Topology Of Neighbor-joining Tree Research Articles

A DNA barcode reference library for the Tipulidae (Insecta, Diptera) of Germany.

Tipulidae, commonly known as true crane flies, represent one of the most species-rich dipteran families, boasting approximately 4,500 known species globally. Their larvae serve as vital decomposers across diverse ecosystems, prompting their frequent and close observation in biomonitoring programs. However, traditional morphological identification methods are laborious and time-consuming, underscoring the need for a comprehensive DNA barcode reference library to speed up species determination. In this study, we present the outcomes of the German Barcode of Life initiative focused on Tipulidae. Our DNA barcode library comprises 824 high-quality cytochrome c oxidase I (COI) barcodes encompassing 76 crane fly species, counting for ca. 54% of the German tipulid fauna. Our results significantly increased the number of European tipulid species available in the Barcode of Life Data System (BOLD) by 14%. Additionally, the number of barcodes from European tipulid specimens more than doubled, with an increase of 118%, bolstering the DNA resource for future identification inquiries. Employing diverse species delimitation algorithms - including the multi-rate Poisson tree processes model (mPTP), Barcode Index Number assignments (BIN), Assemble Species by Automatic Partitioning (ASAP), and the TaxCI R-script - we successfully match 76-86% of the morphologically identified species. Further validation through neighbor-joining tree topology analysis and comparison with 712 additional European tipulid barcodes yield a remarkable 89% success rate for the species identification of German tipulids based on COI barcodes. This comprehensive DNA barcode dataset not only enhances species identification accuracy but also serves as a pivotal resource for ecological and biomonitoring studies, fostering a deeper understanding of crane fly diversity and distribution across terrestrial landscapes.

Description and characterization of questing hard tick, Dermacentor steini (Acari: Ixodidae) in Malaysia based on phenotypic and genotypic traits.

Identifying certain species of Dermacentor ticks in Malaysia is challenging as there is no comprehensive work on their systematics and lack of specific taxonomic keys. In this study, we described and characterized D. steini ticks collected from a forest reserve in the vicinity of the Forest Research Institute of Malaysia using integrated phenotypic and genotypic traits. In total two males and three females of questing D. steini ticks were morphologically identified using specific illustrated taxonomic keys based on their special characters. Further confirmation and characterization of the tick species were then examined using PCR, followed by sequencing partial mitochondrial 16S rDNA gene (mt-rrs). Clustering analysis based on mt-rrs was carried out by constructing neighbor-joining tree topology to clarify the genetic variation of local D. steini. Based on external morphological characterizations, all ticks were successfully identified down to the species as adult D. steini. The molecular traits based on phylogenetic tree provide very strong support for the monophyletic clade of D. steini including high percentages of similarity (97-100%) with available sequences in GenBank. Furthermore, a low intraspecific variation (4%) among the species of D. steini was observed but it was genetically different from other Dermacentor species with high interspecific value (8-15%). These findings produced the first genotypic data of D. steini using 16S rDNA gene which confirmed the presence of this species in Malaysia. Moreover, this study supports the taxonomic status of local D. steini and adds to the knowledge of accurate identification of ticks.

Wing variation in Culex nigripalpus (Diptera: Culicidae) in urban parks

BackgroundCulex nigripalpus has a wide geographical distribution and is found in North and South America. Females are considered primary vectors for several arboviruses, including Saint Louis encephalitis virus, Venezuelan equine encephalitis virus and Eastern equine encephalitis virus, as well as a potential vector of West Nile virus. In view of the epidemiological importance of this mosquito and its high abundance, this study sought to investigate wing variation in Cx. nigripalpus populations from urban parks in the city of São Paulo, Brazil.MethodsFemale mosquitoes were collected in seven urban parks in the city of São Paulo between 2011 and 2013. Eighteen landmark coordinates from the right wing of each female mosquito were digitized, and the dissimilarities between populations were assessed by canonical variate analysis and cross-validated reclassification and by constructing a Neighbor-Joining (NJ) tree based on Mahalanobis distances. The centroid size was calculated to determine mean wing size in each population.ResultsCanonical variate analysis based on fixed landmarks of the wing revealed a pattern of segregation between urban and sylvatic Cx. nigripalpus, a similar result to that revealed by the NJ tree topology, in which the population from Shangrilá Park segregated into a distinct branch separate from the other more urban populations.ConclusionEnvironmental heterogeneity may be affecting the wing shape variation of Cx. nigripalpus populations.

POTYVIRUSES INFECTING VEGETABLE CROPS IN UKRAINE

This paper describes detection of some potyvirus infecting vegetable crops in Ukraine. Collected samples were screened for the presence of Zucchini yellow mosaic virus and Watermelon mosaic virus-2. Obtained isolates of Zucchini yellow mosaic virus were clustered with isolates from Slovenia, Hungary, Czech Republic, Austria and France within subgroup AI. According to the topology of Neighbor-Joining tree based on sequences of NIb-CP genome region obtained WMV-2 isolates showed that belong to group G1. Viruses infecting cucurbits in Ukraine presented by phylogenetic groups widespread in Europe.

Genetic variation in scaly hair-fin anchovy Setipinna tenuifilis (Engraulididae) based on the mitochondrial DNA control region

Scaly hair-fin anchovy (Setipinna tenuifilis) is a small, pelagic and economical species and widely distributed in Chinese coastal water. However, resources of S. tenuifilis have been reduced due to overfishing. For better fishery management, it is necessary to understand the pattern of S. tenuifilis’s biogeography. Genetic analyses were taken place to detect their population genetic variation. A total of 153 individuals from 7 locations (Dongying, Yantai, Qingdao, Nantong, Wenzhou, Xiamen and Beibu Bay) were sequenced at the 5′ end of mtDNA control region. A 39-bp tandem repeated sequence was found at the 5′ end of the segment and a polymorphism of tandem repeated sequence was detected among 7 populations. Both mismatch distribution analysis and neutrality tests showed S. tenuifilis had experienced a recent population expansion. The topology of neighbor-joining tree and Bayesian evolutionary tree showed no significant genealogical branches or clusters of samples corresponding to sampling locality. Hierarchical analysis of molecular variance and conventional pairwise population Fst value at group hierarchical level implied that there might have genetic divergence between southern group (population WZ, XM and BB) and northern group (population DY, YT, QD and NT). We concluded that there might have three different fishery management groups of S. tenuifilis and the late Pleistocene glacial event might have a crucial effect on present-day demography of S. tenuifilis in this region.

On the optimality of the neighbor-joining algorithm

The popular neighbor-joining (NJ) algorithm used in phylogenetics is a greedy algorithm for finding the balanced minimum evolution (BME) tree associated to a dissimilarity map. From this point of view, NJ is "optimal" when the algorithm outputs the tree which minimizes the balanced minimum evolution criterion. We use the fact that the NJ tree topology and the BME tree topology are determined by polyhedral subdivisions of the spaces of dissimilarity maps to study the optimality of the neighbor-joining algorithm. In particular, we investigate and compare the polyhedral subdivisions for n ≤ 8. This requires the measurement of volumes of spherical polytopes in high dimension, which we obtain using a combination of Monte Carlo methods and polyhedral algorithms. Our results include a demonstration that highly unrelated trees can be co-optimal in BME reconstruction, and that NJ regions are not convex. We obtain the l2 radius for neighbor-joining for n = 5 and we conjecture that the ability of the neighbor-joining algorithm to recover the BME tree depends on the diameter of the BME tree.

Genetic variation in Chinese hatchery populations of the Japanese scallop ( Patinopecten yessoensis) inferred from microsatellite data

The Japanese scallop Patinopecten yessoensis was introduced to China about two decades ago from Japan. In aquaculture, there are concerns as to whether genetic variability would have been lost in farmed populations during their subsequent hatchery production. Using six microsatellite loci, three hatchery populations of P. yessoensis in China were compared with one another and with two wild Japanese populations. The hatchery populations were substantially less variable than wild populations. For the hatchery and wild populations, the average numbers of alleles per locus were 5.7 and 7.9, and the average expected heterozygosities were 0.582 and 0.671, respectively. This loss of variation is attributable to about 20 years of isolation and genetic drift. F st values showed significant genetic differentiation among the five populations. Genetic differences between the populations were also detected by pairwise comparison based on allelic distribution. The Neighbor-joining tree topology constructed on the basis of genetic distances among populations showed a clear division between the wild and hatchery populations. The information on the genetic variation and differentiation in cultured and wild populations of P. yessoensis obtained in this study is useful for setting up suitable guidelines for founding and maintaining of cultured stocks, and for future genetic improvement by selective breeding.

Genetic variability assessed by microsatellites in cultured populations of the Pacific oyster ( Crassostrea gigas) in China

Five cultured populations of Pacific oyster, Crassostrea gigas, were examined at seven polymorphic microsatellite loci to assess the levels of allelic diversity and heterozygosity within and differentiation among the populations. The genetic variability of the seven loci was high for all the populations. The average numbers of alleles per locus ranged from 19.1 to 26.0, while the average observed and expected heterozygosity ranged from 0.474 to 0.616, and from 0.916 to 0.949, respectively. F st and R st values showed significant genetic differentiation among the five cultured populations. Genetic differences between the populations were also detected by pairwise comparison based on allelic distribution. The Neighbor-joining tree topology constructed on the basis of genetic distances between populations showed a clear separation of the northern three populations and southern two populations, suggesting that geographically separated cultured populations of C. gigas could be genetically differentiated unless seeds are transplanted among them. The useful information on the genetic variation and differentiation in cultured populations obtained in this study can be applied for future genetic improvement by selective breeding, and to design suitable management guidelines for the Pacific oyster.

HEPATOZOON SAURITUS: A POLYTOPIC HEMOGREGARINE OF THREE GENERA AND FOUR SPECIES OF SNAKES IN NORTH FLORIDA, WITH SPECIFIC IDENTITY VERIFIED FROM GENOME ANALYSIS

Hemogregarines from Thamnophis s. sirtalis, Coluber constrictor priapus, Elaphe obsoleta quadrivittata, and E. g. guttara in northern Florida appeared to be conspecific on the basis of similar gamonts from all the hosts and sporogonic stages obtained from 3 hosts. The resemblance of gamonts to those of Hepatozoon sauritus, described from T. sauritus sackenii in southern Florida, justified comparison of DNA isolates from the type infection of H. sauritus with samples from each of the northern Florida hosts and with a morphologically distinct species, H. sirtalis, from northern Florida. A nucleotide sequence (530 bp) alignment of the 18S ribosomal RNA gene revealed 2 hemogregarine haplotypes that varied at 15 sites (p distance = 2.8%), which included 10 transitions and 5 transversions. Two well-supported clusters (100% bootstrap support) were revealed by a neighbor-joining tree topology. One cluster included the type infection of H. sauritus and all 4 of the other samples from the northern Florida hosts, with samples of H. sirtalis comprising a second cluster. Hepatozoon sauritus, therefore, is a polytopic species in contrast to the 8 other Hepatozoon species thus far described from snakes in Florida, each of which appears to parasitize a single host species.

Loss of genetic variation at microsatellite loci in hatchery strains of the Pacific abalone ( Haliotis discus hannai)

In order to assess the utility of microsatellite DNA markers for detecting changes of genetic diversity in hatchery strains and for estimating their genetic relationships, we used six microsatellite markers to estimate the level of genetic diversity within three hatchery strains and two wild populations of Pacific abalone, and compared the degree of genetic differentiation between them. High polymorphism at the microsatellite loci was found within both hatchery and wild abalone populations. Compared to wild populations, all the hatchery strains showed less genetic variation as revealed in lower number of alleles and lower expected heterozygosity, indicating that bottleneck effects occurred when each strain was founded. Significant differentiation was found between the hatchery strains, and between the hatchery strains and wild populations ( F st range: 0.059–0.427; R st range: 0.056–0.351), and no obvious difference was detected between the wild populations ( F st=0.004; R st=0.007). According to the neighbor-joining tree topology constructed on the basis of genetic distances among individuals, almost all individuals from each hatchery strain were closely clustered, demonstrating the feasibility of microsatellite analysis for discrimination between hatchery strains. The results obtained in this study indicate that it is necessary to genetically characterize the abalone strains that are being released every year in order to monitor the effect on the genetic diversity of wild populations.