Molecular phylogeny and diversity of penaeid shrimps (Crustacea: Decapoda) from South-East Asian waters

The decapod family Penaeidae comprises most of the economically important marine shrimp species. Its members are widespread throughout the world, with its highest species diversity centred in the Indo-West Pacific region. Despite this importance, their taxonomy, classification and phylogeny are not yet settled due in part to incongruence among hypotheses proposed from molecular versus morphological studies. In this study, using a thorough taxonomic sampling of especially the South-East Asian species, we aim to (a) utilize a reconstructed phylogeny to test the monophyly of the Penaeidae and its currently recognized genera and (b) explore its species diversity in South-East Asian waters. To infer the phylogeny, a combined gene data set (including 109 ingroup and six outgroup taxa) of mitochondrial genes, COI and 16S rRNA, and two nuclear genes, NaK and PEPCK, was utilized. To explore its diversity, another data set that included 371 COI gene sequences (231 newly generated and 140 retrieved from public sources) was compiled and subsequently analysed with two different tools (ABGD and bPTP) for species delimitation. Other than supporting the non-monophyly of the Penaeidae with the Sicyoniidae nested within the penaeid tribe Trachypenaeini, the genera Penaeus, Mierspenaeopsis and Parapenaeopsis were also revealed to be polyphyletic. Our species delimitation analysis inferred that 94 putative species actually existed within the 71 morphospecies reviewed, indicating an underestimated biodiversity in this family and the potential presence of new species within the following morphospecies: Kishinouyepenaeopsis cornuta, K. incisa, Mierspenaeopsis sculptilis, M hardwicki, Parapenaeopsis coromandelica and Penaeus monodon.     

Naegleria lovaniensis tarasca New Subspecies, and the Purepecha Strain, a Morphological Variant of N. I. lovaniensis, Isolated from Natural Thermal Waters in Mexico

Amoebae were isolated from a natural thermal water source in Michoacaan, Mexico, in September 1986. Two 500-ml samples were taken from pools with water at 45°C and 46°C and concentrated at 2,000 g for 15 min. The sediment was seeded on nonnutritive agar plates and incubated at 42°C. The isolates were axenized in bactocasitone-serum medium. The identification of the isolates was based on their morphology, total protein and isoenzyme patterns by agarose isoelectric focusing, serology, fine structure, agglutination with Concanavalin A, sensitivity to trimethoprim, capacity to kill mice, and their cytopathic effect in Vero cells. The results showed several morphophysiological, biochemical and serological differences between the isolates and the type strain Aq/9/1/ 45D of Naegleria lovaniensis. These remarkable differences provide sufficient evidence to consider one of the isolates a new subspecies, and the other one a morphological variant of N. l. lovaniensis, which can be differentiated from other Naegleriae by their morphology, biochemistry, serology and physiology. The authors propose the name tarasca for the subspecies and purepecha for the morphological variant.     

A phylogenomic resolution for the taxonomy of Aegean green lizards

Lacerta pamphylica and Lacerta trilineata are two currently recognized green lizard species with a historically problematic taxonomy. In cases of tangled phylogenies, next-generation sequencing and double-digest restriction-site-associated DNA protocols can provide a wealth of genomic data and resolve difficult taxonomic issues. Here, we generated genome-wide SNPs and mitochondrial sequences, and applied molecular species delimitation approaches to provide a stable taxonomy for the Aegean green lizards. Mitochondrial gene trees, genetic cluster delimitation and population structure analyses converged into recognizing the populations of (a) L. pamphylica, (b) east Aegean islands, Anatolia and Thrace (diplochondrodes lineage), (c) central Aegean islands (citrovittata), and (d) remaining Balkan populations and islands (trilineata), as separate clusters. Phylogenomic analyses revealed a split into two major clades, east and west of the Aegean Barrier, unambiguously showing a sister–clade relationship between pamphylica and diplochondrodes, rendering L. trilineata paraphyletic. Species delimitation models were tested in a Bayesian framework using the genomic SNPs: lumping all populations into a single ‘species’ had the lowest likelihood but the current taxonomy was also outperformed by all other models. All lines of evidence support the Pamphylian green lizard as a valid species; thus, east Aegean L. trilineata should also be considered a distinct species under the name Lacerta diplochondrodes. Finally, evidence from the mitochondrial and nuclear genomes is overwhelmingly in favour of recognizing the morphologically distinct Cycladian green lizards as a distinct species. We propose their elevation to full species under the name Lacerta citrovittata. All remaining insular and continental populations of the Balkan Peninsula represent the species L. trilineata.     

A critical rebuttal of the proposed division of the genus Arcobacter into six genera using comparative genomic,phylogenetic, and phenotypic criteria

The proposal to restructure the genus Arcobacter into six distinct genera was critically examined using: comparative analyses of up to 80 Epsilonproteobacterial genome sequences (including 26 arcobacters); phylogenetic analyses of three housekeeping genes and also 342 core genes; and phenotypic criteria. Genome sequences were analysed with tools to calculate Percentage of Conserved Proteins, Average Amino-acid Identity, BLAST-based Average Nucleotide Identity, in silico DNA–DNA hybridisation values, genome-wide Average Nucleotide Identity, Alignment Fractions and G + C percentages. Genome analyses revealed the genus Arcobacter sensu lato to be relatively homogenous, and phylogenetic analyses clearly distinguished the group from other Epsilonproteobacteria. Genomic distinction of the genera proposed by Pérez-Cataluña et al. [2018] was not supported by any of the measures used and a subsequent risk of strain misidentification clearly identified. Similarly, phenotypic analyses supported the delineation of Arcobacter sensu lato but did not justify the position of the proposed novel genera. The present polyphasic taxonomic study strongly supports the continuance of the classification of “aerotolerant campylobacters” as Arcobacter and refutes the proposed genus-level subdivision of Pérez-Cataluña et al. [2018].     

Description of two new species of the leafhopper subgenus Pediopsoides (Pediopsoides) (Hemiptera,Cicadellidae, Macropsinae) from Guangxi Province,Southern China

Two new species of the Macropsinae leafhopper subgenus Pediopsoides (Pediopsoides) Matsumura, 1912, Pediopsoides (Pediopsoides) damingshanensis Li, Dai & Li, sp. n. and Pediopsoides (Pediopsoides) tishetshkini Li, Dai & Li sp. n., are described and illustrated from Guangxi Province of southern China. A key to males is provided to distinguish the species of the subgenus along with a map showing the distribution of the new species.