Pairwise Similarity Indices Research Articles

Technical Note: New similarity index for radiotherapy and medical imaging.

To describe a new similarity index and consider its biomedical applications. Similarity index for a pair of objects is defined by the number of shared features and total number of features in these objects. Similarity measure for more than two objects is commonly defined by using pairwise similarity indices. In the current study we suggest a novel similarity index which depends on the number of features shared between multiple objects and does not have the limitations of the recently described similarity measures. In order to introduce the new index, we consider a concept of "commonality." For a collection of sets , commonality of a given element equals the number of sets this element belongs to. The similarity index for the compared sets is then defined by a weighted sum of normalized commonalities. The considered biomedical applications of the proposed index include comparison of independent delineations of critical cranial structures in MR images and comparison of isodose distributions from different radiotherapy plans. This study describes a novel similarity index which can be used to assess the similarity of multiple independent delineations of the anatomical structure or similarity of multiple dose distributions. Unlike the commonly used pairwise similarity indices, the new index is defined by the number of elements shared between multiple sets. Potential applications of the suggested similarity index for radiotherapy and medical imaging have been described.

Plankton and benthos similarity indices as indicators of the impact of mangrove plantation on the environmental quality of silvofishery ponds

Hastuti ED, Hastuti RB, Darmanti S. 2018. Plankton and benthos similarity indices as indicators of the impact of mangroveplantation on the environmental quality of silvofishery ponds. Biodiversitas 19: 1558-1567. This research was carried out in a coastalarea of Semarang City, Central Java, Indonesia. It aimed to study the composition of plankton and benthos communities in silvofisheryponds, and to analyze the similarity in plankton and benthos composition between ponds as an indicator of variation in pondenvironmental quality. Nine pond treatments were sampled for their plankton and benthos composition. The nine treatments consisted ofa factorial combination of three mangrove species assemblages (Avicennia marina (M1), Rhizophora mucronata (M2), and a mixture ofboth (M3)) at three mangrove populations (5 trees (S1), 10 trees (S2), and 15 trees (S3)). Similarity index analysis was conducted tomeasure the impact of treatments on the plankton and benthos communities. The total number of plankton species identified inobservation periods in May, July and September of 2016, were 23, 16 and 21 species repectively, while for the benthos there were eightsomewhat different species identified in each of the three observation periods. Fluctuation in plankton and benthos composition tendedto achieve a balance in richness by the time of the the third observation period. Diatoms, particularly Gyrosigma sp., were the mostwidely distributed plankton in the first and third observation periods, while Pyramidella sulcata was the only well-distributed benthosspecies in the three observation periods. Pairwise similarity indices between treatments ranged from 0% to 62.5% for plankton and from16.7% to 100% for benthos. The results of the investigation suggested that mangrove species affected plankton and benthos speciesrichness in this initial stage of a silvofishery development: plankton composition appeared to be richer in ponds with A. marina, whilebenthos was richer in ponds with R. mucronata.

ASSESSMENT OF GENETIC COMPONENTS AND GENETIC DIVERSITY OF SIX EGYPTIAN CLOVER (Trifolium alexandrinum L.) GENOTYPES USING ISSR AND URP MARKERS

Six Egyptian clover genotypes, i.e., Helaly, Sakha 4, Gemmeiza 1, Serw1, Giza6 and Sakha composite were used in this study. Data was calculated on four cuts and seasonal yield for fresh and dry forage yield. The results indicated that the mean square values were highly significant for genotypes for all studied traits. Helaly cultivar gave the highest values in four cuts and seasonal yield for fresh forage yield. High heritability values were recorded for all studied traits except 1st fresh yield which recorded moderate value. Phenotypic coefficient of variability (PCV) was higher than genotypic coefficient of variability (GCV) in all cuts and seasonal yields. Genetic variations among the six Egyptian clover cultivars were evaluated using universal rice primers (URP) and inter simple sequence repeat (ISSR) markers. URP fingerprinting detected more polymorphic loci (90%) than the ISSR fingerprinting (77.55%). Mean PIC (polymorphism information content) and band informativness (Ib) for each of these marker systems were (0.21, 0.26 for ISSR and 0.32, 0.46 for URP) respectively, suggested that URP marker systems were effective than ISSR in determining polymorphisms. Pairwise similarity index values ranged from 0.37 to 0.72 for ISSR, 0.23 to 0.62 for URP and 0.29 to 0.65 for combined ISSRs and URP indicated the genetic distinctness among the studied genotypes.

Assessment of Genetic Diversity of Freshwater Mud Eel (Monopterus cuchia) Using RAPD and RFLP Markers

Background: Monopterus cuchia, an economically important eel of Bangladesh, is confronting the challenge of population reduction and germplasm degeneration since the vast majority of fingerlings are collected from natural habitats and artificial cultivation of the fish is yet to be established.Materials and Methods: 30 individuals of M. cuchia from a natural population of Northern-East part of Bangladesh were analyzed using 8 decamer primers and glutamine synthetase gene was digested with 2 restriction enzymes.Results: A total of 735 bands with 228 polymorphic loci were detected among the selected 30 individuals by using RAPD assay while 100% polymorphism was revealed by all the primers. The genetic distance among the individuals was calculated by using the data from pair-wise similarity index where 36 groups of genetic diversities were measured while the lowest and highest genetic distance were found 0.58 and 0.97 respectively with an average genetic diversity of 0.81. The Nei’s genetic similarity values were found from 0.06 to 0.6 where average value was recorded 0.301746 which was found significant regarding genetic distance. Phylogenetic relationships using UPGMA clustering revealed linkage distance ranged from 3.6 to 6.24 and generated 6 clusters by 11 clades with the involvement of 22 individuals while the rest of the samples were connected to those clades with specific linkage distances. Genetic diversity of glutamine synthetase gene was analyzed with two restriction enzymes, e.g. +CfrI and +Hpy178III while both the enzymes digested the gene fragment at a length of 541 bp and polymorphism was detected in terms of wild type homogygotes, polymorphic homozygote and heterozygosity. The genetic diversity was observed by using the RFLP band analysis and four different groups of individuals were identified with the p-values of 0, 0.033, 0.05 and 1 respectively whereas different distances were found among the groups indicating the polymorphism among experimental individuals of glutamine synthetase gene.Conclusion: Herein, RAPD and RFLP analysis indicating the rich genetic diversity of this fish in the experimental ecological habitat and this would come helpful for the conservation of germplasm diversity and to support the sustainable breeding program of M. cuchia.

Characterization of ten date palm (Phoenix dactylifera L.) cultivars from Saudi Arabia using AFLP and ISSR markers

Date palm is the most economically important plant in the Middle East due to its nutritionally valuable fruit. The development of accurate DNA fingerprints to characterize cultivars and the detection of genetic diversity are of great value for breeding programs. The present study explores the usefulness of ISSR and AFLP molecular markers to detect relationships among 10 date palm (Phoenix dactylifera L.) cultivars from Saudi Arabia. Thirteen ISSR primers and six AFLP primer combinations were examined. The level of polymorphism among cultivars for ISSRs ranged from 20% to 100% with an average of 85%. Polymorphism levels for AFLPs ranged from 63% to 84% with an average of 76%. The total number of cultivar-specific markers was 241, 208 of which were generated from AFLP analysis. AJWA cultivar had the highest number of cultivar-specific ISSR markers, whereas DEK, PER, SUK-Q, SHA and MOS-H cultivars had the lowest. RAB and SHA cultivars had the most and least AFLP cultivar-specific markers, respectively. The highest pairwise similarity indices for ISSRs, AFLPs and combined markers were 84% between DEK (female) and PER (female), 81% between SUK-Q (male) and RAB (male), and 80% between SUK-Q (male) and RAB (male), respectively. The lowest similarity indices were 65% between TAB (female) and SUK-Q (male), 67% between SUK-A (female) and SUK-Q (male), and 67% between SUK-A (female) and SUK-Q (male). Cultivars of the same sex had higher pairwise similarities than those between cultivars of different sex. The Neighbor-Joining (NJ) tree generated from the ISSR dataset was not well resolved and bootstrap support for resolved nodes in the tree was low. AFLP and combined data generated completely resolved trees with high levels of bootstrap support. In conclusion, AFLP and ISSR approaches enabled discrimination among 10 date palm cultivars of from Saudi Arabia, which will provide valuable information for future improvement of this important crop.

Epigeal Spider (Araneae) Communities in Moist Acidic and Dry Heath Tundra at Toolik Lake, Alaska

For the 2004–2006 growing seasons, we trapped a total of 6980 spiders (5066 adults, 1914 immatures) using pitfall traps at the Arctic Long Term Experimental Research (LTER) site in Toolik Lake, Alaska. We found 10 families and 51 putative species, with 45 completely identified, in two distinct habitats: Moist Acidic Tundra (MAT) and Dry Heath (DH) Tundra. We captured spiders belonging to the following families (number of species captured): Araneidae (1), Clubionidae (1), Dictynidae (1), Gnaphosidae (4), Linyphiidae (26), Lycosidae (11), Philodromidae (2), Salticidae (1), Theridiidae (1), and Thomisidae (3). Statistical comparisons of families captured at MAT and DH Tundra indicate that the habitats have significantly different spider communities (Chi Square Test: p < 0.0001, and Fisher’s Exact Test: p = 0.0018). This finding is further supported by differences in similarity, diversity, evenness, and species richness between the two habitats. In this report, we present eight new state records and five extensions of previously described ranges for spider species. The following species are new state records for Alaska: Emblyna borealis (O.P.-Cambridge 1877), Horcotes strandi (Sytschevskaja 1935), Mecynargus monticola (Holm 1943), Mecynargus tungusicus (Eskov 1981), Metopobactrus prominulus (O.P. -Cambridge 1872), Poeciloneta theridiformis Emerton 1911, and Poeciloneta vakkhanka (Tanasevitch 1989). The following five species have been reported previously in Alaska, but not near Toolik Lake: Hypsosinga groenlandica Simon 1889, Gnaphosa borea Kulczyn’ski 1908, Gnaphosa microps Holm 1939, Haplodrassus hiemalis (Emerton 1909), and Islandiana cristata Eskov 1987. Pairwise similarity indices were calculated across 13 other arctic and subarctic spider communities and statistical tests show that all sites are dissimilar (p = 0.25). These results fit the general pattern of both the patchiness and habitat specificity of arctic spider fauna.

Comparative evaluation of genetic diversity using RAPD, SSR and cytochrome P450 gene based markers with respect to calcium content in finger millet (Eleusine coracana L. Gaertn.)

Genetic relationships among 52 Eleusine coracana (finger millet) genotypes collected from different districts of Uttarakhand were investigated by using randomly amplified polymorphic DNA (RAPD), simple sequence repeat (SSR) and cytochrome P450 gene based markers. A total of 18 RAPD primers, 10 SSR primers, and 10 pairs of cytochrome P450 gene based markers, respectively, revealed 49.4%, 50.2% and 58.7% polymorphism in 52 genotypes of E. coracana. Mean polymorphic information content (PIC) for each of these marker systems (0.351 for RAPD, 0.505 for SSR and 0.406 for cyt P450 gene based markers) suggested that all the marker systems were effective in determining polymorphisms. Pair-wise similarity index values ranged from 0.011 to 0.999 (RAPD), 0.010 to 0.999 (SSR) and 0.001 to 0.998 (cyt P450 gene based markers) and mean similarity index value of 0.505, 0.504 and 0.499, respectively. The dendrogram developed by RAPD, SSR and cytochrome P450 gene based primers analyses revealed that the genotypes are grouped in different clusters according to high calcium (300-450 mg/100 g), medium calcium (200-300 mg/100 g) and low calcium (100-200 mg/100 g). Mantel test employed for detection of goodness of fit established cophenetic correlation values above 0.95 for all the three marker systems. The dendrograms and principal coordinate analysis (PCA) plots derived from the binary data matrices of the three marker systems are highly concordant. High bootstrap values were obtained at major nodes of phenograms through WINBOOT software. Comparison of RAPD, SSR and cytochrome P450 gene based markers, in terms of the quality of data output, indicated that SSRs and cyt P450 gene based markers are particularly promising for the analysis of plant genome diversity. The genotypes of finger millet collected from different districts of Uttarakhand constitute a wide genetic base and clustered according to calcium contents. The identified genotypes could be used in breeding programmes and amajor input into conservation biology of cereal crops.

Efficiency of RAPD and ISSR Markers in Differentiation of Homo- and Heterokaryotic Protoclones of Agaricus bisporus

Morphologically, nine different slow-growing protoclones were screened from regenerated protoplast of heterokaryotic Agaricus bisporus. The present study is the first report of fingerprinting on differentiating homo- and heterokaryotic protoclones using random amplified polymorphic DNA (RAPD) and inter-simple sequence repeat (ISSR) markers. Among 80 primers tested, the seven ISSR and seven RAPD primers selected for the analysis generated a total of 94 ISSR and 52 RAPD fragments, respectively. ISSR fingerprinting detected more polymorphic loci (38.29%) than RAPD fingerprinting (34.61%). Principal coordinate analysis (PCA) was employed to evaluate the resolving power of the markers to differentiate protoclones. The mean polymorphism information content (PIC) for each of these marker systems (i.e., 0.787 for RAPD and 0.916 for ISSR, respectively) suggests that the ISSR marker system was more effective in determining polymorphisms. The dendrograms constructed using RAPD, ISSR, and integrated RAPD, and ISSR marker systems were highly correlated with each other as revealed by the high Mantel correlation (r = 0.98). Pair-wise similarity index values ranged from 0.64 to 0.95 (RAPD), 0.67 to 0.98 (ISSR), and 0.67 to 0.98 (RAPD and ISSR), and mean similarity index values of 0.82, 0.81, and 0.84 for RAPD, ISSR, and combined data, respectively, were obtained. As there was a good correspondence between RAPD and ISSR similarity matrices, ISSR may be used as an alternative to replace RAPD in the genetic diversity assessment and accurate differentiation of homo- and heterokaryotic protoclones of A. bisporus.

A Two‐Stage Probabilistic Approach to Multiple‐Community Similarity Indices

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.

Do humans homogenize or differentiate biotas? It depends

Do humans homogenize or differentiate biotas? It depends

Assessment of Genetic Variation Within Indian Mustard (Brassica juncea) Germplasm Using Random Amplified Polymorphic DNA Markers

Genetic diversity among 45 Indian mustard (Brassica juncea L.) genotypes comprising 37 germplasm collections, five advance breeding lines and three improved cultivars was investigated at the DNA level using the random amplified polymorphic DNA (RAPD) technique. Fifteen primers used generated a total of 92 RAPD fragments, of which 81 (88%) were polymorphic. Of these, 13 were unique to accession 'Pak85559'. Each primer produced four to nine amplified products with an average of 6.13 bands per primer. Based on pairwise comparisons of RAPD amplification products, Nei and Li's similarity coefficients were calculated to evaluate the relationships among the accessions. Pairwise similarity indices were higher among the oilseed accessions and cultivars showing narrow ranges of 0.77-0.99. An unweighted pair-group method with arithmetic averages cluster analysis based on these genetic similarities placed most of the collections and oilseed cultivars close to each other, showing a low level of polymorphism between the accessions used. However, the clusters formed by oilseed collections and cultivars were comparatively distinct from that of advanced breeding lines. Genetically, all of the accessions were classified into a few major groups and a number of individual accessions. Advanced breeding lines were relatively divergent from the rest of the accessions and formed independent clusters. Clustering of the accessions did not show any pattern of association between the RAPD markers and the collection sites. A low level of genetic variability of oilseed mustard was attributed to the selection for similar traits and horticultural uses. Perhaps close parentage of these accessions further contributed towards their little diversity. The study demonstrated that RAPD is a simple and fast technique to compare the genetic relationship and pattern of variation among the gene pool of this crop.

Improved Strategy for Comparing Microbial Assemblage Fingerprints

Microbial fingerprinting techniques permit the rapid visualization of entire assemblages in single assays, allowing direct comparison of communities in different samples, where the null hypothesis of such analyses is that all samples are the same. The comparison of fingerprints relies upon the precise estimation of all amplified DNA fragment lengths, which correspond to operational taxonomic units (OTU; analogous, but not equal to, a taxon in macroorganism studies). However, computer interpolation of size standards (and consequently OTU size calling) can be imprecise between gel runs, which can lead to imprecise calculation of similarity indices between multiple assemblages. To account for OTU size calling imprecision, all fragments within a range of sizes (a window) can be combined (i.e., "binned") where the window is as wide as the imprecision of OTU size calling. However, artifacts may occur upon binning samples that may cause samples to appear less similar to each other, caused by splitting of OTU between adjacent bin windows. In this work we present an improved binning technique that accounts for OTU size calling imprecision in the comparison of multiple fingerprints. This technique comprises binning all pairwise comparisons in multiple bin window frames, where the starting size of the window (i.e., frame) is shifted by +1 bp for a total of x frames, where x bp is the width of the maximum bin window size in any binning scheme. Pairwise similarity indices between different community fingerprints are calculated for each of the x frames. To best address the null hypothesis of the community comparison, the maximum similarity value of all x frames is then used in downstream analyses to compare the communities. We believe this binning technique provides the most accurate and least biased comparison between different microbial fingerprints.

A genetic bottleneck in the ’evolution under domestication’ of upland cotton Gossypium hirsutum L. examined using DNA fingerprinting

Reliable information about the evolutionary and genetic relationships of various germplasm resources is essential to the establishment of rational strategies for crop improvement. We used AFLPs to study the genetic relationships of 43 cultivars of Gossypium hirsutum representative of the genomic composition of modern ’Upland’ cotton. The study also included representatives of the related tetraploid species Gossypium barbadense, as well as the diploid species Gossypium raimondii, Gossypium incanum, Gossypium herbaceum and Gossypium arboreum. We tested 20 primer combinations that resulted in a total of 3,178 fragments. At the species level, and above, genetic similarities based on AFLPs were in agreement with the known taxonomic relationships. Similarity indices ranged from 0.25 to 0.99. Representatives of the G. hirsutum germplasm resources utilized in North America, including secondary accessions collected by breeders in Central America (’Acala’, ’Tuxtla’, ’Kekchi’) and the southwestern US (’Hopi Moencopi’), formed a single cluster with exceedingly limited genetic diversity (with many pairwise similarity indices >0.96) We concluded that these accessions were derived from the same genetic pool. The early maturing or ’latifolium’ or ’Mexican Highlands’ cultigens from which these cultivars were derived appear to have had extremely limited genetic diversity, perhaps as a result of a severe genetic bottleneck resulting from the selection pressures of domestication. Outside of the major G. hirsutum cluster, well-supported phylogenies were inferred. Inside this cluster, phylogenies were obscured by limited diversity, reticulation and lineage sorting. The implications of these findings for cotton improvement are discussed.

Genetic status of Acanthamoeba spp. Korean isolates on the basis of RAPD markers

Genetic status of Acanthamoeba spp. were tested on the basis of random amplified polymorphic DNA (RAPD) marker analysis. Four previously established Acanthamoeba species, 4 Korean isolates of Acanthamoeba sp., and one American isolate of Acanthamoeba sp. were analyzed by RAPD-PCR using an arbitrary decamer primers. Amplification products were fractionated by agarose gel electrophoresis and stained by ethidium bromide. Eighteen primers produced DNA amplification profiles revealing clear differences among 4 species. Nine of them also produced DNA amplification profiles which included some isolate-specific amplification products. On the basis of amplified fragments by 18 primers, the pairwise similarity indices between A. culbertsoni and other species (i.e., A. hatchetti, A. triangularis, A. polyphaga) were 0.300, 0.308, and 0.313, respectively. Similarity index between A. hatchetti and A. triangularis was 0.833. The mean similarity index among the 3 Korean isolates (YM-2, -3, -4) was 0.959 and 0.832 among them and 2 other species (A. hatchetti and A. triangularis). The mean similarity index among YM-5 and other Korean isolates (YM-2, -3, -4) was 0.237. However, the similarity index between YM-5 and A. culbertsoni was 0.857, which suggests that YM-5 is genetically more similar to A. culbertsoni than other Korean isolates. Phenogram reconstructed by UPGMA method revealed that there are two groups: one group consists of A. hatchetti, A. triangularis, and 3 Korean isolates (YM-2, -3, -4), and the other group consists of A. culbertsoni, A. polyphaga, HOV, and YM-5.