Bayesian Research Articles

Molecular identification of ecologically relevant hoverflies (Diptera, Syrphidae) from eastern India

Syrphid identification keys that cover all life cycle stages of the taxonomy are insufficient, and there are problems with the morphological identification of these flies. Cytochrome oxidase I (COI) is widely used for molecular identification and phylogenetic reconstruction. The study examined the effectiveness of COI in identifying 18 specimens containing 13 agriculturally important species of syrphids collected from different geo-climatic regions of West Bengal. Phylogenetic analysis was performed using Maximum Likelihood (ML) and Bayesian (BA) trees, which were almost congruent. Barcodes were generated for Dasysyrphus orsua and Eristalinus polychromata for the first time. This is the first study to use the COI for barcoding ecologically and agriculturally relevant syrphid flies from eastern India and their phylogeny. The findings contribute to the basic understanding of the diversity of syrphids across West Bengal and the molecular characterization of hoverflies, promoting their conservation and thus leading to the augmentation of crops.

Machine learning for accurate detection of small airway dysfunction-related respiratory changes: an observational study

BackgroundThe use of machine learning(ML) methods would improve the diagnosis of small airway dysfunction(SAD) in subjects with chronic respiratory symptoms and preserved pulmonary function(PPF). This paper evaluated the performance of several ML algorithms associated with the impulse oscillometry(IOS) analysis to aid in the diagnostic of respiratory changes in SAD. We also find out the best configuration for this task.MethodsIOS and spirometry were measured in 280 subjects, including a healthy control group (n = 78), a group with normal spirometry (n = 158) and a group with abnormal spirometry (n = 44). Various supervised machine learning (ML) algorithms and feature selection strategies were examined, such as Support Vector Machines (SVM), Random Forests (RF), Adaptive Boosting (ADABOOST), Navie Bayesian (BAYES), and K-Nearest Neighbors (KNN).ResultsThe first experiment of this study demonstrated that the best oscillometric parameter (BOP) was R5, with an AUC value of 0.642, when comparing a healthy control group(CG) with patients in the group without lung volume-defined SAD(PPFN). The AUC value of BOP in the control group was 0.769 compared with patients with spirometry defined SAD(PPFA) in the PPF population. In the second experiment, the ML technique was used. In CGvsPPFN, RF and ADABOOST had the best diagnostic results (AUC = 0.914, 0.915), with significantly higher accuracy compared to BOP (p < 0.01). In CGvsPPFA, RF and ADABOOST had the best diagnostic results (AUC = 0.951, 0.971) and significantly higher diagnostic accuracy (p < 0.01). In the third, fourth and fifth experiments, different feature selection techniques allowed us to find the best IOS parameters (R5, (R5-R20)/R5 and Fres). The results demonstrate that the performance of ADABOOST remained essentially unaltered following the application of the feature selector, whereas the diagnostic accuracy of the remaining four classifiers (RF, SVM, BAYES, and KNN) is marginally enhanced.ConclusionsIOS combined with ML algorithms provide a new method for diagnosing SAD in subjects with chronic respiratory symptoms and PPF. The present study’s findings provide evidence that this combination may help in the early diagnosis of respiratory changes in these patients.

Modicellaguangxiensis (Mortierellomycota, Mortierellaceae), a new species from south-western karst areas of China.

Modicella Kanouse (1936) is the only genus of Mortierellaceae known to produce macroscopic fruiting bodies in the form of small, whitish, round sporocarps. Specimens which belong to Modicella were collected during our field investigations in tropical karst areas of China. Based on morphological characteristics and phylogenetic analysis, a new species is introduced. Modicellaguangxiensis is described as a new species from tropical karst areas of China. The main distinguishing characteristics of M.guangxiensis are the number of sporangiospores per sporangium (11-18), the size of sporangiospores (14-34 × 12-27.5 μm) and the surface of some hyphae with hemispherical tuber. The phylogenetic analyses, based on the internal transcribed spacer (ITS) and the large subunit (LSU) regions of rDNA sequences using Bayesian (BA) and Maximum Likelihood (ML) methods showed that the new taxon is closely related to M.reniformis.

Parametric Bootstrap Confidence Interval Estimation for the Percentile and Difference between the Percentiles of Delta-Lognormal Distributions with Application to Rainfall Data in Thailand

In Thailand, flooding often occurs during the summer monsoon when many tropical storms affect the country. The motivation of this study was to plan for and mitigate the damage caused by flooding in the future. The confidence interval (CI) for the percentile of a precipitation dataset can be used to estimate the intensity of rainfall in a particular area whereas the CI for the difference between the percentiles of two datasets can be used to compare the rainfall intensities in two areas. To this end, the performances of several approaches to estimate the CI for the percentile and difference between the percentiles of delta-lognormal distributions were constructed and compared. These estimates were constructed based on the Bayesian (BS) and parametric bootstrap (PB) approaches, as well as two fiducial generalized confidence interval (FGCI) approaches. The performances of the methods were evaluated using Monte Carlo simulation, the results of which indicate that the PB approach for both CIs performed the best in all scenarios tested. Its suitability was confirmed via two illustrative examples using daily rainfall datasets for Chiang Mai and Lampang provinces in Thailand.

The Himalayan uplift and evolution of aquatic biodiversity across Asia: Snowtrout (Cyprininae: Schizothorax) as a test case.

Global biodiversity hotspots are often remote, tectonically active areas undergoing climatic fluctuations, such as the Himalaya Mountains and neighboring Qinghai-Tibetan Plateau (QTP). They provide biogeographic templates upon which endemic biodiversity can be mapped to infer diversification scenarios. Yet, this process can be somewhat opaque for the Himalaya, given substantial data gaps separating eastern and western regions. To help clarify, we evaluated phylogeographic and phylogenetic hypotheses for a widespread fish (Snowtrout: Cyprininae; Schizothorax) by sequencing 1,140 base pair of mtDNA cytochrome-b (cytb) from Central Himalaya samples (Nepal: N = 53; Bhutan: N = 19), augmented with 68 GenBank sequences (N = 60 Schizothorax/N = 8 outgroups). Genealogical relationships (N = 132) were analyzed via maximum likelihood (ML), Bayesian (BA), and haplotype network clustering, with clade divergence estimated via TimeTree. Snowtrout seemingly originated in Central Asia, dispersed across the QTP, then into Bhutan via southward-flowing tributaries of the east-flowing Yarlung-Tsangpo River (YLTR). Headwaters of five large Asian rivers provided dispersal corridors from Central into eastern/southeastern Asia. South of the Himalaya, the YLTR transitions into the Brahmaputra River, facilitating successive westward colonization of Himalayan drainages first in Bhutan, then Nepal, followed by far-western drainages subsequently captured by the (now) westward-flowing Indus River. Two distinct Bhutanese phylogenetic groups were recovered: Bhutan-1 (with three subclades) seemingly represents southward dispersal from the QTP; Bhutan-2 apparently illustrates northward colonization from the Lower Brahmaputra. The close phylogenetic/phylogeographic relationships between the Indus River (Pakistan) and western tributaries of the Upper Ganges (India/Nepal) potentially implicate an historic, now disjunct connection. Greater species-divergences occurred across rather than within-basins, suggesting vicariance as a driver. The Himalaya is a component of the Earth's largest glacial reservoir (i.e., the "third-pole") separate from the Arctic/Antarctic. Its unique aquatic biodiversity must be defined and conserved through broad, trans-national collaborations. Our study provides an initial baseline for this process.

E‐Bayesian estimation for the parameters and hazard function of Gompertz distribution based on progressively type‐II right censoring with application

AbstractE‐Bayesian inference is of incremental significance in the area related to the reliability of industrial products dealing with censored data sets. In this article, based on the progressive Type‐II right censored order statistics (PTIIRCOS), the E‐Bayesian estimates (E‐BE) for the parameters of Gompertz distribution (GD) and its hazard function are obtained and compared with the maximum likelihood (MLE) and Bayesian (BE) estimates. The squared error loss function (SE), linear‐exponential loss function (LINEX), and Al‐Bayyati loss function (ALB) are considered for the methods of BE and E‐BE. Some properties for the E‐BE estimates are discussed based on PTIIRCOS. Real data is established to clear the theoretical procedures. Akaike information criterion (AIC) is used to prove that GD is the best to model the data compared to other competitors and could potentially be very adequate in describing and modeling industrial products data. Finally, simulation study has been operated for comparing the E‐BEs with the MLEs and BEs.

‘Where is my family?’ Molecular and morphological data reveal the phylogenetic position and diversity of the enigmatic handsome fungus beetle genus Anamycetaea Strohecker, 1975 (Coleoptera, Coccinelloidea)

The genus Anamycetaea Strohecker, 1975, established for Anamycetaea keralae, a single species from India, was originally placed in the diverse endomychid subfamily Mycetaeinae and has subsequently been considered a member of the subfamily Anamorphinae based on closed mesocoxal cavities, a postulated synapomorphy of this group. Recent molecular research resulted in raising Anamorphinae to family level and revealed this group to be distantly related to Endomychidae sensu stricto. However, Anamycetaea has been ‘neglected’ since description. Our detailed study of this genus has been possible due to new material collected from Oriental and Australian regions. Striking overall similarity to the endomychine genus Tharina and a tentorium with anterior arms fused medially (separated in almost all Anamorphidae) have raised our doubts and led to further investigation of the phylogenetic placement of this enigmatic genus within Endomychidae sensu lato (handsome fungus beetles). Phylogenetic analyses of molecular and morphological datasets were conducted under Bayesian (BI), maximum likelihood (ML) and parsimony (MP) frameworks. Our results recovered Anamycetaea as belonging to the family Endomychidae, in the subfamily Endomychinae, distant from Anamorphidae. The close affinity to Stenotarsus and allies was strongly supported in all analyses. Based on material studied, A. keralae is described in detail here and includes description of previously unknown male genitalia. Four new species are also described, extending the ragne of the genus to the Australian region: Anamycetaea borneensis sp. nov. (from Borneo), A. novoguineensis sp. nov. and A. papuensis sp. nov. (from Papua New Guinea) and A. queenslandica sp. nov. (from Australia). Illustrations of morphological details and diagnoses are provided for each species. A key to the species of the genus is also presented. ZooBank: urn:lsid:zoobank.org:pub:90BAA954-7849-4FA9-997B-061FE7BB5702

Mitochondrial DNA and Distribution Modelling Evidenced the Lost Genetic Diversity and Wild-Residence of Star Tortoise, Geochelone elegans (Testudines: Testudinidae) in India.

The Indian star tortoise (Geochelone elegans) is a massively traded animal in South Asia. To mitigate this risk, the conservation agencies recommended guidelines to safeguard this charismatic species in nature. We adopted mitochondrial DNA-based investigation and performed species distribution modeling of G. elegans throughout its distribution range in the Indian subcontinent. The genetic analyses revealed weak genetic landscape shape interpolations, low intraspecific distances (0% to 1.5%) with mixed haplotype diversity, and a single molecular operational taxonomic unit (MOTU) in the cytochrome b gene dataset. The star tortoise, G. elegans, and its sister species Geochelone platynota showed a monophyletic clustering in the Bayesian (BA) phylogeny. We also attempt to understand the habitat suitability and quality of G. elegans in its distribution range. Our results suggest that, out of the extant area, only 56,495 km2 (9.90%) is suitable for this species, with regions of highest suitability in Sri Lanka. Comparative habitat quality estimation suggests the patch shape complexity and habitat fragmentation are greater in the western and southern ranges of India, which have been greatly influenced by an increased level of urbanization and agriculture practices. We have also provided a retrospect on the potential threat to G. elegans related to the wildlife trade on the regional and international spectrum. Our results detected multiple trading hubs and junctions overlying within the suitable ranges which need special attention in the vicinity. The present study calls for a proper conservation strategy to combat the fragmented distribution and explicitly recommends intensive genetic screening of founder individuals or isolated adult colonies, implementing scientific breeding, and subsequent wild release to restore the lost genetic diversity of star tortoises.

The resurrection of Cerasommatidiidae, an enigmatic group of coccinelloid beetles (Coleoptera: Coccinelloidea) based on molecular and morphological evidence

Abstract The family Cerasommatidiidae was proposed by Brèthes in 1925 for his new genus Cerasommatidia from Brazil, described as an intermediate taxon between Endomychidae and Coccinellidae (Coccinelloidea). This group was neglected for decades until 1994 when the resemblance of Cerasommatidia with the eupsilobiine genus Ibicarella was noticed, and Cerasommatidiidae was synonymized with Eupsilobiinae (Endomychidae). Based on the newly discovered material from the Neotropical and Afrotropical regions with clear resemblance to Cerasommatidia and Ibicarella, the phylogenetic placement of these taxa and new allied genera was reassessed based on phylogenetic analyses of molecular, morphological and combined datasets. The data were analysed under Bayesian (BI), maximum likelihood (ML) and parsimony (MP) frameworks. Our results support the restoration of Cerasommatidiidae as a distinct family in Coccinelloidea. Close affinity of Cerasommatidiidae with Coccinellidae, Eupsilobiidae and Mycetaeidae is recovered and the sister-relationship to Mycetaeidae is highly supported. Ibicarella is found to be a junior synonym of Cerasommatidia. Three new genera and six new species are described and illustrated: Yamuy gen. nov. (type species, Y. marginatus sp. nov.; and Y. constratus sp. nov.) and Karumbe gen. nov. (type species, K. geiseri sp. nov.; K. brethesi sp. nov. and K. pakaluki sp. nov.) from the Neotropics and Mahavelo gen. nov. (type species, M. madagasus sp. nov.) from Madagascar.

Effective differentiation between depressed patients and controls using discriminative eye movement features

BackgroundDepression is a common debilitating mental disorder caused by various factors. Identifying and diagnosing depression are challenging because the clinical evaluation of depression is mainly subjective, lacking objective and quantitative indicators. The present study investigated the value and significance of eye movement measurements in distinguishing depressed patients from controls. MethodsNinety-five depressed patients and sixty-nine healthy controls performed three eye movement tests, including fixation stability, free-viewing, and anti-saccade tests, and eleven eye movement indexes were obtained from these tests. The independent t-test was adopted for group comparisons, and multiple logistic regression analysis was employed to identify diagnostic biomarkers. Support vector machine (SVM), quadratic discriminant analysis (QDA), and Bayesian (BYS) algorithms were applied to build the classification models. ResultsDepressed patients exhibited eye movement anomalies, characterized by increased saccade amplitude in the fixation stability test; diminished saccade velocity in the anti-saccade test; and reduced saccade amplitude, shorter scan path length, lower saccade velocity, decreased dynamic range of pupil size, and lower pupil size ratio in the free-viewing test. Four features mentioned above entered the logistic regression equation. The classification accuracies of SVM, QDA, and BYS models reached 86.0%, 81.1%, and 83.5%, respectively. ConclusionsDepressed patients exhibited abnormalities across multiple tests of eye movements, assisting in differentiating depressed patients from healthy controls in a cost-effective and non-invasive manner.

Asproinocybaceae fam. nov. (Agaricales, Agaricomycetes) for Accommodating the Genera Asproinocybe and Tricholosporum, and Description of Asproinocybe sinensis and Tricholosporum guangxiense sp. nov.

Asproinocybe and Tricholosporum are not well known, and their placement at the family level remains undetermined. In this study, we conducted molecular phylogenetic analyses based on nuc rDNA internal transcribed spacer region (ITS) and nuc 28S rDNA (nrLSU), and a dataset with six molecular markers (ITS, LSU, RNA polymerase II largest subunit (RPB1), RNA polymerase II second largest subunit (RPB2), 18S nuclear small subunit ribosomal DNA (nrSSU), and translation elongation factor 1-alpha (TEF1-α)) using Bayesian (BA) and Maximum Likelihood (ML) methods, we found that the species of Asproinocybe and Tricholosporum formed an independent family-level clade (0.98/72). Asproinocybaceae fam. nov., a new family, is established here for accommodating this clade. Two new species, Asproinocybe sinensis and Tricholosporum guangxiense, from subtropical and tropical karst areas of China, are also described here.

Comparative Analysis of Mitogenomes among Five Species of Filchnerella (Orthoptera: Acridoidea: Pamphagidae) and Their Phylogenetic and Taxonomic Implications.

Simple SummaryFilchnerella belongs to Insecta, Orthoptera and Pamphagidae, of which there are 19 recorded species. The wings of Filchnerella are diverse, including three grasshopper wing types: longipennate, short wings and small wings. The previous studies of Filchnerella are more about the description of species morphology, and few about exploring the phylogenetic relationships with limited number of species and DNA fragments, which are insufficient to study the phylogeny of the entire genus, especially in order to understand the evolution of wing types in Filchnerella. To better understand the mitogenomic characteristics of Filchnerella and reveal its internal phylogenetic relationships, the complete mitochondrial genomes of Filchnerella sunanensis, Filchnerella amplivertica, Filchnerella dingxiensis, Filchnerella pamphagoides and Filchnerella nigritibia were sequenced and comparatively analyzed in this study. The mitogenomes of these five Filchnerella species were found to be highly conserved. Phylogenetic analyses, based on mitogenome data of 16 species of Pamphagidae, using both the maximum likelihood (ML) and Bayesian inference (BI) methods, supported the monophyly of Filchnerella and produced valuable data for the phylogenetic study of the genus.Mitogenomes have been widely used for exploring phylogenetic analysis and taxonomic diagnosis. In this study, the complete mitogenomes of five species of Filchnerella were sequenced, annotated and analyzed. Then, combined with other seven mitogenomes of Filchnerella and four of Pamphagidae, the phylogenetic relationships were reconstructed by maximum likelihood (ML) and Bayesian (BI) methods based on PCGs+rRNAs. The sizes of the five complete mitogenomes are Filchnerella sunanensis 15,656 bp, Filchnerella amplivertica 15,657 bp, Filchnerella nigritibia 15,661 bp, Filchnerella pamphagoides 15,661 bp and Filchnerella dingxiensis 15,666 bp. The nucleotide composition of mitogenomes is biased toward A+T. All tRNAs could be folded into the typical clover-leaf structure, except that tRNA Ser (AGN) lacked a dihydrouridine (DHU) arm. The phylogenetic relationships of Filchnerella species based on mitogenome data revealed a general pattern of wing evolution from long wing to increasingly shortened wing.

Plectania lutea (Sarcosomataceae), a new species from southwestern karst areas of China

Plectania lutea, is described as a new species from subtropical karst areas of China. The main distinguishing characteristics of P. lutea are the yellow hymenium, the external surface with ridges, the gelatinous but not semifluid medullary excipulum, and the large finely warted ascospores. The phylogenetic analyses based on internal transcribed spacer (ITS) and the large subunit (LSU) regions of rDNA sequences using Bayesian (BA) and Maximum Likelihood (ML) methods showed that the new taxon can be distinguished from phenotypically similar and phylogenetically related species.

Phylogenetic Relationships of Flounders from the Family Pleuronectidae (Ostichties: Pleuronectiformes) Based on 16S rRNA Gene

The systematics and phylogeny of flatfish is investigated on the basis of an incomplete nucleotide sequence of 16S rRNA and the complete Co-1 and Cyt-b sequences. In total 62 specimens of 14 species of our own collections were submitted to the GenBank/BOLD repositories and studied. Four types of gene trees were reconstructed: Bayesian (BA), maximum likelihood (ML), minimum evolution (ME), and neighbor joining (NJ). These trees showed basically similar topology. Two separate branches on the trees support the previously identified subfamilies Hippoglossoidinae and Pleuronectinae with the monophyletic status of these taxa. The subfamily Pleuronectinae can be considered monophyletic if the tribe Microstomini is excluded from it and genus Lepidopsetta is moved into the tribe Pleuronectini. Three sets of nucleotide sequences were formed and independently studied. One set included all the obtained 16S rRNA gene sequences (291 bp), the second set included a sample of longer 16S rRNA sequences (617 bp), and the third set consisted of three gene sequences: 16S rRNA, Co-1, and Cyt-b (2926 bp). All three data sets gave a similar phylogenetic signal, which is consistent with the traditional concept of the taxonomy of the Pleuronectiformes order; however, the second and third sets provided better resolution of topology.

The complete mitochondrial genome sequence of Oryctes rhinoceros (Coleoptera: Scarabaeidae) based on long-read nanopore sequencing.

BackgroundThe coconut rhinoceros beetle (CRB, Oryctes rhinoceros) is a severe and invasive pest of coconut and other palms throughout Asia and the Pacific. The biocontrol agent, Oryctes rhinoceros nudivirus (OrNV), has successfully suppressed O. rhinoceros populations for decades but new CRB invasions started appearing after 2007. A single-SNP variant within the mitochondrial cox1 gene is used to distinguish the recently-invading CRB-G lineage from other haplotypes, but the lack of mitogenome sequence for this species hinders further development of a molecular toolset for biosecurity and management programmes against CRB. Here we report the complete circular sequence and annotation for CRB mitogenome, generated to support such efforts.MethodsSequencing data were generated using long-read Nanopore technology from genomic DNA isolated from a CRB-G female. The mitogenome was assembled with Flye v.2.5, using the short-read Illumina sequences to remove homopolymers with Pilon, and annotated with MITOS. Independently-generated transcriptome data were used to assess the O. rhinoceros mitogenome annotation and transcription. The aligned sequences of 13 protein-coding genes (PCGs) (with degenerate third codon position) from O. rhinoceros, 13 other Scarabaeidae taxa and two outgroup taxa were used for the phylogenetic reconstruction with the Maximum likelihood (ML) approach in IQ-TREE and Bayesian (BI) approach in MrBayes.ResultsThe complete circular mitogenome of O. rhinoceros is 20,898 bp in length, with a gene content canonical for insects (13 PCGs, two rRNA genes, and 22 tRNA genes), as well as one structural variation (rearrangement of trnQ and trnI) and a long control region (6,204 bp). Transcription was detected across all 37 genes, and interestingly, within three domains in the control region. ML and BI phylogenies had the same topology, correctly grouping O. rhinoceros with one other Dynastinae taxon, and recovering the previously reported relationship among lineages in the Scarabaeidae. In silico PCR-RFLP analysis recovered the correct fragment set that is diagnostic for the CRB-G haplogroup. These results validate the high-quality of the O. rhinoceros mitogenome sequence and annotation.

Research on Bayesian fault diagnosis model of traditional Chinese medicine dry granulation based on failure model and effect analysis (FMEA)

This paper aims to construct a Bayesian(BN) fault diagnosis model of traditional Chinese medicine dry granulation based on the failure model and effect analysis(FMEA), effectively control risk factors and ensure the quality of granules.Firstly, the risk ana-lysis of dry granulation process was carried out with FMEA, and the selected medium and high risk factors were taken as node variables to establish corresponding BN network with causality.According to the mathematical reasoning method of probability theory, the model was accurately inferred and verified by Netica, and the granule nonconformance was used as the evidence for reversed reasoning to determine the most likely cause of the failure that affected the granule quality.The BN fault diagnosis model of traditional Chinese medicine dry gra-nulation was established based on the medium and high risk factors of process, prescription and equipment screened out by FMEA, such as roller pressure, raw material viscosity, clearance between rollers in the paper.The fault diagnosis of traditional Chinese medicine dry granulation process was then carried out according to the model, and the posterior probability of each node under the premise of nonconforming granule quality was obtained.This method could provide strong support for operators to quickly eliminate faults and make decisions, so as to improve the efficiency and accuracy for fault diagnosis and prediction, with innovation in its application.

Multi-algorithm based machine learning and structural pattern studies for hERG ion channel blockers mediated cardiotoxicity prediction

The development of novel bioactive molecules without hERG ion channel blocking activities is one of the important tasks for the drug discovery scientists. Both experimental and in silico techniques are applied for screening/assaying of novel molecules and existing molecules against hERG ion channel to study its cardiotoxicity. Hence, in the present investigation, QSAR and multialgorithm based classification analysis such as Random Forest (RF), Decision Tree (DT), Support Vector Machine (SVM) and Naive Bayesian (BN) were performed on the data set possessed hERG ion channel blocking activity using different variable (MOE-descriptors and MACCS Fingerprints). The models developed with the MLR and the machine learning techniques provided significant results which were confirmed by their acceptable statistical parameter values. Further, the sum of ranking differences (SRDs) calculated for the models showed that the Model 6-MOE, Model 7-MOE, Model 4-SVM, Model 7-SVM and Model 9-SVM are having smaller SRD values and are placed as top ranked models. The MOE-descriptors and the MACCS Fingerprints contributed in these models revealed that the volume-surface area properties, negative charge on the vdW surface area, number of fluorine atom, number of aromatic ring/atoms, less number of oxygen and hydrogen bonding and donor atoms are contributed for the activity. Furthermore the MACCS Fingerprints such as MACCSFP42, MACCSFP85, MACCSFP122 and MACCSFP139 also explain the polarity of the compounds. The structural pattern analysis with the MACCS Fingerprint revealed that the aromatic rings responsible for hydrophobicity, halogen and heteroatoms provide polarity to the compounds and the asymmetric carbon make the compounds are highly flexible. These studies concluded that the derived results can be used for prediction of hERG ion channel blocking activity of novel molecules.

LINEAR, GENERALIZED, HIERARCHICAL, BAYESIAN AND RANDOM REGRESSION MIXED MODELS IN GENETICS/GENOMICS IN PLANT BREEDING

This paper presents the state of the art of the statistical modelling as applied to plant breeding. Classes of inference, statistical models, estimation methods and model selection are emphasized in a practical way. Restricted Maximum Likelihood (REML), Hierarchical Maximum Likelihood (HIML) and Bayesian (BAYES) are highlighted. Distributions of data and effects, and dimension and structure of the models are considered for model selection and parameters estimation. Theory and practical examples referring to selection between models with different fixed effects factors are given using the Full Maximum Likelihood (FML). An analytical FML way of defining random or fixed effects is presented to avoid the subjective or conceptual usual definitions. Examples of the applications of the Hierarchical Maximum Likelihood/Hierarchical Generalized Best Linear Unbiased Prediction (HIML/HG-BLUP) procedure are also presented. Sample sizes for achieving high experimental quality and accuracy are indicated and simple interpretation of the estimates of key genetic parameters are given. Phenomics and genomics are approached. Maximum accuracy under the truest model is the key for achieving efficacy in plant breeding programs.

Chloroplast Genome Analysis of Two Medicinal Coelogyne spp. (Orchidaceae) Shed Light on the Genetic Information, Comparative Genomics, and Species Identification.

Although the medicinal properties of Coelogyne spp. have been previously studied, there is little genomic information providing a valuable tool for the plant taxonomy, conservation, and utilization of this genus. This study used the next-generation MiSeq sequencing platform to characterize the chloroplast (cp) genomes of Coelogyne fimbriata and Coelogyne ovalis. The Maximum Likelihood (ML) and Bayesian (BI) methods were employed to confirm the phylogenetic position of two Coelogyne species based on the whole chloroplast genome sequences. Additionally, we developed eight new primers based on the two cp genomes’ medium variable regions and evaluated the transferability to another 16 Coelogyne species. We constructed phylogenetic trees including 18 Coelogyne species and four outgroup species using the chloroplast fragments with the ML method. Our results showed that the cp genomes of C. fimbriata and C. ovalis contained a small single-copy region (18,839 and 18,851 bp, respectively) and a large single-copy region (87,606 and 87,759 bp, respectively), separated by two same-length inverted-repeat regions (26,675 bp in C. fimbriata and 26,715 bp C. ovalis, respectively). They all contained 86 protein-coding genes, 38 tRNA genes, and eight rRNA genes, revealing strong structure and gene content similarities. The phylogenetic analysis indicated a close relationship between the genera Coelogyne and Pleione. The newly developed primers revealed good transferability among the Coelogyne taxa and provided enough variable sites to distinguish C. fimbriata and C. ovalis. The two complete cp genomes and the eight new primers of Coelogyne provide new genomic data for further studies on phylogenomics, population genetics, and evolutionary history of Coelogyne taxa.

Comparative analysis of mitogenomes among three species of Haplotropidini grasshoppers and a new species of the genus Sulcotropis (Orthoptera: Acridoidea: Pamphagidae) from China.

The complete mitochondrial genomes of three species of Haplotropidini were sequenced, annotated and analyzed. Then, combined with 18 species mitogenomes of Acridoidea and 1 species of Tridactyloidea, the phylogenetic relationships were reconstructed by maximum likelihood (ML) and Bayesian (BI) methods based on PCGs. The phylogenetic relationship tree showing that Sulcotropis Yin et Chou is a valid genus and not a synonym of Haplotropis Saussure, 1888. A new species Sulcotropis xiaowutaiensis sp. nov. is described in this paper from China, it is allied to Sulcotropis cyanipes Yin et Chou, 1979, but differs from latter by median carina of pronotum cut by posterior transverse sulcus slightly, epiphallus with middle part equal both sides in high, cercus of male gradually widened at base, interspace of mesosternum narrowed in the base slightly and subgenital plate of female oblong, hind margin with small acute angle in the middle. Type specimens are deposited in the College of Life Sciences, Hebei University, Baoding, Hebei, China.