Population Structure and Phylogeny of Some U.S. Peach Cultivars

Peach (Prunus persica) cultivars maintained at the U.S. Department of Agriculture program at Byron, GA, have never been characterized with any molecular markers. In this study, 20 microsatellite markers were used to genotype 112 cultivars and the data were analyzed to discern their population structure and phylogenetic relationships. STRUCTURE simulations revealed four K clusters and broad genetic admixture among the cultivars. Principal coordinate analysis (PCoA) showed the cultivar groups from western, northeastern, and southeastern U.S. states were adjacent to each other except cultivars from Michigan (close to most southeastern state groups) and Florida (most distant from the other groups). Principal component analysis (PCA) showed that these cultivars had no obvious PCA partitioning boundaries. The intertwined distribution in both PCoA and PCA partitions suggested many of them were genetically closely related to each other largely because most shared same ancestral parentages. Most pairwise distance means within and between the cultivar groups were relatively low, suggesting close phylogenetic relations among those cultivars, as were demonstrated in the phylogenetic tree. Limiting factors and perspectives relevant to peach breeding are discussed.

Acanthosaura meridiona sp. nov. (Squamata: Agamidae), a new short-horned lizard from southern Thailand

A new short – horned lizard species of the genus Acanthosaura from southern Thailand, is described herein. The species was previously recognised as Acanthosaura crucigera and has been reported to present a wide distribution across mainland south-east Asia. The combination of modern morphological studies of Acanthosaura meridiona sp. nov. allows its separation from closely related species A. crucigera, on the basis of presenting more nuchal scales, more scales between diastema, more scales bordering rostral scales and more midline ventral scales. Mitochondrial DNA analysis also indicated a sister relationship between A. meridiona sp. nov. and A. crucigera with a 100 % probability according to Bayesian and maximum – likelihood analyses. The pairwise distance between A. meridiona sp. nov. and A. crucigera ranges from 9.9 – 11.1 %, while the distance between A. meridiona populations ranges from 0 – 0.9 %. This new discovery contributes to the redescription of the distribution of A. crucigera under Kra Isthmus and its replacement by A. meridiona sp. nov.

Mobile Data-Mule Optimal Path Planning for Wireless Sensor Networks

This article is concerned with collecting stored sensor data from a static Wireless Sensor Network utilizing a group of mobile robots that act as data mules. In this scenario, the static sensor nodes’ locations are known a priori, and the overall optimization problem is formulated as a variation of the Traveling Salesman Subset-tour Problem (TSSP). The constraints that are taken into account include: (a) the pairwise distance between static nodes, (b) the maximum time interval between consecutive visits of each static node, (c) the service time that is required for the collection of the sensor data from the mobile element that visits this sensor node, and (d) the energy efficiency for the mobile nodes. The optimal mobile robot paths are computed using an enhanced Mobile Element Scheduling scheme. This scheme extracts the sequential paths of the mobile elements in an attempt to eliminate any sensor data loss.

Single-Molecule Clustering for Super-Resolution Optical Fluorescence Microscopy

Molecular assembly in a complex cellular environment is vital for understanding underlying biological mechanisms. Biophysical parameters (such as single-molecule cluster density, cluster-area, pairwise distance, and number of molecules per cluster) related to molecular clusters directly associate with the physiological state (healthy/diseased) of a cell. Using super-resolution imaging along with powerful clustering methods (K-means, Gaussian mixture, and point clustering), we estimated these critical biophysical parameters associated with dense and sparse molecular clusters. We investigated Hemaglutinin (HA) molecules in an Influenza type A disease model. Subsequently, clustering parameters were estimated for transfected NIH3T3 cells. Investigations on test sample (randomly generated clusters) and NIH3T3 cells (expressing Dendra2-Hemaglutinin (Dendra2-HA) photoactivable molecules) show a significant disparity among the existing clustering techniques. It is observed that a single method is inadequate for estimating all relevant biophysical parameters accurately. Thus, a multimodel approach is necessary in order to characterize molecular clusters and determine critical parameters. The proposed study involving optical system development, photoactivable sample synthesis, and advanced clustering methods may facilitate a better understanding of single molecular clusters. Potential applications are in the emerging field of cell biology, biophysics, and fluorescence imaging.

A new species of the Gekko japonicus group (Squamata: Gekkonidae) from Khammouane Province, central Laos

A new species of the Gekko (Japonigekko) japonicus group from Khammouane Province, central Laos is described based on morphological characters and molecular evidence. Morphologically, Gekko khunkhamensis sp. nov. can be distinguished from the remaining congeners by a combination of the following characters: size moderate (SVL 69.7–75.2 mm); nares in contact with rostral; internasals absent; postmentals enlarged; interorbital scales between anterior corners of the eyes 31 or 32; dorsal tubercles absent; ventrals between mental and cloacal slit 181–185; midbody scales 127–138; ventral scales 42–45; subdigital lamellae on first toe 13 or 14, on fourth toe 14 or 15; tubercles on upper surface of fore and hind limbs absent; precloacal pores absent in the male and females; postcloacal tubercles 2; tubercles absent on dorsal surface of tail base; subcaudals distinctly enlarged; dorsal surface of body with five dark grey bands, which become irregular posteriorly. Genetically, the new species is placed in a clade, consisting of G. bonkowskii, G. nadenensis, G. scientiadventura, G. sengchanthavongi, and G. thakhekensis and differs from other congeners by at least 13% in terms of pairwise distance based on a fragment of the mitochondrial ND2 gene.

Incongruent molecular and morphological variation in the crab spider Synema globosum (Araneae, Thomisidae) in Europe

Establishing species boundaries is one of the challenges taxonomists around the world have been tackling for centuries. The relation between intraspecific and interspecific variability is still under discussion and in many taxa it remains understudied. Here the hypothesis of single versus multiple species of the crab spider Synema globosum (Fabricius) is tested. The wide distribution range as well as its high morphological variability makes this species an interesting candidate for re-evaluation using an integrative approach. This study combines information from barcoding, phylogenetic reconstruction based on mitochondrial CO1 and ITS2 of more than 60 specimens collected over a wide range of European localities, and morphology. The findings show deep clades with up to 6% mean pairwise distance in the CO1 barcode without any biogeographical pattern. The nuclear ITS2 gene did not support the CO1 clades. Morphological assessment of somatic and genital characters in males and females and a morphometric analysis of the male palp uncovered high intraspecific variation that does not match the CO1 or ITS2 phylogenies or biogeography either. Screening for endosymbiotic Wolbachia bacteria was conducted and only a single infected specimen was found. Several scenarios might explain these inconsistent patterns. While the deep divergences in the barcoding marker might suggest cryptic or ongoing speciation or geographical isolation in the past, the lack of congruent variation in the nuclear ITS2 gene or the studied morphological character systems, especially the male palp, indicates that S. globosum might simply be highly polymorphic both in terms of its mtDNA and morphology. Therefore, more data on ecology and behaviour and full genome sequences are necessary to ultimately resolve this taxonomically intriguing case.

Reconstructing mitochondrial genomes from ancient DNA through iterative mapping: an evaluation of software, parameters, and bait reference

(1) Within evolutionary biology, mitochondrial genomes (mitogenomes) provide useful insights at both population and species level. Several approaches are available to assemble mitogenomes. However, most are not suitable for divergent, extinct species, due to the requirement of a reference mitogenome from a conspecific or close relative, and relatively high-quality DNA. (2) Iterative mapping can overcome the lack of a close reference sequence, and has been applied to an array of extinct species. Despite its widespread use, the accuracy of the reconstructed assemblies are yet to be comprehensively assessed. Here, we investigated the influence of mapping software (BWA or MITObim), parameters, and bait reference phylogenetic distance on the accuracy of the reconstructed assembly using two simulated datasets: (i) spotted hyena and various mammalian bait references, and (ii) southern cassowary and various avian bait references. Specifically, we assessed the accuracy of results through pairwise distance (PWD) to the reference conspecific mitogenome, number of incorrectly inserted base pairs (bp), and total length of the reconstructed assembly. (3) We found large discrepancies in the accuracy of reconstructed assemblies using different mapping software, parameters, and bait references. PWD to the reference conspecific mitogenome, which reflected the level of incorrect base calls, was consistently higher with BWA than MITObim. The same was observed for the number of incorrectly inserted bp. In contrast, the total sequence length was lower. Overall, the most accurate results were obtained with MITObim using mismatch values of 3 or 5, and the phylogenetically closest bait reference sequence. Accuracy could be further improved by combining results from multiple bait references. (4) We present the first comprehensive investigation of how mapping software, parameters, and bait reference influence mitogenome reconstruction from ancient DNA through iterative mapping. Our study provides information on how mitogenomes are best reconstructed from divergent, short-read data. By obtaining the most accurate reconstruction possible, one can be more confident as to the reliability of downstream analyses, and the evolutionary inferences made from them.

Hepatitis C subtyping assay failure in UK patients born in Sub-Saharan Africa: implications for global treatment and elimination

The newly developed direct-acting antivirals (DAAs) have revolutionised the treatment of chronic hepatitis C virus (HCV), where cohort studies have shown that cure rates as high as 98% can be achieved. Whilst genome sequencing has demonstrated that some subtypes of HCV naturally harbour drug resistance associated substitutions (RAS), these have not been considered important as previous molecular epidemiological studies have suggested that such difficult-to-treat subtypes are rare. Therefore, to optimise and streamline molecular detection and sequence-based typing of diverse RAS-containing subtypes, a novel panel of single round PCR assays was applied to HCV derived from 146 individuals, whose likely source of infection was from regions of sub-Saharan Africa (SSA). Partial NS5A and NS5B sequences were obtained from 135 HCV-positive patients born in 19 different countries from SSA but attending clinics in the UK. Virus subtype assignments were determined by pairwise-distance analysis and compared to both diagnostic laboratory assignments and free-to-use online typing tools. We determined that routine clinical diagnostic methods incorrectly subtyped 59.0% of samples, with a further 6.8% incorrectly genotyped. Of five commonly used online tools, Geno2Pheno performed most effectively in determining a subtype in agreement with pairwise distance analysis. Considering the estimated number of HCV infections to have occurred in across Africa, this study provides a simple low-cost pathway to guide regional therapeutic choice and assist global eradication programmes.

Putative novel avian paramyxoviruses identified from wild bird surveillance (United States, 2016?2018) and retrospective analysis of APMV-2s and APMV-6s in GenBank

Avian paramyxoviruses (APMVs) (subfamily Avulavirinae) have been isolated from over 200 species of wild and domestic birds from around the world. The International Committee on Taxonomy of Viruses (ICTV) currently defines 22 different APMV species, with Avian orthoavulavirus 1 (whose viruses are designated as APMV-1) being the most frequently studied due to its economic burden to the poultry industry. Less is known about other APMV species, including limited knowledge on the genetic diversity in wild birds and there is a paucity of public whole genome sequences for APMV-2 to -22. The goal of this study was to use MinION sequencing to genetically characterize APMVs isolated from wild bird swab samples collected during 2016–2018 in the United States. Multiplexed MinION libraries were prepared using a random strand-switching approach using 37 egg-cultured, influenza-negative, hemagglutination-positive samples. Thirty-five APMV isolates that had complete polymerase coding sequences were speciated using ICTV’s current Paramyxoviridae phylogenetic methodology. Viruses from APMV-1, -4, -6, -8 were classified, one putative novel species (Avian orthoavulavirus 23) was identified from viruses isolated in this study, two putative new APMV species (Avian metaavulavirus 24 and 27) were identified from viruses isolated in this study and from retrospective GenBank sequences, and two putative new APMV species (Avian metaavulavirus 25 and 26) were identified solely from retrospective GenBank sequences. Furthermore, co-infections of APMVs were identified in a subset of the samples. The potential limitations of the branch length being the only speciation criterion and the potential benefit of a group pairwise distance analysis are discussed.

Estimation of linkage disequilibrium levels and allele frequency distribution in crossbred Vrindavani cattle using 50K SNP data

The objective of this study was to calculate the extent and decay of linkage disequilibrium (LD) in 96 crossbred Vrindavani cattle genotyped with Bovine SNP50K Bead Chip. After filtering, 43,821 SNPs were retained for final analysis, across 2500.3 Mb of autosome. A significant percentage of SNPs was having minor allele frequency of less than 0.20. The extent of LD between autosomal SNPs up to 10 Mb apart across the genome was measured using r2 statistic. The mean r2 value was 0.43, if pairwise distance of marker was less than10 kb and it decreased further to 0.21 for 25–50 kb markers distance. Further, the effect of minor allele frequency and sample size on LD estimate was investigated. The LD value decreased with the increase in inter-marker distance, and increased with the increase of minor allelic frequency. The estimated inbreeding coefficient and effective population size were 0.04, and 46 for present generation, which indicated small and unstable population of Vrindavani cattle. These findings suggested that a denser or breed specific SNP panel would be required to cover all genome of Vrindavani cattle for genome wide association studies (GWAS).