Tree Distance Research Articles

Computing RF Tree Distance over Succinct Representations

There are several tools available to infer phylogenetic trees, which depict the evolutionary relationships among biological entities such as viral and bacterial strains in infectious outbreaks or cancerous cells in tumor progression trees. These tools rely on several inference methods available to produce phylogenetic trees, with resulting trees not being unique. Thus, methods for comparing phylogenies that are capable of revealing where two phylogenetic trees agree or differ are required. An approach is then proposed to compute a similarity or dissimilarity measure between trees, with the Robinson–Foulds distance being one of the most used, and which can be computed in linear time and space. Nevertheless, given the large and increasing volume of phylogenetic data, phylogenetic trees are becoming very large with hundreds of thousands of leaves. In this context, space requirements become an issue both while computing tree distances and while storing trees. We propose then an efficient implementation of the Robinson–Foulds distance over tree succinct representations. Our implementation also generalizes the Robinson–Foulds distances to labelled phylogenetic trees, i.e., trees containing labels on all nodes, instead of only on leaves. Experimental results show that we are able to still achieve linear time while requiring less space. Our implementation in C++ is available as an open-source tool.

Deep Learning based flower detection and counting in highly populated images: A peach grove case study

Farmers and producers need to estimate crop yield in order to plan and allocate human and economic resources during the harvesting season. For many crops, such as peach groves, the number of fruits is correlated with the number of flowers produced by each tree. Therefore, estimating the number of flowers in peach groves can serve as a good indicator of crop yield, disregarding climate hazards. However, in peach groves, tree images present several challenges, including a high number of flowers, interference from distant trees, and occlusion between elements. These issues pose a difficult task for computer vision and machine learning techniques. In this study, we propose the utilization of state-of-the-art deep learning techniques for image detection purposes; namely the YOLO architectures on its versions 5, 7, and 8 and their different size models (n, s, m, l, x); as well as predicting object density using multi-column in densely populated images, using a multi-column deep neural network. The methodology was tested on a new dataset comprising 600 images of peach trees during the blooming season, in the region of Catalonia, Spain. Out of these, 400 images were used to train the model, while 100 were allocated for testing and another 100 for validation. The counting results were evaluated using metrics such as Mean Squared Error (MSE), Mean Absolute Error (MAE), and percentage error (%Err). For the detection algorithms, metrics such as accuracy, precision, recall, and mean average precision were utilized, alongside metrics for evaluating the counting process.The experiments demonstrated that predicting the density map yielded better results in the counting process, achieving an MAE of 39.13, RMSE of 69.69, and a percentage error of 9.98. The detection algorithm that exhibited superior performance was YOLOv7x, with metrics of MAE 152.7, RMSE 212.9, and a percentage error of 29.7 %. These results indicate that, for counting purposes, predicting the density map produced better overall outcomes.

Consensus Tree Under the Ancestor-Descendant Distance is NP-Hard.

Due to uncertainty in tumor phylogeny inference from sequencing data, many methods infer multiple, equally plausible phylogenies for the same cancer. To summarize the solution space of tumor phylogenies, consensus tree methods seek a single best representative tree S under a specified pairwise tree distance function. One such distance function is the ancestor-descendant (AD) distance [Formula: see text] , which equals the size of the symmetric difference of the transitive closures of the edge sets [Formula: see text] and [Formula: see text] . Here, we show that finding a consensus tree S for tumor phylogenies that minimizes the total AD distance [Formula: see text] is NP-hard.

Tessaracoccus caeni sp. nov., a novel member of Propionibacteriaceae isolated from activated sludge in Hefei, PR China.

A floc-forming bacterial strain, designated HF-7T, was isolated from the activated sludge of an industrial wastewater treatment plant in Hefei, PR China. Cells of this strain were Gram-stain-positive, catalase- and oxidase-negative, facultatively anaerobic, and rod-shaped. Growth occurred at 20-42 °C (optimum, 28 °C), at pH 5.5-10.5 (optimum, pH 7.5) and with 0-8.0 % (w/v) NaCl (optimum, 1 %). The major fatty acid was anteiso-C15 : 0. The polar lipid profile contained phosphatidylglycerol, diphosphatidylglycerol and phosphatidylinositol. The DNA G+C content was 67 mol% from whole genomic sequence analysis. Based on the results of 16S rRNA gene sequence analysis, this strain should be assigned to the genus Tessaracoccus and is closely related to Tessaracoccus arenae CAU 1319T (95.87 % similarity), Tessaracoccus lapidicaptus IPBSL-7T (95.19 %) and Tessaracoccus bendigoensis Ben 106T (94.63 %) but separated from them by large distances in different phylogenetic trees. Based on whole genome analysis, the orthologous average nucleotide identity and in silico DNA-DNA hybridization values against two of the closest relatives were 75.21-76.50 % and 14.2-24.4 %, respectively. The phylogenetic, genotypic, phenotypic and chemotaxonomic data demonstrated that strain HF-7T could be distinguished from its phylogenetically related species and represents a novel species within the genus Tessaracoccus, for which the name Tessaracoccus caeni sp. nov. is proposed. The type strain is HF-7T (=KCTC 49959T=CCTCC AB 2023019T).

Comparison of chloroplast genomes and phylogenetic analysis of four species in Quercus section Cyclobalanopsis

The identification in Quercus L. species was considered to be difficult all the time. The fundamental phylogenies of Quercus have already been discussed by morphological and molecular means. However, the morphological characteristics of some Quercus groups may not be consistent with the molecular results (such as the group Helferiana), which may lead to blurring of species relationships and prevent further evolutionary researches. To understand the interspecific relationships and phylogenetic positions, we sequenced and assembled the CPGs (160,715 bp-160842 bp) of four Quercus section Cyclobalanopsis species by Illumina pair-end sequencing. The genomic structure, GC content, and IR/SC boundaries exhibited significant conservatism. Six highly variable hotspots were detected in comparison analysis, among which rpoC1, clpP and ycf1 could be used as molecular markers. Besides, two genes (petA, ycf2) were detected to be under positive selection pressure. The phylogenetic analysis showed: Trigonobalanus genus and Fagus genus located at the base of the phylogeny tree; The Quercus genus species were distincted to two clades, including five sections. All Compound Trichome Base species clustered into a single branch, which was in accordance with the results of the morphological studies. But neither of group Gilva nor group Helferiana had formed a monophyly. Six Compound Trichome Base species gathered together in pairs to form three branch respectively (Quercus kerrii and Quercus chungii; Quercus austrocochinchinensis with Quercus gilva; Quercus helferiana and Quercus rex). Due to a low support rate (0.338) in the phylogeny tree, the interspecies relationship between the two branches differentiated by this node remained unclear. We believe that Q. helferiana and Q. kerrii can exist as independent species due to their distance in the phylogeny tree. Our study provided genetic information in Quercus genus, which could be applied to further studies in taxonomy and phylogenetics.

Variability in Water Capacity of Small-Leaved Linden Associated with Both the Presence of Honeydew and Various Sources of Pollution.

The process of water retention on the surface of the assimilation apparatus of plants is inextricably linked with the water capacity of tree crowns and depends mainly on the condition of the leaf itself. The main objective of the present study was to investigate how the honeydew coverage and the location of trees related to the content of polycyclic aromatic hydrocarbons affected the differences in the capability of small-leaved linden leaves to capture water. Honeydew coverage was determined with the use of AutoCAD, whereas the content of polycyclic aromatic hydrocarbons was determined using gas chromatography. The value of S (water capacity) was much lower before the appearance of honeydew on the leaf than at the peak moment of honeydew collection. This is due to the hydrophobic properties of the substance. It was also found that the content of polycyclic aromatic hydrocarbons (PAH) in leaves varied depending on the distance of trees from pollution sources, and it was found that the amount of PAHs increased with the growth of honeydew on leaves and in locations exposed to pollution. The highest S and the total amount of PAHs occurred with the combination of the largest amount of pyrogenic impurities with the highest amount of honeydew. Combing pollutants from the air by plants is a very important function, but it may also change the physical properties of leaves, such as wettability.

Riparian forests throwback at the Eurasian beaver era: a woody vegetation assessment for Mediterranean regions

Several biotic and abiotic interactions will contribute to riparian ecosystem changes. The impact of Eurasian beaver (Castor fiber) on woody vegetation is still unknown for the Mediterranean biogeographical area. Through a replicable approach applied on a cluster of three rivers, we studied how the tree layer of Mediterranean riparian sites is impacted by the beaver's recent comeback. For each site, we collected data (e.g., stem diameter, species, distance from riverbank) for all standing trees and additional information only for gnawed trees at plot level. Data elaboration allowed to characterise impacts on riparian vegetation. Salix spp. and Populus spp. are the main gnawed species, but sporadically other species can be selected based on their size and spatial distribution (e.g., Alnus glutinosa). Diameter means of gnawed trees are significantly lower than the not gnawed ones. Most of the selected trees have low diameter classes (< 12 cm), even if diameter preferences may vary on the basis of overall stand tree size range and distribution. Over 90% of the gnawed trees are entirely harvested, with stumps as the remaining standing element. Main changes on the overall forest stand occurred in the first ten metres from the riverbank, as beaver gnawing activity is significantly influenced by the interaction among tree distance from the river and diameter size. Our approach can be used as a model system to be implemented in other Mediterranean sites where beaver is expanding, with the aim of predicting mid-term riparian forests vegetation changes.Graphical abstract

Rampant chloroplast capture in Sarracenia revealed by plastome phylogeny.

Introgression can produce novel genetic variation in organisms that hybridize. Sympatric species pairs in the carnivorous plant genus Sarracenia L. frequently hybridize, and all known hybrids are fertile. Despite being a desirable system for studying the evolutionary consequences of hybridization, the extent to which introgression occurs in the genus is limited to a few species in only two field sites. Previous phylogenomic analysis of Sarracenia estimated a highly resolved species tree from 199 nuclear genes, but revealed a plastid genome that is highly discordant with the species tree. Such cytonuclear discordance could be caused by chloroplast introgression (i.e. chloroplast capture) or incomplete lineage sorting (ILS). To better understand the extent to which introgression is occurring in Sarracenia, the chloroplast capture and ILS hypotheses were formally evaluated. Plastomes were assembled de-novo from sequencing reads generated from 17 individuals in addition to reads obtained from the previous study. Assemblies of 14 whole plastomes were generated and annotated, and the remaining fragmented assemblies were scaffolded to these whole-plastome assemblies. Coding sequence from 79 homologous genes were aligned and concatenated for maximum-likelihood phylogeny estimation. The plastome tree is extremely discordant with the published species tree. Plastome trees were simulated under the coalescent and tree distance from the species tree was calculated to generate a null distribution of discordance that is expected under ILS alone. A t-test rejected the null hypothesis that ILS could cause the level of discordance seen in the plastome tree, suggesting that chloroplast capture must be invoked to explain the discordance. Due to the extreme level of discordance in the plastome tree, it is likely that chloroplast capture has been common in the evolutionary history of Sarracenia.

Distribution of pinned distance trees in the plane [formula omitted

The recent result of Guth, Iosevich, Ou, and Wang (2019) on the Falconer distance problem states that for a compact set A⊂R2, if the Hausdorff dimension of A is greater than 54, then the distance set Δ(A) has positive Lebesgue measure. With a completely different approach, Murphy, Petridis, Pham, Rudnev, and Stevens (2022) proved the prime field version of this result, namely, for E⊂Fp2 with |E|≫p5/4, there exist many points x∈E such that the number of distinct distances from x is at least cp. The main purpose of this paper is to prove extensions in the more general structure of pinned trees. The case of distances on small sets will also be addressed in this paper.

Urban Green Development and Resilient Cities: A First Insight into Urban Forest Planning in Italy

The research proposes an application of a modification of the 3–30–300 rule to identify areas that require Urban Forestry implementation in small and medium-sized Roman and/or medieval urban areas. The selected case study is that of Asti in Piedmont, Italy. An open source, cross-platform desktop geographic information system is used to process geospatial datasets via qualitative analyses of electoral sections (or wards). An analysis of the number and distribution of trees around each building is performed, in addition to the calculation of tree canopy cover and distance between buildings and green spaces. Findings reveal that 64 out of 70 wards have an average of at least three trees per building and sufficient green areas of at least 0.5 hectares within 300 m of the buildings. Additionally, the tree canopy cover ranges from approximately 0.6% (lowest) to about 55% (highest) for the electoral sections. Lastly, findings suggest that the highly built-up urban fabric in these areas may significantly affect the availability and quality of green spaces. In conclusion, the case study proves the benefits of applying the 3–30–300 rule to small and medium-sized urban areas using an integrated assessment approach based on nature-based solutions and ecosystem services.

Surveyor and analyst biases in forest density estimation from United States Public Land Surveys

AbstractAccurate forest density estimates based on United States Public Land Surveys have long been questioned because of doubts about randomness of both the surveyors' selection of witness trees and the underlying tree dispersion. This study analyzes the surveyor sampling of witness trees in six Midwestern states in the mid‐1800s. It develops universal methods for identification, quantification, and correction of bias, and then calculation of unbiased density. Applying these techniques produces unbiased site‐specific densities before Euro‐American settlement, which are the essential baseline for determining historic changes in forest structure. Previous analysts used untested assumptions, inaccurate estimators, unknown or unrealistic sampling designs, and omitted or poorly corrected surveyor bias, resulting in hundreds of unreliable density estimates. The surveyors' recording of the empirical distance, bearing, and diameter of witness trees documented the exact sampling design. The intended design and deviation from it are investigated with a combination of descriptive statistics, probability theory, computer simulations, analogue geometric models, and modern stand conditions. Herein, analyst bias is eliminated using the robust Morisita II density estimator matching the predominant sampling design of two trees in opposing semicircles. Six widespread surveyor biases deviating from the nearest tree to the corner are evaluated. Quadrant bias and diameter bias for medium‐sized trees are subsumed under newly framed design and small tree biases. Two novel surveyor positional biases (pair angle and near‐post) are introduced here. Previously recognized azimuthal and species biases are analyzed with new techniques. Widely postulated surveyor bias for certain species was found to be minimal. Bias correction and density estimation are applied in detail over 68 townships in northern Wisconsin. The estimated historical forest density in northern Wisconsin, corrected for bias and small tree truncation, averaged 323 trees/ha ≥20 cm. Over 80 Midwestern subregions, surveyors bypassed an estimated 17% of the nearest trees due to their position, resulting in an average bias correction of +24% over the base density. If censored trees below a 20‐cm “veil‐line” are considered, the surveyors bypassed 48% of the nearest trees &gt;12.7 cm in diameter. This study resolves a 70‐year‐old conundrum of surveyor and analyst biases in historical density estimation.

Population structure and genetic diversity of rainbow trout (Oncorhynchus mykiss) broodstocks from Brazil using SNP markers

Rainbow trout (Oncorhynchus mykiss) are native to the Pacific Ocean coast of North America and the Kamchatka Peninsula of Russia. Brazilian populations of rainbow trout derive from various imports from European countries, the United States of America (U.S.A.) and Canada, from the 1950 s onwards. A total of 347 samples from nine commercial broodstock groups sampled from five farms in Brazil were genotyped with a panel of 96 SNPs to analyze the genetic diversity and structure of commercial rainbow trout farmed in Brazil. Pairwise coefficients of relatedness of individual animals and coefficients of genetic differentiation and inbreeding of broodstock groups were obtained, in addition to tests of genetic allocation of animals to their respective group. The mean observed and expected heterozygosities were 0.405 and 0.398, respectively. The total Fst was 0.172 and the pairwise Fst estimates considering all strains ranged from 0.036 to 0.338. The UPGMA genetic distance tree shows that broodstocks declared to be originally from Canada (Kamloops region) and from Northern California (Mount Shasta) are the most genetically distant from each other and from the remaining studied groups. Genetic structure analyses suggest a best value of K= 2, separating broodstock groups originally from the U.S.A. and Canada. Structure and Principal Component Analyses (PCA) indicate that the management practices of one of the farms was efficient in properly maintaining different broodstocks separated, while in another farm unwanted admixture has been occurring. Reclassification of these animals using Structure analysis results were corroborated with PCA and GeneClass2 analyses, providing evidence that advanced analyzes with low-density SNP data can be used to improve farm management practices and even correct past errors. The present study represents the first analysis of diversity and genetic structure of commercial rainbow trout farmed in Brazil using SNP markers.

DNA barcoding of recently diverging legume genera: Assessing the temperate Asian Caragana (Fabaceae: Papilionoideae)

AbstractObtaining reliable species identification of the legume genus Caragana has been challenging. Until now, species identification was mostly carried out utilizing diagnostic morphological characteristics, in addition to some successful applications of secondary chemical compounds. This study was designed to establish a DNA barcoding protocol enabling unambiguous identification of 238 accessions belonging to 67 species of Caragana. The performance of four DNA barcoding regions nrITS, trnH‐psbA, matK, and rbcL was explored using three analytical approaches, Pairwise Genetic Distance, Sequence Similarity and Phylogenetic Tree method. The chloroplast regions rbcL and matK showed lower discriminatory power compared with the nuclear region internal transcribed spacer (ITS) and the chloroplast region trnH‐psbA. The nrITS outperformed the other regions in the resolution rate. The present study brings forth an efficient barcode locus for Caragana. A barcode based either on a single‐locus nrITS or the combination of nrITS and trnH‐psbA was found to be most suitable for species discrimination with distinctive barcoding gaps. An attempt has also been made to resolve taxonomic issues in the Caragana opulens complex. DNA barcoding tools when complemented with alpha taxonomic evidence can aid in solving complex systematic problems, especially when taxa are characterized by overlapping traits, such as species belonging to the Fabaceae family.

The difficulty of aligning intrinsically disordered protein sequences as assessed by conservation and phylogeny.

Intrinsically disordered proteins (IDPs) are proteins that lack a stable 3D structure but maintain a biological function. It has been frequently suggested that IDPs are difficult to align because they tend to have fewer conserved residues compared to ordered proteins, but to our knowledge this has never been directly tested. To compare the alignments of ordered proteins to IDPs, their multiple sequence alignments (MSAs) were assessed using two different methods. The first compared the similarity between MSAs produced using the same sequences but created with Clustal Omega, MAFFT, and MUSCLE. The second assessed MSAs based on how well they recapitulated the species tree. These two methods measure the "correctness" of an MSA with two different approaches; the first method measures consistency while the second measures the underlying phylogenetic signal. Proteins that contained both regions of disorder and order were analyzed along with proteins that were fully disordered and fully ordered, using nucleotide, codon and peptide sequence alignments. We observed that IDPs had less similar MSAs than ordered proteins, which is most likely linked to the lower sequence conservation in IDPs. However, comparisons of tree distances found that trees from the ordered sequence MSAs were not significantly closer to the species tree than those inferred from disordered sequence MSAs. Our results show that it is correct to say that IDPs are difficult to align on the basis of MSA consistency, but that this does not equate with alignments being of poor quality when assessed by their ability to correctly infer a species tree.

Classification of ancient glassware based on K-means and decision trees

In this paper, the relation between the chemical composition of different types of glass objects was analyzed, and the differences between the chemical compositions were used to classify the glass objects, mainly by K-means, decision tree, and Euclidean distance analysis. For the classification of glass artifacts, this article analyzed the chemical composition of different types of glass artifacts and the changes of chemical composition before and after weathering, and then obtained the differences of chemical composition of different types of glass artifacts to obtain the classification law. The model was tested for reasonableness by giving the classification criteria, and the sensitivity of the model was determined by the change in the number of classification species K.The sensitivity of the model was analyzed by calculating the Euclidean distances between the object and the cluster centers, and the variance of the model by calculating the Euclidean distances between the object and the cluster centers before and after the weathering of the glass objects.

Identification and Characterization of Pseudomonas aeruginosa 16S rRNA Gene Isolated from Contaminated Soil With Oil Residues

Pseudomonas aeruginosa was isolated from fifty soil samples were collected from different sites of contaminated soil with oil residues in Ministry of science& technology. Morphological, biochemical tests and 16S rRNA genes sequencing was performed for bacterial isolates identification. Thirty (30) isolates of P. aeruginosa bacteria were confirmed according to morphological, biochemical tests. For molecular analysis, all isolates that tested positive for P. aeruginosa underwent amplification of the 16S rRNA gene using previously described primers that amplified a particular DNA fragment of 956 bp. PCR product was delivered to Macrogen Corporation - Korea for Sanger sequencing utilizing an automated DNA sequencer called the ABI3730XL. The results were emailed to us, and we used geneious software to analyze them. The investigation of phylogenetic relationships between different strains of Pseudomonas aeruginosa has frequently been conducted on the sequencing of the 16S rRNA gene region, which is a viable technique for species identification. To determine the degree of genetic similarity between the organisms, a distance tree was built. Consequently, gene sequencing of the 16S rRNA region was an appropriate method for isolating isolates at the molecular level. The a novel local strain of Ps. aeruginosa which isolated from contaminated soil with oil residues samples (MSZ. IRQ20) and we will registration of isolate in GenBank under accession number of MT832126.1. Distance Tree Using Blast Tool in the Geneious software.

MOLECULAR STUDY TO SOME FUNGI ISOLATED FROM PHONE COVER AND IT'S USERS

60 samples were randomly isolated 30 samples from the cover of a mobile phone and 30 samples from the finger of its users for people from the city of Mosul - Iraq, most of them are pioneers of life sciences, College of Science, University of Mosul, with a ratio of 15 females and 15 males of different ages, occupation, region, type of device, number of hours of use, and the last date taken. Washing the hands and the user's hand, right or left. The results showed that the cover of the mobile device of a female student in the Department of Life Sciences, College of Science, University of Mosul, at the age of 27 years, was contaminated with the fungus Chaetomium globosum, which grew on PDA medium.it was also noticed that the finger of the mobile device was contaminated by a female student in the Department of life Sciences College of sciences, University of Mosul,28 years old with The yeast Meyerozyma caribbica, and these two samples were recorded in the Gen Bank of the National Center for Biotechnology Information NCBI, the fungus was recorded as Chaetomium globosum B-M1 and given an identification number LC723824.1, while the yeast Meyerozyma caribbica was recorded as Meyerozyma caribbica B-M2 and with definition number is LC723825, .By studying the genetic distance and affinity tree of the fungus Chaetomium globosum B-M1 it was observed that it was identical (2.283), while the affinity ratio with the Chinese one was (2.582) and it was genetically far from the Iranian isolate by (2.852). As for the American isolate, there was genetic divergence with the Iraqi local isolate by (3326.), while it was found from the tree of distance and genetic affinity for the yeast Meyerozyma caribbica B-M2 that it was identical by ( 0.001) with its Japanese counterpart and was genetically far from the Australian isolate by (2.086) . As for the Italian and Dutch isolates there was a genetic divergence with the Iraqi local isolate by (2.304).

On the fractal patterns of language structures.

Natural Language Processing (NLP) makes use of Artificial Intelligence algorithms to extract meaningful information from unstructured texts, i.e., content that lacks metadata and cannot easily be indexed or mapped onto standard database fields. It has several applications, from sentiment analysis and text summary to automatic language translation. In this work, we use NLP to figure out similar structural linguistic patterns among several different languages. We apply the word2vec algorithm that creates a vector representation for the words in a multidimensional space that maintains the meaning relationship between the words. From a large corpus we built this vectorial representation in a 100-dimensional space for English, Portuguese, German, Spanish, Russian, French, Chinese, Japanese, Korean, Italian, Arabic, Hebrew, Basque, Dutch, Swedish, Finnish, and Estonian. Then, we calculated the fractal dimensions of the structure that represents each language. The structures are multi-fractals with two different dimensions that we use, in addition to the token-dictionary size rate of the languages, to represent the languages in a three-dimensional space. Finally, analyzing the distance among languages in this space, we conclude that the closeness there is tendentially related to the distance in the Phylogenetic tree that depicts the lines of evolutionary descent of the languages from a common ancestor.

Biological characterization of isolated pigeon Paramyxovirus-1 and its pathogenicity analysis in SPF chickens

Pigeon paramyxovirus type 1 (PPMV-1) is considered as an antigenic variant of Newcastle Disease leading to high mortality and significant economic losses to the poultry industry. However, the pathogenicity of PPMV-1 to chickens is still unclear. Herein, we reported the biological characterization of the isolated PPMV-1 from the diseased pigeons suspected to Newcastle Disease and studied its pathogenicity in SPF chickens. The phylogenetic tree and evolution distances revealed that the new isolate belonged to a VI.2.1.1.2.2 sub-genotype of NDV. Despite the cleavage motif of the F protein containing the 112RRQKR↓F117 sequence associated with virulent NDV strains, and the value of MDT and ICPI of the isolate showing mesogenic characteristics, the challenge trial showed that the isolate had weak pathogenicity to chickens while causing lesions in multiple tissues and organs in pigeons.

Plant phylogenetic relatedness and herbivore specialization interact to determine pest biocontrol efficiency in mixed plantations

Pest herbivory regulation is one of the key functions provided by diverse ecosystems, especially when compared to species depauperate agro-ecosystems and in the context of increased pest outbreaks due to global change. The dilution effect of host diversity on insect herbivory suggests that mixed plantations are feasible for regulating pest herbivory in agroecosystems. Dilution effect of increased plant diversity on insect herbivory has been widely observed, yet little is known about how it may change with plant phylogenetic relatedness and herbivore specialization, especially at the community level. Here, we compared herbivore richness, abundance, and degree of herbivory (i.e., the ratio of trees damaged by pest and total trees in a given area) among the two monocultures and the four mixed plantations in Wenchang city, Hainan Province, China. We also respectively assessed the effects of phylogenetically close or distant species on generalist and specialist herbivores in monocultures and mixture. We found that increasing the number of phylogenetically closely-related tree species could dilute generalist herbivore richness, abundance, and degree of herbivory but amplify specialist herbivore richness, abundance, and degree of herbivory. In contrast, increasing the number of phylogenetically distant tree species increased generalist herbivore richness, abundance, and degree of herbivory, while reducing specialist herbivore richness, abundance, and degree of herbivory. Our results suggest that plant phylogenetic relatedness and herbivore specialization can indeed interact to influence pest control efficiency when using mixed plantations to manage pest herbivory in agroecosystems. Thus, both herbivore specialization and plant phylogenetic relatedness should be taken into account in the management of agro-ecosystems and biodiversity conservation with respect to herbivory.