Parsimonious Phylogenetic Tree Research Articles

First Report of a New Species, Chrysofolia galloides sp. nov., Causing Black Spots on Gallnuts of Rhus punjabensis var. sinica in China

In June 2021 and 2022, 30-40% ensiform galls of Rhus punjabensis var. sinica (Diels) Rehd. et Wils. showing similar black spots were observed at a same woodland in Zhuyu town (E 107"42', N 32"10', altitude 560 m), Wanyuan, Southwest China. The lesions were usually dotted, rounded to irregular black or blackish brown spots, and scattered to gather into patches on the gall surfaces; the central areas of the lesions were often depressed. The infected galls often grow slowly or even fall off early. Fresh symptomatic galls were randomly collected in June 2021 (9 galls) and 2022 (13 galls). Tissues from the infected galls (ca. 3×5 mm) were surface-disinfected by 75% ethyl alcohol and 10% sodium hypochlorite (NaOCl), then plated on potato dextrose agar (PDA) at 25°C in the dark for six days. Nine isolates from different galls showed similar colony morphology. Similar dominant fungal colonies were isolated from 44.0% and 38.5% of the infected galls in 2021 and 2022, respectively. After sub-culturing of hyphal tips on PDA and oat meal agar (OA)，the colonies showed cottony-felty, annular, whitish to grey-brown after 10 days. Four isolates, IFRDCC1022 and IFRDCC1023 from 2021, and IFRDCC1024 and IFRDCC1025 from 2022 were randomly selected for molecular and morphological evaluations. Selected isolates were cultured on OA and incubated at 21°C at a 12 h/12 h day/night regime to induce sporulation (Jiang et al. 2020). Pycnidia (up to 500 µm diam.) developed within six days or longer. Conidiogenous cells lined the inner cavity of base, which were hyaline, occasionally brownish, ampulliform, 6-12 × 2-4.5 µm. Conidia were solitary, hyaline, guttulate, elliptic, sometimes subcylindric or ovoid, straight to curved, aseptate, (3.5-) 4-6.5 (-8) × 2-3.5 (-4) µm (n=60). Respective DNA fragments were amplified and sequenced with primers ITS1/ITS4 for ITS, LR0R/LR5 for LSU, EF1-728F (Carbone and Kohn 1999) /EF-2 (O’Donnell et al. 1998) for tef1-α, and Bt2a/ Bt2b for tub2 (Glass and Donaldson 1995). The obtained sequences were deposited in GenBank (accession Nos. ITS: OR363211 - OR363214, LSU: OR363215 - OR363218, tef1-α: OR344509 - OR344512, and tub2: OR344513 - OR344516). The morphological characteristics of the new isolates were consistent with the genus Chrysofolia (Crous et al. 2015). The conidiogenous cells (6-12 × 2-4.5 µm) are larger than those of C. colombiana Crous, Rodas & M.J. Wingf. 2015 (5–8 × 2–3 μm) and C. barringtoniae Suwannar., Kumla & Lumyong 2016 (3–7.5 × 2–3 μm), while shorter and wider than those of C. coriariae S.Y. Wang, Yong Wang bis, and Y. Li 2022 (5–20 × 1–3.5 μm). Maximum likelihood (ML), Maximum parsimony (MP) and Bayesian phylogenetic trees generated from the datasets all showed similar topologies, four strains formed a well-supported clade (BS = 99-100%, PP=0.99-1) in Chrysofolia genus, and clearly separated from the other three Chrysofolia spp. and clustered as sister to C. coriariae with high supported values (BS = 97-100%, PP=0.97-1). Based on morphological characteristics and DNA phylogeny, the new isolates were described as a new species, Chrysofolia galloides T. Ma & Z. X. Yang, sp. nov. (Mycobank: MB850312). The two isolates from 2021 (IFRDCC1022 and IFRDCC1023) were randomly selected for pathogenicity tests. Mycelial plugs (ca. 6×6 mm) of a two-week-old colony were placed onto the surface of wounded and unwounded healthy ensiform galls with six or seven replicates. Sterile PDA agar plugs were used as controls. The inoculated galls were incubated at 25°C in sterile plastic containers (21.4×14.0×5.0 cm) lined with wet filter paper for high humidity. The typical symptom appeared within 3 days on 83.3-100% wounded galls, while the unwounded galls and the controls remained asymptomatic. All wounded galls and 20.0-85.7% of unwounded galls showed symptoms within 5 days, while the controls remained asymptomatic. The fungus was reisolated from the lesions and showed identical morphology and 100% sequence similarity of ITS, LSU, tef1-α and tub2 with the initial isolates. No fungus was isolated from the controls. Neofusicoccum parvum is the first fungal pathogen demonstrated to induce brown spots on Chinese gallnuts (Ma and Yang 2022). Therefore, C. galloides is the second fungus confirmed to cause black spots lesions on gallnuts. These findings provide foundations for the comprehensive management of gall production, which have significant economical implication for Chinese gallnut production.

Bioactivity Features of Novel Actinobacteria Isolated from Lichen and Orchid Plant

A total of 10 actinobacterial strains were isolated from a lichen and an orchid species by employing a selective isolation procedure for actinobacteria. Antimicrobial activities of the isolates were evaluated against Aspergillus niger ATCC 16404, Candida albicans ATCC 10231, Enterococcus faecalis ATCC 29212, Bacillus subtilis ATCC 6633, Escherichia coli ATCC 25922, Klebsiella pneumoniae ATCC 700603, Pseudomonas aeroginosa ATCC 27853, Salmonella enterica ATCC 13311, Staphylococcus aureus ATCC 29213 and Listeria monocytogenes NCTC 5348. Out of the 10 isolates, eight showed antimicrobial activity against at least one pathogen. For molecular identification of the strains, 16S rRNA gene sequence analysis was performed. The pairwise comparison of the 16S rRNA gene sequences of the strains with the databases showed that the strains are members of the genus Streptomyces by sharing 98.9 – 100% gene sequence similarities. Phylogenetic relationships of the strains within the genus Streptomyces were revealed by maximum likelihood and maximum parsimony phylogenetic trees. The results revealed that unexplored environmental habitats like lichens and plant tissues may represent a potential reservoir for novel actinobacteria with promising bioactivity features.

Occurrence of leaf rust disease in Oxalis triangularis caused by Puccinia oxalidis in Valdivia, Chile.

False shamrock (Oxalis triangularis), native to South America, is an ornamental and popular plant bulb, commercialized for their attractive shape and color (purple triangular leaves) (Taha et al., 2013). In Chile, a rust was detected in O. triangularis plants growing from April to June in several gardens (n=10) in the city of Valdivia, estimating a disease incidence between 80 and 100%. The symptoms appeared as diffuse chlorotic spots from the upperside of leaves, where infected tissues eventually become completely necrotic, and yellow rust pustules were observed on the underside of leaves. Severe symptoms on infected leaves were consistently observed, showing necrosis on entire leaves. Symptomatic plants (n=50) were collected, and three representative isolates from different localities (OX1, OX2, and OX3) were used for morphological and genetic identification. Uredinia (n=20) were hypophyllous, erumpent, yellow, and irregularly distributed, with sizes from 340 to 850 μm in diameter. Urediniospores (n=150) were yellow, subglobose to globose, equinulate, with measures of 14.2 - 17.7 x 14.7 - 17.2 µm. Teliospores were absent. Based on morphological characters, this rust was identified as a Puccinia sp. These morphological characteristics coincided with those indicated by Šafránková (2014), Abbasi et al. (2018), and Khouader et al. (2018). To classify this rust genetically, sequences analyses were performed using the ITS region of the rDNA (ITS4/ITS5) (White et al., 1990). The DNA was extracted using a commercial kit. The results indicated 99% similarity with two reference sequences of P. oxalidis (MH325473 and MH325474) available at GenBank (NCBI http://www.ncbi.nlm.nih.gov/BLAST/). The sequences obtained were deposited in GenBank (ON259085 to ON259087). Based on the maximum parsimony phylogenetic tree, the sequences of Chilean isolates were clustered with those of P. oxalidis references. Pathogenicity tests were conducted using three isolates (OX1 to OX3). Surface disinfection of leaves of O. triangularis (n=36 plants), were performed by spraying 1% NaOCl solution for 1 min. Subsequently, 2 mL of urediniospores suspensions of each isolate (OX1 to OX3) at a concentration of 106 urediniospores/mL, were sprayed with an atomizer on the underside of the leaves of all plants. Urediniospores were obtained following the methodology proposed by Ferrada et al. (2020). Control leaves were disinfested and inoculated with sterile distilled water. Plants of O. triangularis of 90-day-old were incubated in a humid chamber (24°C, 80% HR), with a photoperiod of 12 light /12 dark. At 11 days post-inoculation, all leaves inoculated developed chlorosis spots and pulverulent pustules (averaged 10.9 to 25.4 pustules per leaf), and then at 26 days post-inoculation, affected leaves showed necrotic tissues. The identity of these isolates was confirmed morphologically. The symptoms in the control leaves were negative. To our knowledge, this is the first report of multiple occurrences of the leaf rust disease on gardens of false shamrock caused by P. oxalidis in Valdivia, south of Chile. Previously, P. oxalidis has been reported to cause leaf rust disease in O. triangularis in the Czech Republic (Šafránková, 2014) and O. debilis in Korea (Lee et al., 2018). The leaf rust disease could represent a threat to the ornamental gardens of O. triangularis in Valdivia. Currently, epidemiological studies of leaf rust disease are necessary to develop management strategies in gardens of O. triangularis.

Molecular Characterization of Dehydrin in Azraq Saltbush among Related Atriplex Species

Atriplex spp. (saltbush) is known to survive extremely harsh environmental stresses such as salinity and drought. It mitigates such conditions based on specialized physiological and biochemical characteristics. Dehydrin genes (DHNs) are considered major players in this adaptation. In this study, a novel DHN gene from Azrak (Jordan) saltbush was characterized along with other Atriplex species from diverse habitats. Intronless DHN-expressed sequence tags (495-761 bp) were successfully cloned and sequenced. Saltbush dehydrins contain one S-segment followed by three K-segments: an arrangement called SK3-type. Two substantial insertions were detected including three copies of the K2-segemnet in A. canescens. New motif variants other than the six-serine standard were evident in the S-segment. AhaDHN1 (A. halimus) has a cysteine residue (SSCSSS), while AgaDHN1 (A. gardneri var. utahensis) has an isoleucine residue (SISSSS). In contrast to the conserved K1-segment, both the K2- and K3-segment showed several substitutions, particularly in AnuDHN1 (A. nummularia). In addition, a parsimony phylogenetic tree based on homologs from related genera was constructed. The phylogenetic tree resolved DHNs for all of the investigated Atriplex species in a superclade with an 85% bootstrap value. Nonetheless, the DHN isolated from Azraq saltbush was uniquely subclustred with a related genera Halimione portulacoides. The characterized DHNs revealed tremendous diversification among the Atriplex species, which opens a new venue for their functional analysis.

A Thermococci-to-Clostridia Pathway for the Evolution of the Bacteria Domain

With the identification of an archaeal Last Universal Common Ancestor (LUCA) related to the archaeon Methanopyrus, the origin of Bacteria became a choice between autonomic development versus descent from Archaea. The similarity bitscores between paralogous valyl-tRNA synthetase (VARS) and isoleucyl-tRNA synthetase (IARS) suggest that the five oldest bacteria were Mahella australiensis, Thermincola potens, Halobacteroides halobius, Desulfosporosinus orientis and Caldicellulosiruptor lactoaceticus, which were all Clostridia species and hydrogen producers. A search for archaea that could be a candidate Progenitor of Bacteria endowed with an Emden-Myerhof-Parnas type glycolytic pathway and a clostridial-like dark-fermentation mechanism for generating hydrogen pointed to such a role for the anaerobic chemoorganotroph Thermococci, which were known to engage in rapid evolutionary changes at high-biodiversity sites abundant in sugars and other small molecular substrates, and constituted together with Clostridia the two most powerful microbial generators of hydrogen. Moreover, two-domain maximum-likelihood and maximum- parsimony phylogenetic trees for VARS showed that Thermococci and Clostridia formed sister clades on both trees, and close similarity was evident between their VARS sequences, which were consistent with kinship between them. On this basis, it was proposed that the Bacteria domain emerged from a thermocococal or thermococcal-like Progenitor of Bacteria possibly at some high-biodiversity site, through the formation of a Thermincola-proximal Last Bacterial Common Ancestor (LBCA).

A comparison of gene organisations and phylogenetic relationships of all 22 squamate species listed in South Korea using complete mitochondrial DNA.

Studies using complete mitochondrial genome data have the potential to increase our understanding on gene organisations and evolutionary species relationships. In this study, we compared complete mitochondrial genomes between all 22 squamate species listed in South Korea. In addition, we constructed Maximum Parsimony (MP), Maximum Likelihood (ML) and Bayesian Inference (BI) phylogenetic trees using 13 mitochondrial protein-coding genes. The mitochondrial genes for all six species in the suborder Sauria followed the same organisation as the sequenced Testudines (turtle) outgroup. In contrast, 16 snake species in the suborder Serpentes contained some gene organisational variations. For example, all snake species contained a second control region (CR2), while three species in the family Viperidae had a translocated tRNA-Pro gene region. In addition, the snake species, Elapheschrenckii, carried a tRNA-Pro pseudogene. We were also able to identify a translocation of a tRNA-Asn gene within the five tRNA (WANCY gene region) gene clusters for two true sea snake species in the subfamily Hydrophiinae. Our BI phylogenetic tree was also well fitted against currently known Korean squamate phylogenetic trees, where each family and genus unit forms monophyletic clades and the suborder Sauria is paraphyletic to the suborder Serpentes. Our results may form the basis for future northeast Asian squamate phylogenetic studies.

A taxonomic revision of Northeast Pacific softnose skates (Rajiformes: Arhynchobatidae: Bathyraja Ishiyama)

Softnose skates (Rajiformes: Arhynchobatidae: Bathyraja Ishiyama) are the most diverse skate genus, with 54 species, and are readily distinguishable from other genera in the family by their poorly calcified, flexible rostral cartilages. Six Bathyraja species are considered valid in the eastern North Pacific, including: B. abyssicola, B. aleutica, B. kincaidii, microtrachys, B. spinosissima, and B. trachura. Similar to other skate genera, eastern North Pacific Bathyraja lack a robust species-specific identification, which leads to issues with setting catch limits and creating management plans. This study identifies and formally redescribes the eastern North Pacific softnose skate species based on morphometric and meristic measurements and includes an Alaskan species, Bering Skate, B. interrupta due to its close morphological relationship to B. kincaidii. A lectotype for B. interrupta is designated. Multivariate tests determined that significant differences existed between the study species. Parsimonious phylogenetic trees showed that B kincaidii represents the basal condition, with B. abyssicola and B. aleutica being the most derived species in the study. The formerly synonymized species B. interrupta and B. kincaidii were shown to be separate, as were the previously synonymized species B. microtrachys and B. trachura. Improved Bathyraja species identification will hopefully assist fisheries managers in developing conservation policies easing the impacts of deep-sea fishing expansion.

Preliminary study: Species identification of Rasbora sumatrana through the cytochrome oxidase subunit I DNA barcoding marker

Rasbora sumatrana or locally known as “seluang” in Malaysia is a pelagic fish. Unlike its other congeneric species is not categorized as an ornamental fish. Samples of the presumed R. sumatrana was obtained from an abandoned swamp in Hulu Langat, Selangor. Initial identification of the samples was conducted based on meristic and morphometric analyses, which showed congruence with R. sumatrana when referenced to FishBase. To complement the analysis, a molecular study was conducted based on the cytochrome oxidase subunit I (COI) DNA barcoding marker. Confirmation of the species identity was done by BLAST results with six voucher sequences of R. sumatrana and other Rasbora species from GenBank. The relationship of Rasbora spp. was analysed by phylogenetic and Automatic Barcode Gap Discovery (ABGD) analysis. Contradicting with morphological and meristic data analysis, both Maximum-Likelihood and Maximum Parsimony phylogenetic tree showed that the currently studied samples did not cluster with R. sumatrana. We believe that they may represent cryptic diversity and are tentatively classified as Rasbora spp.

The molecular taxonomy of three endemic Central Asian species of Ranunculus(Ranunculaceae)

Worldwide, the genus Ranunculus includes approximately 600 species and is highly genetically diverse. Recent taxonomic reports suggest that the genus has a monophyletic origin, divided into two subgenera, and consists of 17 sections. The Central Asian country of Kazakhstan has 62 species of the genus that have primarily been collected in the central part of the country. The latest collection trips in southern parts of the country have led to the description of a wider distribution area for Ranunculus and the identification of a new species Ranunculus talassicus Schegol. et A.L. Ebel from Western Tien Shan. Therefore, in this study, attempts were made to assess the molecular taxonomic positions of R. talassicus and two other species endemic to the Central Asian region R. karkaralensis Schegol. and R. pskemensis V.N. Pavlov in relation to other species of the genus, using internal transcribed spacer (ITS) molecular genetic markers. The ITS-aligned sequences of 22 local Central Asian accessions and 43 accession sequences available in the National Center for Biotechnology Information (NCBI) database allowed the construction of a maximum parsimony phylogenetic tree and a Neighbor-Net network. The results indicated that R. talassicus and R. pskemensis could be assigned to section Ranunculastrum. Additionally, an assessment of the network suggested that R. pskemensis was the rooting taxon for the group of species containing R. talassicus, and that R. illyricus L. and R. pedatus Waldst. & Kit. were founders of a prime rooting node for the Ranunculastrum section of the genus. The ITS-aligned sequences showed that R. karkaralensis was indifferent with respect to three other species in the Ranunculus section of the genus, i.e., R. acris L., R. grandifolius C.A. Mey., and R. subborealis Tzvelev. The study indicated that the assessments of ITS-based phylogenetic tree and Neighbor-Net network provided new insights into the taxonomic positions of three endemic species from Central Asia.

Diaphorina citri (Hemiptera: Psylloidea) in China: Two Invasion Routes and Three Transmission Paths.

Diaphorina citri Kuwayama (Hemiptera: Liviidae) is one of the most common pests impacting citrus orchards in southern China. Samples of D. citri were collected in southern China in order to systematically explore the genetic architecture of the species. Mitochondrial cytochrome b (Cytb) and cytochrome coxidase subunit I (COI) were amplified by polymerase chain reaction (PCR) which allowed highlighting low haplotype and nucleotide diversities among the population. Two clades could be observed in the haplotype network. Moreover, Bayesian and maximum parsimony phylogenetic trees were constructed based on the sequences of Cytb and COI. Here, we report on the significant genetic variation of the species when comparing southwestern China with other regions of southern China (southern and southeastern). This analysis also suggested that the genetic structure of D. citri in China originates may from long-term climate fluctuations concomitant with recent disturbances resulting from human activity. Combined with previous data, the present work indicates that D. citri potentially entered China through two distinct invasion routes and spread within the country via three transmission paths.

The complete chloroplast genome of Comastoma falcatum (Gentianaceae)

Here in this work, we have sequenced the complete chloroplast genome of Comastoma falcatum. The complete chloroplast genome size of C. falcatum is 151,423 bp with 81721 bp of LSC, 25727 bp of IRa/IRb and 18248 bp of SSC. The GC contents of its chloroplast genomes are 38.26%. Their chloroplast has a total of 133 unique genes, including 88 of protein-coding genes, 8 of rRNA genes, and 37 of tRNA genes. In the maximum parsimony phylogenetic tree, C. falcatum clustered with Swertia mussotii. This sequenced chloroplast genome of C. falcatum will help to further study the phylogenetic position of Comastoma.

Finding a most parsimonious or likely tree in a network with respect to an alignment

Phylogenetic networks are often constructed by merging multiple conflicting phylogenetic signals into a directed acyclic graph. It is interesting to explore whether a network constructed in this way induces biologically-relevant phylogenetic signals that were not present in the input. Here we show that, given a multiple alignment A for a set of taxa X and a rooted phylogenetic network N whose leaves are labelled by X, it is NP-hard to locate a most parsimonious phylogenetic tree displayed by N (with respect to A) even when the level of N—the maximum number of reticulation nodes within a biconnected component—is 1 and A contains only 2 distinct states. (If, additionally, gaps are allowed the problem becomes APX-hard.) We also show that under the same conditions, and assuming a simple binary symmetric model of character evolution, finding a most likely tree displayed by the network is NP-hard. These negative results contrast with earlier work on parsimony in which it is shown that if A consists of a single column the problem is fixed parameter tractable in the level. We conclude with a discussion of why, despite the NP-hardness, both the parsimony and likelihood problem can likely be well-solved in practice.

Verticillium Wilt Caused by Verticillium dahliae and V. nonalfalfae in Potato in Northern China.

Potato (Solanum tuberosum L.) is one of the most important staple foods in many parts of the world including China. In recent years, Verticillium wilt has become a severe threat to potato production in China. During 2015 to 2016, 287 samples of symptomatic potato plants were collected from 15 counties in five provinces from northern China. One hundred and eighty-seven Verticillium-like colonies were isolated from these samples and identified to species based on cultural and morphological characteristics, and multigene phylogeny based on the partial sequences of actin (ACT), elongation factor 1-alpha (EF1α), glyceraldehyde-3-phosphate dehydrogenase (GPD), and tryptophan synthase (TS) genes. A consensus-rooted most parsimonious phylogenetic tree was generated from the data. One hundred and fifteen isolates comprising 61.5% of the total were identified as Verticillium dahliae, and the remaining 38.5% of the isolates were identified as V. nonalfalfae. V. dahliae was widely distributed in Shaanxi (84.1%), Inner Mongolia (76.7%), Gansu (12.8%), and Qinghai (100%, representing a single isolate). V. dahliae was not recovered from the samples in Ningxia. V. nonalfalfae dominated the collections from Gansu (87.2%) and Ningxia (100%) but was also recovered from Shaanxi (15.9%) and Inner Mongolia (23.3%) at lower frequencies. Neither V. albo-atrum nor V. alfalfae was recovered from the sampled areas. The V. nonalfalfae isolates were predominantly isolated from the samples collected from altitudes above 1,800 m, and in contrast, V. dahliae isolates were mainly recovered from fields sampled below 1,800 m. The optimum temperature for the colony growth of V. nonalfalfae was lower (20°C) than that for V. dahliae (25°C). Pathogenicity tests demonstrated that V. dahliae and V. nonalfalfae were both pathogens of potato Verticillium wilt, with V. dahliae isolates exhibiting higher virulence than V. nonalfalfae isolates regardless of the collection area of the species. This is the first documentation of V. nonalfalfae infecting S. tuberosum in China and the higher altitudes associated with infections of V. nonalfalfae anywhere in the world.

Phylogenetic relationship of a fossil macaque (Macaca cf. robusta) from the Korean Peninsula to extant species of macaques based on zygomaxillary morphology

Little is known about the biogeographical and evolutionary histories of macaques (Macaca spp.) in East Asia because the phylogenetic positions of fossil species remain unclear. Here we examined the zygomaxillary remains of a fossil macaque (M. cf. robusta) from the Durubong Cave Complex, South Korea, that dates back to the late Middle to Late Pleistocene, to infer its phylogenetic relationship to extant species. We took 195 fixed- and semi-landmarks from the zygomaxillary regions of the fossil specimen and from 147 specimens belonging to 14 extant species. We then conducted a generalized Procrustes analysis followed by a multivariate statistical analysis to evaluate the phenetic affinities of the fossil to the extant species and reconstructed the most parsimonious phylogenetic tree using a phylogenetic morphometric approach. We found that the fossil was most similar to Macaca fuscata (Japanese macaque) in the zygomaxillary morphospace although it was at the limit of the range of variation for this species. The second closest in the morphospace was the continental Macaca mulatta (rhesus macaque). Parsimonious reconstruction confirmed that the fossil was most closely related to M. fuscata, even after controlling for the effects of allometry. These findings suggest that in the late Middle to Late Pleistocene, close relatives of M. fuscata that looked like the extant species were distributed on the Korean Peninsula, where no species of macaques are found today. Thus, some morphological characteristics of M. fuscata may have developed before its ancestor dispersed into the Japanese archipelago.

Genetic divergence and speciation within Ziziphora capitata (Lamiaceae): Molecular and micromorphological evidences

Tabaripour R, Sheidai M, Talebi SM, Noormohammadi Z. 2018. Genetic divergence and speciation within Ziziphora capitata (Lamiaceae): Molecular and micromorphological evidences. Biodiversitas 19: 747-755. Ziziphora capitata is a member of the Mint family (Lamiaceae) that naturally grows in various regions. Different subspecies have been reported for this species, from which two are recorded from Iran: Z. capitata subsp. capitata, and Z. capitata subsp. orientalis. In the present study, morphological, palynological and molecular (ISSR and cp-DNA) data were used to reveal speciation within this species and reconsider taxonomic rank of its presumed subspecies. The obtained results revealed a great difference between two presumed subsp. of Z. capitata. These taxa differed in morphological, palynological and molecular characteristics. Statistical and bioinformatics tests revealed significant genomic difference between them and phylogenetic analyses showed that they have a close affinity to some other Ziziphora species (out-groups used), then to each other. Bayesian and maximum parsimony phylogenetic trees differentiated the presumed sub-species of Z. capitata. Moreover, K-Means clustering and Bayesian analysis of genetic groups by Evanno test (optimal k) supported the presence of two distinct genetic groups within Z. capitata. This approach objectively defines a threshold separating intraspecific population substructure from interspecific divergence, which is the general aim of species delimitation studies. Therefore, the present study provides enough evidence for introducing two separate species within Z. capitata based on the traditional taxonomy as well as combination of molecular and micro-morphological data.

First Report of Nothophoma quercina Causing Trunk Canker on Crabapple (Malus micromalus) in China

HomePlant DiseaseVol. 102, No. 7First Report of Nothophoma quercina Causing Trunk Canker on Crabapple (Malus micromalus) in China PreviousNext DISEASE NOTES OPENOpen Access licenseFirst Report of Nothophoma quercina Causing Trunk Canker on Crabapple (Malus micromalus) in ChinaM. Liu, W. Zhang, I. S. Manawasinghe, Y. Zhou, Q. K. Xing, X. H. Li, J. Y. Yan, and S. WangM. Liu†Corresponding author: M. Liu; E-mail: E-mail Address: liumeidmw@163.comhttp://orcid.org/0000-0002-6785-8090Search for more papers by this author, W. ZhangSearch for more papers by this author, I. S. ManawasingheSearch for more papers by this author, Y. ZhouSearch for more papers by this author, Q. K. XingSearch for more papers by this author, X. H. LiSearch for more papers by this author, J. Y. YanSearch for more papers by this author, and S. WangSearch for more papers by this authorAffiliationsAuthors and Affiliations M. Liu † W. Zhang I. S. Manawasinghe Y. Zhou Q. K. Xing X. H. Li J. Y. Yan , Institute of Plant and Environment Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China S. Wang , Administrative Office of the Summer Palace, Beijing Municipal Administration Center of Parks, Beijing 100080, China. Published Online:23 May 2018https://doi.org/10.1094/PDIS-11-17-1866-PDNAboutSectionsSupplemental ToolsAdd to favoritesDownload CitationsTrack Citations ShareShare onFacebookTwitterLinked InRedditEmailWechat Malus micromalus (crabapple) is an ornamental plant mainly distributed in northern China, where the spring climate is warm and dry (mean temperature 1.0 to 12.0°C). Typical trunk cankers on crabapple were observed at the Summer Palace, Beijing, in March 2017. The symptoms included warts on trunk, cracked periderm around warts, roughed bark with scaled periderm, and cankers often expanded and coalesced during dry weather, affecting the ornamental value of crabapple. Symptomatic tissues from the trunk were cut into small pieces (4 × 4 mm), surface-sterilized in 75% alcohol for 1 min, 1% NaClO for 1 min, and then rinsed three times with sterilized water. The sterilized tissues were cultured on potato dextrose agar (PDA) plates (three pieces of tissue per plate) and incubated at 25°C with a 12-h photoperiod for 7 days. Pure cultures of the suspected pathogen were obtained by hyphal-tip and single spore isolation techniques. The colonies on PDA were greenish olivaceous to olivaceous, with pure white, floccose to wooly aerial mycelium. Fifteen days post incubation, abundant, black, solitary, globose, peroblate to suboblate, and 50 to 175 µm (n = 50) diameter pycnidia were scattered over the medium. Conidia were aseptate, hyaline to brown, oval to obtuse, and 4.5 to 7.0 × 2.5 to 4.0 µm (n = 50). For molecular characterization, two representative isolates based on similar morphology characters were selected and four phylogenetic markers (LSU, ITS, TUB2, and RPB2) were amplified by PCR (Chen et al. 2015). The amplicons were sequenced and deposited in GenBank under accession numbers KY887674, KY887675, KY887672, KY887673, KY887678, KY887679, KY887676, and KY887677. Maximum parsimony and Bayesian inference phylogenetic trees were constructed using PAUP (phylogenetic analysis using parsimony) v. 4.0b10 and MrBayes v. 3.1.2. The isolates JZB380007 and JZB380009 clustered together with ex-type culture of Nothophoma quercina (CBS 633.92) with 100% bootstrap support and 1.00 Bayesian posterior probabilities support. Based on the morphological and molecular data, the isolates were identified as N. quercina (Aveskamp et al. 2010; Chen et al. 2015). To confirm pathogenicity, shoots were surface sterilized and wounds (4 mm diam., 1 mm depth) were made with a cork borer. The mycelial plug from mother colonies was placed on the wound, which was then covered with a Parafilm (BEMIS, U.S.A.). Wounded shoots were inoculated with only PDA plugs as controls. Inoculated shoots were placed under dark and moist conditions (70 to 90% RH) at 25°C. Fourteen days later, wounded shoots produced warts and showed peeling symptoms, but controls remained asymptomatic. The same fungus was reisolated from the inoculated shoots, confirming Koch’s postulates. N. quercina has been reported previously in the U.S.A., Tunisia, and Korea (Chen et al. 2013; Taieb et al. 2014; Yun et al. 2016). To our knowledge, this is the first report of N. quercina causing trunk canker in China. Therefore, our report would be useful for its management.

Sequence analysis and typing of Saprolegnia strains isolated from freshwater fish from Southern Chinese regions

Saprolegniasis, caused by Saprolegnia infection, is one of the most common diseases in freshwater fish. Our study aimed to determine the epidemiological characteristics of saprolegniasis in Chinese regions of high incidence. Saprolegnia were isolated and identified by morphological and molecular methods targeting the internal transcribed spacer (ITS) ribosomal DNA (rDNA) and building neighbor-joining (NJ) and maximum parsimony (MP) phylogenetic trees. The ITS sequences of eight isolated strains were compared with GenBank sequences and all strains fell into three clades: CLADE1 (02, LP, 04 and 14), CLADE2 (S1), and CLADE3 (CP, S2, L5 and the reference ATCC200013). Isolates 02 and LP shared 80% sequence similarity with S. diclina, S. longicaulis, S. ferax, S. mixta, and S. anomalies. Further, isolates 04 and 14 shared 80% similarity with S. bulbosa and S. oliviae. Finally, extremely high ITS sequence similarities were identified between isolates S1 and S. australis (100%); CP and S. hypogyna (96%); and S2, L5, ATCC200013 and S. salmonis (98%). This research provides insights into the identification, prevention and control of saprolegniasis pathogens and the potential development of effective drugs.

Live phylogeny with polytomies: Finding the most compact parsimonious trees

Construction of phylogenetic trees has traditionally focused on binary trees where all species appear on leaves, a problem for which numerous efficient solutions have been developed. Certain application domains though, such as viral evolution and transmission, paleontology, linguistics, and phylogenetic stemmatics, often require phylogeny inference that involves placing input species on ancestral tree nodes (live phylogeny), and polytomies. These requirements, despite their prevalence, lead to computationally harder algorithmic solutions and have been sparsely examined in the literature to date. In this article we prove some unique properties of most parsimonious live phylogenetic trees with polytomies, and their mapping to traditional binary phylogenetic trees. We show that our problem reduces to finding the most compact parsimonious tree for n species, and describe a novel efficient algorithm to find such trees without resorting to exhaustive enumeration of all possible tree topologies.

DTL reconciliation repair

BackgroundMaximum parsimony phylogenetic tree reconciliation is an important technique for reconstructing the evolutionary histories of hosts and parasites, genes and species, and other interdependent pairs. Since the problem of finding temporally feasible maximum parsimony reconciliations is NP-complete, current methods use either exact algorithms with exponential worst-case running time or heuristics that do not guarantee optimal solutions.ResultsWe offer an efficient new approach that begins with a potentially infeasible maximum parsimony reconciliation and iteratively “repairs” it until it becomes temporally feasible.ConclusionsIn a non-trivial number of cases, this approach finds solutions that are better than those found by the widely-used Jane heuristic.

Oceanic currents drove population genetic connectivity of the brown alga Sargassum thunbergii in the north‐west Pacific

AbstractAimOceanic currents are among the most pervasive hydrodynamic features in shaping community dynamics, population connectivity and phylogeographical structure of intertidal species. Here, we test whether population structure and biogeographical gradients of genetic diversity in the brown alga Sargassum thunbergii are correlated with oceanic currents in the north‐west Pacific (NWP).LocationNorth‐west Pacific (25.07°N–43.36°N).MethodsNuclear internal transcribed spacer‐2 and mitochondrial cox3 sequences were obtained from 835 and 810 individuals of S. thunbergii respectively. Parsimony networks and phylogenetic trees (maximum parsimony and Bayesian inference) were constructed to evaluate phylogeographical structure. Pairwise FST estimates and analyses of molecular variance (AMOVA) at various hierarchical levels (latitude, longitude, marine provinces, biogeographical basins and zoogeographical zones) were conducted to elucidate population genetic differentiation. migrate software was used to estimate the number of migrants between adjacent populations.ResultsSeveral lines of evidence indicate that S. thunbergii is characterized by shallow population structure. Geographical distances do not correlate with population pairwise genetic differentiations. The corridor/stepping‐stone model‐based coalescent analyses reveal high levels of asymmetric gene flow among S. thunbergii populations, with the numbers of migrants largely corresponding to the directions of oceanic current systems in the NWP. Genetic signatures also indicate that Jeju Island, Korea might act as a transition zone for dispersal of S. thunbergii in the NWP driven by the Kuroshio Current, thus facilitating subsequent transportation northward into the Sea of Japan and the Yellow‐Bohai Sea.Main conclusionsPopulation genetic homogeneity in S. thunbergii was mainly structured by oceanic currents rather than palaeoclimatic events. Our study illustrates an important phylogeographical case of how coastal hydrodynamic factors contributed to population connectivity and geographical shifts of genetic diversity for marine organisms without a pelagic stage.