Low Dissimilarity Research Articles

Histogram-based standardization of intravascular optical coherence tomography images acquired from different imaging systems.

Intravascular optical coherence tomography (OCT) is widely used for analysis of the coronary artery disease. Its high spatial resolution allows for visualization of arterial tissue components in detail. There are different OCT systems on the market, each of which produces data characterized by its own intensity range and distribution. These differences should be taken into account for the development of image processing algorithms. In order to overcome this difference in the intensity range and distribution, we developed a framework for matching intensities based on the exact histogram matching technique. In our method, the key step for using the exact histogram matching is to determine the target histogram. For this, we proposed two schemes: a global scheme that uses a single histogram as the target histogram for all the pullbacks, and a local scheme that selects for each single image a target histogram from a predefined database. These two schemes are compared on a unique dataset containing pairs of pullbacks that were acquired shortly after each other with systems from two vendors, St. Jude and Terumo. Pullbacks were aligned according to anatomical landmarks, and a database of matched histogram pairs was created. A leave-one-out cross validation was used to compare performance of the two schemes. The matching accuracy was evaluated by comparing: (a) histograms using Euclidean (dx2 ) and Kolmogorov-Smirnov (dKS ) distances, and (b) median intensity level within anatomical regions of interest. Leave-one-out validation indicated that both matching schemes yield comparably high accuracies across the entire validation dataset. The local scheme outperforms the global scheme with marginally lower dissimilarities at both histogram level and intensity level. High visual similarity was observed when comparing the matched images to their aligned counterparts. Both local and global schemes are robust and produce accurate intensity matching. While local scheme performs marginally better than the global scheme, it requires a predefined histogram dataset and is more time consuming. Thus, for offline standardization of the images, the local scheme should be preferred for being more accurate. For online standardization or when another system is involved, the global scheme can be used as a simple and nearly-as-accurate alternative.

Image-based perceptual analysis of lit environments

Modern lighting systems typically provide a number of control parameters, e.g. colour and intensity, which allows nearly infinite possible configurations in one single room. The growing complexity of control makes it increasingly challenging for the user to configure the system and fully utilize the additional degrees of freedom. In contrast, an intuitive control interface takes into account the perceptual meaning of the lighting configurations. Unfortunately, collecting user ratings to construct perceptual models for lit spaces is cumbersome. To address this problem, we introduce an image-based mapping method that can rapidly evaluate the perceptual impression of lighting scenes using photographs or renderings. We discuss potential applications, guidelines and limitations of this method. In summary, we were able to closely approximate ratings-based mapping (normalized dissimilarity value <0.04). Among three dimensionality reduction methods, principal component analysis achieved the lowest dissimilarity and required the least images with a resolution as low as six by six pixels. Furthermore, simulations revealed that one perceptual model might suffice for the same type of offices. Offices of different types, on the other hand, require new mapping.

Heuristic analysis influence of saliency in the color diversity of natural images

AbstractThe estimation of chromatic diversity of natural images is commonly quantified through the computation of the number of discernible colors and has received much attention because of the different implications it has. However, the relationship between that number and the number of colors that really attracts the attention from an observer is still not clear and has been given little attention. New concepts about salient discernible colors‐the salient chromatic diversity of images‐ and remarkable salient colors‐connected colors in the same salient image area‐are introduced as opposed to the classical number of discernible object colors, which is usually evaluated for the global image without differentiating between probable attended and non‐attended image regions. We have used different well‐known saliency models to locate the salient regions in the scenes and have heuristically studied the extent to which those models preserve the chromatic diversity of natural images. Based on a bottom‐up approach, a reduction of around 40%‐55% in the number of discernible colors were obtained, and not all saliency algorithms preserved a uniform sampling of the original color gamut. Thus, our results suggests that particularly the graph‐based visual saliency model got good low dissimilarity values in comparison with other approaches that put emphasis solely on color as the main low‐level feature. Furthermore, we have introduced a quantification scheme of the average number of remarkable salient colors appearing in the images, and have proved how the heuristic‐based analysis of salient image areas can be used to create segmented images automatically according to their salient chromatic diversity.

Forecasting the impact of an invasive macrophyte species in the littoral zone through aquatic insect species composition

Invasive macrophytes threaten freshwater ecosystem biodiversity. We analyzed the impact of the invasive white ginger lily ( Hedychium coronarium Konig J, 1783.– Zingiberaceae) on aquatic insect assemblages living in the littoral zone of a tropical reservoir. We took aquatic insect samples in the littoral zone on four main vegetal profile banks: white ginger monotypic bank, forest partially invaded, native macrophyte monotypic bank and riparian forest. At each vegetal bank, we measured abiotic variables such as dissolved oxygen, pH, water temperature and depth. We analyzed the aquatic insects through abundance, richness and Simpson diversity. We used the non-Metric Multidimensional Scaling (nMDS) analysis to analyze the spatial distribution of each assemblage, and Analysis of similarities (ANOSIM) to verify differences amongst dissimilarity distances. Additionally, we analyzed the main taxa associated with invasive macrophytes through indicator species analyses using IndVal index. We observed that the invasive macrophyte banks presented higher abundance of associated specimens, as well as lower dissimilarity of aquatic insect assemblages. Additionally, invasive macrophytes shifted the water pH and littoral depth of reservoir banks. The IndVal index indicated eight aquatic insects as indicator species. Labrundinia unicolor Silva, 2013 , Ablabesmyia depaulai Neubern, 2013 and Diastatops Rambur, 1842 were indicator species on banks. We concluded that invasion of white ginger lily caused loss of shallow littoral habitat and altered the pH of the surrounding water probably by high decomposition rate and high production of plant biomass. We suggest the use of species of aquatic insects as indicator species to monitor white ginger lily impact in freshwater systems.

Deep-Sea Mega-Epibenthic Assemblages from the SW Portuguese Margin (NE Atlantic) Subjected to Bottom-Trawling Fisheries

Bottom trawling fisheries are a common threat to the health of continental margins worldwide. Together with numerous environmental and biological processes, physical disturbance induced by trawlers can largely shape the benthic habitats and their associated assemblages. At the SW Portuguese Margin, crustacean bottom trawlers have exploited deep-sea habitats for a few decades, but its effects on the benthic biodiversity are practically unknown. During the spring-summer of 2013 and 2014, several Remotely Operated Vehicle (ROV) video transects were used to investigate mega-epibenthic abundance, composition and diversity in soft-sediment areas subjected to varying trawling pressures off Sines and Setubal (200-800 m). Differences in mega-epibenthic assemblages were linked with environmental changes (depth, grain size, primary productivity) and trawling disturbance. The effect of trawling was assessed between segments with similar habitat characteristics, i.e. muddy-sand bottoms between 300–500 m. Areas subjected to intensive trawling pressure showed a generally flattened seabed, with abundant recent trawl marks (up to 3 scars/100 m), indicating that the seabed physical integrity was compromised. Significant negative correlations were detected between various mega-epibenthic diversity indices (S, H’ and ET(20)) and trawling pressure (h.cell-1.y-1). Furthermore, the distinct mega-epibenthic assemblages and absence of several sessile erect morphospecies at both low and highly disturbed locations by trawling off Sines, namely all seapen morphospecies found in non-trawled areas, demonstrates the negative influence of trawling fisheries on the benthic component of the study area. Also, low dissimilarity between assemblages from the main fishing grounds and the adjacent low-disturbance locations, suggests that the potentially negative influence of trawling can extend beyond the targeted areas (e.g. by the plumes of re-suspended sediments). The observed deleterious effects of trawling on mega-epibenthic fauna together with the intensification of trawling pressure in the study area, stress the need for adequate monitoring programs and regulatory measures to halt the long-term loss of biodiversity and allow the sustainability of fisheries at the SW Portuguese Margin.

A hybrid method based on ensemble WELM for handling multi class imbalance in cancer microarray data

DNA microarray technology provides an efficient way to diagnose cancer. However, microarray gene expression data face the challenges of class imbalance and high dimension. The class imbalance problem usually leads to inaccurate results when using traditional feature selection and classification algorithms. Due to fast learning speed and good classification performance, extreme learning machine (ELM) has become one of the best classification algorithms and weighted ELM has been recently presented to deal with the class imbalance. However, they ignored the negative impact of imbalanced feature set. This paper proposes a hybrid method based on WELM to handle the multi class imbalance problem of cancer microarray data at both feature and algorithmic levels. At feature level, a corrected feature subset is searched for each class using class oriented feature selection method, so that the features correlated with the minority class are explicitly selected. At algorithmic level, WELM is further modified to strengthen the input nodes with high discrimination power, and an ensemble model is trained to improve the generalization. That is, multiple modified WELM models are trained on the datasets characterized by different feature subsets; in order to encourage the ensemble diversity, the models with low dissimilarity are removed and the reserved ones are combined as an ensemble model. The experiments are conducted on eight gene expression datasets with multiple cancer types and classification results show that our method significantly outperforms ELM and several recent works.

The morphological and molecular identity of Longidorus piceicola Lišková, Robbins & Brown, 1997 from Romania (Nematoda, Dorylaimida).

Longidorus piceicola, a new geographical and host record from Romania, was described and illustrated on the basis of two populations originating from a coniferous and a deciduous forest. The main morphological characters of specimens from Romania correspond very well with the type material collected from the soil around Picea abies L. (Slovakia) except for the shorter body and tail. The D2-D3 fragment of 28S rDNA from both populations was amplified and sequenced, and the sequences were identical to L. piceicola sequence from Slovakia. The partial 18S-ITS1-5.8S-ITS2 rDNA regions from one of the populations were sequenced for the first time. The evolutionary relationships between L. piceicola and the closest species L. intermedius based on D2-D3 sequence divergence and single-nucleotide polymorphisms are discussed. Although having very low sequence dissimilarity (0.3–0.9 %) both species have distinct morphology and biology. Longidorus piceicola differs from L. intermedius in having a much longer odontostyle, body, distance anterior end - guide ring, a wider lip region, more ventromedian supplements (11 vs 5–7) in the male, and develops through four rather than three juvenile stages. Furthermore, L. piceicola occurs more frequently in association with conifers, while L. intermedius is found mainly in oak forests.

Research Article Genetic diversity between and within half-sib families of Brazil nut tree (Bertholletia excelsa Bonpl.) originating from native forest of the Brazilian Amazon

Brazil nut tree is a species of economic importance for the Amazon region, known for the commercialization of its almonds. The objective of this work was to study the genetic diversity among half-sib progenies from different Brazil nut trees present in native forest in the municipality of Itauba, MT, belonging to the Brazilian Amazon. In a native forest area of nine hectares, fruits of nine parent trees, randomly selected in the plot, were collected. The seeds were planted at greenhouse and they were named, according to their origin, identifying seed tree and fruit. After the seed germination and initial development of the seedlings, leaves were collected for DNA extraction and analyzed with microsatellite molecular markers. It was performed analysis of molecular variance and cluster analysis of progenies and seed trees. There is greater genetic diversity between families than among progenies from the same family. The clustering of progenies from different families in the same group can be explained by the low dissimilarity between the seed trees. Among the loci analyzed in this study, eight were informative for evaluations of genetic diversity in Brazil nut, except BET12 and BET16 loci

Urban biodiversity in China: Who are winners? Who are losers?

Rapid urbanization in the last three decades has impacted biogeographic patterns of wildlife in China profoundly. Large areas of natural habitats have been converted into concentrated industrial and residential areas [1]. Remaining habitats in vicinities of cities are often fragmented and degraded [2]. Besides land use/land cover changes, anthropogenic disturbances such as the introduction of exotic species further add pressure on local biodiversity [3]. How does wildlife respond to these impacts? Who will win and who will lose in this urbanization process in China? Answers to these questions will help conservation agencies to manage the impacts of urbanization on biodiversity more effectively. A general finding from urban biodiversity studies is that urbanization favors exotic species over native species because of the environmental filtering effect and anthropogenic influences [3]. The temporal change of species composition of birds in Beijing serves as a good example. By comparing the species composition of birds in Beijing recorded during 1954–1978 [4, 5] to those recorded during 2003–2013 (Chinese Bird Reports, http://www.chinabirdnet. org/report.html; eBird, http://www.ebird.org/), one can find that the proportion of species whose distribution ranges are outside of Beijing increased significantly, up from 22 % of the 172 observed species to 46 % of the 409 observed species. Three species whose distribution ranges encompass Beijing could not be observed in the later time (Names of species listed in supplementary Table S1). The gain of exotic species and loss of native species cause biotic homogenization, which is considered one of the most prominent forms of biotic impoverishment worldwide [6]. The diversity pattern of urban woody plants in China bears the evidence of this trend. Assemblages of urban woody plants from 35 Chinese cities had lower dissimilarities of species composition between urban areas than these of woody plants in natural areas (Fig. 1a, b, paired t test, P 0.001), which indicated that urbanization had a homogenization effect. This effect was significant and detectable as social factors explained 11 % of variation in the composition dissimilarity (Fig. 1c). Species from families like Prunus, Populus, and Magnolia have contributed to the homogenization of urban woody plants, which may be due to their wide use in landscaping. That rapid urbanization in China has caused negative impacts on urban biodiversity is supported bymore andmore evidences. The question is: ‘‘Why bother?’’ China has the largest urban population in the world—670 million and an additional 100million by 2020 is expected [7].Many of them experience ‘‘nature’’ primarily in urban areas. Preservation of urban biodiversity will increase their awareness to the importance of biodiversity conservation in nature [8]. Values of urban biodiversity are not restrict to psychological and educational benefits. Urban biodiversity is the foundation of a healthy urban ecosystem. Preserving biodiversity in urban ecosystems can sustain the supply of much-needed Electronic supplementary material The online version of this article (doi:10.1007/s11434-016-1187-7) contains supplementary material, which is available to authorized users.

Analysis of bacterial composition in marine sponges reveals the influence of host phylogeny and environment.

Bacterial communities associated with sponges are influenced by environmental factors; however, some degree of genetic influence of the host on the microbiome is also expected. In this work, 16S rRNA gene amplicon sequencing revealed diverse bacterial phylotypes based on the phylogenies of three tropical sponges (Aplysina fulva, Aiolochroia crassa and Chondrosia collectrix). Despite their sympatric occurrence, the studied sponges presented different bacterial compositions that differed from those observed in seawater. However, lower dissimilarities in bacterial communities were observed within sponges from the same phylogenetic group. The relationships between operational taxonomic units (OTUs) recovered from the sponges and database sequences revealed associations among sequences from unrelated sponge species and sequences retrieved from diverse environmental samples. In addition, one Proteobacteria OTU retrieved from A. fulva was identical to sequences previously reported from A. fulva specimens collected along the Brazilian coast. Based on these results, we conclude that bacterial communities associated with marine sponges are shaped by host identity, while environmental conditions seem to be less important in shaping symbiont communities. This is the first study to assess bacterial communities associated with marine sponges in the remote St. Peter and St. Paul Archipelago using amplicon sequencing of the 16S rRNA gene.

Salient Object Detection via Adaptive Region Merging

Most existing salient object detection algorithms commonly employed segmentation techniques to eliminate background noise and reduce computation by treating each segment as a processing unit. However, individual small segments provide little information about global contents. Such schemes have limited capability on modeling global perceptual phenomena. In this paper, a novel salient object detection algorithm is proposed based on region merging. An adaptive-based merging scheme is developed to reassemble regions based on their color dissimilarities. The merging strategy can be described as that a region R is merged with its adjacent region Q if Q has the lowest dissimilarity with Q among all Q’s adjacent regions. To guide the merging process, superpixels that located at the boundary of the image are treated as the seeds. However, it is possible for a boundary in the input image to be occupied by the foreground object. To avoid this case, we optimize the boundary influences by locating and eliminating erroneous boundaries before the region merging. We show that even though three simple region saliency measurements are adopted for each region, encouraging performance can be obtained. Experiments on four benchmark datasets including MSRA-B, SOD, SED and iCoSeg show the proposed method results in uniform object enhancement and achieve state-of-the-art performance by comparing with nine existing methods.

Effects of irrigation treatments on the quality of table olives produced with the Greek-style process

The irrigation of olive orchards is commonly applied to produce table olives with optimal size. No data have been published on the microbiological quality of drupes from irrigated olive groves during fermentation. The trials T100 and T50 (receiving a water amount equivalent to 100 % and 50 % of the required amount, respectively) and control T0 (rainfed trial) were monitored during two consecutive years. The results showed a significant increase of equatorial diameter and flesh:pit ratio of irrigated drupes. The decrease of pH and the numbers of lactic acid bacteria (LAB) registered for the irrigated trials during the fermentation were more consistent than those displayed by control T0. Lactobacillus pentosus, Lactobacillus plantarum, Lactobacillus coryniformis, and Pediococcus pentosaceus for LAB and Candida boidinii, Candida diddensiae, and Wickerhamomyces anomalus for yeasts were isolated at the highest concentrations. The global sensory acceptance was better for irrigated trials than control T0. The statistical multivariate analysis showed that the effect of irrigation was independent of the seasonal variability and it clearly distinguished the T100 and T50 trials from rainfed control. Irrigation improves significantly the quality of table olives. Interestingly, all explorative multivariate analyses showed low dissimilarity between irrigated trials; thus, the thesis T50 represents an effective approach to save water in olive orchards without compromising the quality of table olives.

Global mammal beta diversity shows parallel assemblage structure in similar but isolated environments.

The taxonomic, phylogenetic and trait dimensions of beta diversity each provide us unique insights into the importance of historical isolation and environmental conditions in shaping global diversity. These three dimensions should, in general, be positively correlated. However, if similar environmental conditions filter species with similar trait values, then assemblages located in similar environmental conditions, but separated by large dispersal barriers, may show high taxonomic, high phylogenetic, but low trait beta diversity. Conversely, we expect lower phylogenetic diversity, but higher trait biodiversity among assemblages that are connected but are in differing environmental conditions. We calculated all pairwise comparisons of approximately 110 × 110 km grid cells across the globe for more than 5000 mammal species (approx. 70 million comparisons). We considered realms as units representing geographical distance and historical isolation and biomes as units with similar environmental conditions. While beta diversity dimensions were generally correlated, we highlight geographical regions of decoupling among beta diversity dimensions. Our analysis shows that assemblages from tropical forests in different realms had low trait dissimilarity while phylogenetic beta diversity was significantly higher than expected, suggesting potential convergent evolution. Low trait beta diversity was surprisingly not found between isolated deserts, despite harsh environmental conditions. Overall, our results provide evidence for parallel assemblage structure of mammal assemblages driven by environmental conditions at a global scale.

Effect of Partnership Status on Preferences for Facial Self-Resemblance.

Self-resemblance has been found to have a context-dependent effect when expressing preferences for faces. Whereas dissimilarity preference during mate choice in animals is often explained as an evolutionary adaptation to increase heterozygosity of offspring, self-resemblance can be also favored in humans, reflecting, e.g., preference for kinship cues. We performed two studies, using transformations of facial photographs to manipulate levels of resemblance with the rater, to examine the influence of self-resemblance in single vs. coupled individuals. Raters assessed facial attractiveness of other-sex and same-sex photographs according to both short-term and long-term relationship contexts. We found a preference for dissimilarity of other-sex and same-sex faces in single individuals, but no effect of self-resemblance in coupled raters. No effect of sex of participant or short-term vs. long-term attractiveness rating was observed. The results support the evolutionary interpretation that dissimilarity of other-sex faces is preferred by uncoupled individuals as an adaptive mechanism to avoid inbreeding. In contrast, lower dissimilarity preference of other-sex faces in coupled individuals may reflect suppressed attention to attractiveness cues in potential alternative partners as a relationship maintenance mechanism, and its substitution by attention to cues of kinship and psychological similarity connected with greater likelihood of prosocial behavior acquisition from such persons.

Arctiinae (Lepidoptera: Erebidae) in the state of Rio de Janeiro, Brazil

This study describes the composition and distribution of the Arctiinae species (Lepidoptera: Erebidae) in Rio de Janeiro, generating the first list of Arctiinae species in the state. We assessed the variations in species composition and the different vegetation types in the municipalities of Rio de Janeiro. Data were collected primarily through surveys of museums and publication lists of species. We also conducted field sampling in March and September 2010. Of the 2,077 records covering 28 municipalities, 679 Arctiinae species were found in Rio de Janeiro state and were divided into two tribes and 220 genera. The location with the highest number of species recorded was Itatiaia, with 362 species, followed by Petrópolis and Angra dos Reis, with 320 and 306 species, respectively. Thirty-four percent (n = 230) of the species recorded were exclusive, i.e., occurred in only one location. The lowest dissimilarity values were observed between neighboring municipalities with the same type of plant formation, such as Petrópolis and Teresópolis (19%) or Itatiaia and Resende (24%). Some municipalities slightly further apart geographically, but with the same type of plant formation, also showed low levels of dissimilarity, for example, Petropolis and Resende (29%). However, most locations showed intermediate dissimilarity values of 40-60%, and in some cases, this figure rose to 96%. In the state of Rio de Janeiro, irrespective of its small geographical size and the predominance of a unique ecosystem, the Atlantic Forest shows a wide variation in relief, which may explain the high beta diversity values. Despite the large number of Arctiinae species recorded in Rio de Janeiro, few species were identified in areas with important forest remnants, such as Guapimirim, Nova Iguaçu, and Campos dos Goitacazes. Some regions of the northwestern part of the state were also subsampled. It is likely that new records of Arctiinae still exist in these locations, further increasing the list of Arctiinae species in Rio de Janeiro.

Limited differences among habitats in deep‐sea macro‐infaunal communities off New Zealand: implications for their vulnerability to anthropogenic disturbance

AbstractThe spread of human activities into the deep sea may pose a high risk to benthic communities and affect ecosystem integrity. The deep sea is characterized by physical and biological heterogeneity and different habitat types are likely to differ in their vulnerability to anthropogenic impacts. However, across‐habitat comparisons are rare, and no comprehensive ecological risk assessment has yet been developed. To address this gap in our knowledge, we compared macro‐infaunal community structure in four habitats (slope, canyons, seamounts and methane seeps) at depths between 700 and 1500 m in the Hikurangi Margin and Bay of Plenty regions off New Zealand. The most striking contrast in community structure was between the two study regions, due to an order of magnitude difference in macro‐infaunal abundance that we believe was caused by differences in surface productivity and food availability at the sea bed. We found differences in structural and functional attributes of macro‐infaunal communities among some habitats in the Hikurangi Margin (slope, canyon and seep), but not in the Bay of Plenty. We posit that differences between canyon and slope communities on the Hikurangi Margin are due to enhanced food availability inside canyons compared with adjacent slope habitats. Seep communities were characterized by elevated abundance of both symbiont‐bearing and heterotrophic taxa, and were the most distinct, and variable, among the habitats that we considered on the Hikurangi Margin. Communities of seamounts were not distinct from slope or canyon communities on the Hikurangi Margin, probably reflecting similar environmental conditions in these habitats. The communities of deep‐sea canyon and seep habitats on the Hikurangi Margin were sufficiently dissimilar from each other and from slope habitats to warrant separate management consideration. By contrast, the low dissimilarity between communities of canyon and slope habitats in the Bay of Plenty suggests that habitat‐based management is not required in this region, for macro‐infauna at least. Although the two study regions share similar species pools, populations of the Hikurangi Margin region may be less vulnerable than the sparser populations of the Bay of Plenty due to the higher availability of potential colonizers and faster population growth. Thus regions, and habitats in some regions, should be subject to separate ecological risk assessment to help identify the key risks and consequences of human activities, and to inform options for reducing or mitigating impacts.

Multivariate analyses of Antarctic and sub-Antarctic seaweed distribution patterns: An evaluation of the role of the Antarctic Circumpolar Current

Biogeographic barriers and ecological corridors are fundamental in defining macroecological and evolutionary processes. Ocean circulation, considering present and past patterns of continental drift, can isolate or connect many groups of marine organisms, including seaweeds. These benthic organisms present spores and propagules as planktonic stages that drift with currents and or tides, and have been a sensible indicator of changes to biogeographical distribution patterns. Phycological studies have been exhaustive in the sub-Antarctic and Antarctic seaweed communities. However, the role of the Antarctic Circumpolar Current (ACC) in shaping marine phytogeographic diversity has been poorly investigated. The ACC connects the major world oceans and redistributes oceanic properties, such as heat, salt, and nutrients, consisting of three major circumpolar fronts (in order of north to southward): the Sub-Antarctic Front (SAF), the Antarctic Polar Front (PF), and the Southern Antarctic Circumpolar Front (SACF). This paper's aim is to understand the role of the ACC fronts as a constraint on seaweed distribution patterns in different taxonomic levels, in relation to the southern Sub-Tropical areas, as well as to compare sections connected with South America (1: north), influenced by the Ross Sea Gyre (2: Western Antarctica Peninsula) and by the Weddell Sea Gyre (3: Eastern Antarctica Peninsula). nMDS showed differences in the distributional patterns of species and genera in relation to the zones and sections. The predicted latitudinal gradient of species richness was observed, and by comparing biogeographic zones, two main clusters were observed: Sub-tropical and Sub-Antarctica; and Polar Front (Antarctic Peninsula) and SACF (areas surrounding continental Antarctica), suggesting, for this sort of macroscale analysis, that ACC still has a role of “watershed barrier”. However, a lower dissimilarity (higher similarity) was observed between the 2nd (Eastern Antarctica Peninsula – EAP – or under influence of the Weddell Sea Gyre, and some sub-Antarctic islands as South Orcadas, South Georgia and Crozet Archipelago) and the 1st sectors (Chilean and Argentinean Patagonia and surrounding islands, Falklands, South Shetlands and including Antarctic Peninsula). When considering recently reported changes in diversity patterns of these locations, this result could demonstrate the existence of a clear species distributional flux, despite evidence of the ACC being a limit to dispersal. Therefore, this contribution has used previously published data to provide a tool for monitoring future biogeographical changes to the flora and fauna of this region of the Antarctic and sub-Antarctic areas due to changes in biogeographical distribution, resulting either from natural dispersion due to global meteoceanographic changes, and or biological invasions related to anthropogenic activities. We could be witness to a period of changes in Antarctic diversity, suggesting that Antarctica may not be as isolated as was once thought.

Low Phylogenetic Beta Diversity and Geographic Neo‐endemism in Amazonian White‐sand Forests

AbstractOver the past three decades, many small‐scale floristic studies of white‐sand forests across the Amazon basin have been published. Nonetheless, a basin‐wide description of both taxonomic and phylogenetic alpha and beta diversity at regional scales has never been achieved. We present a complete floristic analysis of white‐sand forests across the Amazon basin including both taxonomic and phylogenetic diversity. We found strong regional differences in the signal of phylogenetic community structure with both overall and regional Net Relatedness Index and Nearest Taxon Index values found to be significantly positive leading to a pattern of phylogenetic clustering. Additionally, we found high taxonomic dissimilarity but low phylogenetic dissimilarity in pairwise community comparisons. These results suggest that recent diversification has played an important role in the assembly of white‐sand forests causing geographic neo‐endemism patterns at the regional scale.

Comparison of two commercial DNA extraction kits for the analysis of nasopharyngeal bacterial communities

Characterization of microbial communities via next-generation sequencing (NGS) requires an extraction ofmicrobial DNA. Methodological differences in DNA extraction protocols may bias results and complicate inter-study comparisons. Here we compare the effect of two commonly used commercial kits (Norgen and Qiagen)for the extraction of total DNA on estimatingnasopharyngeal microbiome diversity. The nasopharynxis a reservoir for pathogens associated with respiratory illnesses and a key player in understandingairway microbial dynamics. Total DNA from nasal washes corresponding to 30 asthmatic children was extracted using theQiagenQIAamp DNA and NorgenRNA/DNA Purification kits and analyzed via IlluminaMiSeq16S rRNA V4 ampliconsequencing. The Norgen samples included more sequence reads and OTUs per sample than the Qiagen samples, but OTU counts per sample varied proportionallybetween groups (r = 0.732).Microbial profiles varied slightly between sample pairs, but alpha- and beta-diversity indices (PCoAand clustering) showed highsimilarity between Norgen and Qiagenmicrobiomes. Moreover, no significant differences in community structure (PERMANOVA and adonis tests) and taxa proportions (Kruskal-Wallis test) were observed betweenkits. Finally, aProcrustes analysis also showed low dissimilarity (M 2 = 0.173; P < 0.001) between the PCoAs of the two DNA extraction kits. Contrary to what has been observed in previous studies comparing DNA extraction methods, our 16S NGS analysis of nasopharyngeal washes did not reveal significant differences in community composition or structure between kits. Our findingssuggest congruence between column-based chromatography kits and supportthe comparison of microbiomeprofilesacross nasopharyngeal metataxonomic studies.

Plant community response to nitrogen and phosphorus enrichment varies across an alpine tundra moisture gradient

Background: The extent to which nutrient availability influences plant community composition and dynamics has been a focus of ecological enquiry for decades.Aims: Results from a long-term nitrogen (N) and phosphorus (P) addition experiment in alpine tundra were used to evaluate the importance of the two nutrients in structuring plant communities in three communities that differed in their snow cover amounts and duration and soil moisture characteristics.Methods: A factorial N and P experiment was established in three meadows differing in initial vegetation composition and soil moisture. Plant and soil characteristics were measured after 20 years, and the dissimilarity among meadows and treatments were measured using permutational analysis of variance.Results: Plant species richness declined uniformly across the three meadow types and in response to N and N + P additions, while both evenness and the Shannon diversity index finding indicated that nutrient additions had the highest impact on moister habitats. Overall, N impacts overshadowed changes attributed to P additions, and the N and N + P plots in wet meadow sites were the least diverse and scored the lowest dissimilarity averages among treatments. Dissimilarity estimates indicated that the control and P plots in the dry meadow community were more distinct in composition than all other plots, and especially those in the moist or wet meadows. Above-ground biomass of grasses and sedges (graminoids) increased with N additions while forbs appeared to show responses dictated in part by the graminoid responses. The most abundant grass species of moist and wet meadow, Deschampsia cespitosa, dominated N and N + P plots of the wet sites, but did not show a N response in moist areas in spite of its general abundance in moist meadow. Competition from other plant species in the moist areas likely diminished the D. cespitosa response and contributed to the resilience of the community to nutrient enrichment.Conclusions: Initial community composition, as influenced by the specific moisture regime, appears to control the extent to which changes in nutrient resources can alter plant community structure. Long-term fertilization tends to support most but not all findings obtained from shorter-termed efforts, and wet meadows exhibit the largest changes in plant species numbers and composition when chronically enriched with N.