARTIs) and yet little is known about the prevalence, recurrence, structure and clinical impact of individual members. During 2007, the complete coding sequences of six previously unknown and highly divergent HRV strains were reported. To catalogue the molecular and clinical features distinguishing the divergent HRV strains, we undertook, for the first time, in silico analyses of all available polyprotein sequences and performed retrospective reviews of the medical records of cases in which variants of the prototype strain, HRV-QPM, had been detected.

Methodology/Principle Findings

Genomic analyses revealed that the six divergent strains, residing within a clade we previously called HRV A2, had the shortest polyprotein of all picornaviruses investigated. Structure-based amino acid alignments identified conserved motifs shared among members of the genus Rhinovirus as well as substantive deletions and insertions unique to the divergent strains. Deletions mostly affected regions encoding proteins traditionally involved in antigenicity and serving as HRV and HEV receptor footprints. Because the HRV A2 strains cannot yet be cultured, we created homology models of predicted HRV-QPM structural proteins. In silico comparisons confirmed that HRV-QPM was most closely related to the major group HRVs. HRV-QPM was most frequently detected in infants with expiratory wheezing or persistent cough who had been admitted to hospital and required supplemental oxygen. It was the only virus detected in 65% of positive individuals. These observations contributed to an objective clinical impact ranging from mild to severe.

Conclusions

The divergent strains did not meet classification requirements for any existing species of the genus Rhinovirus or Enterovirus. HRV A2 strains should be partitioned into at least one new species, putatively called Human rhinovirus C, populated by members detected with high frequency, from individuals with respiratory symptoms requiring hospital admission.