A new insular species of the Cyrtodactylus pulchellus group (Reptilia, Gekkonidae) from Tarutao Island, southern Thailand revealed by morphological and genetic evidence

The bent-toed geckos of the Cyrtodactylus pulchellus group are widely distributed along the Thai-Malay Peninsula. Although taxonomic and phylogenetic studies of this species group have been continuously conducted, only some populations from Thailand have been included, resulting in hidden diversity within this group. In this study, we used morphological and molecular data to clarify the taxonomic status and describe a new population from Tarutao Island, Satun Province, southern Thailand. Cyrtodactylus stellatussp. nov. can be distinguished from its congeners by the combination of the following morphological characters: body size; tuberculation; number of dark body bands, ventral scales, and femoroprecloacal pores in males; presence of precloacal pores in females; and scattered pattern on dorsum. Phylogenetic analyses of the mitochondrial ND2 gene recovered the new species as the sister species to C. astrum, with an uncorrected pairwise divergence of 9.78–12.37%. Cyrtodactylus stellatussp. nov. is currently only known from Tarutao Island, Thailand. The discovery of this species suggests that the diversity within the C. pulchellus group remains underestimated and future exploration of unsurveyed areas are needed to further the understanding of this group and its geographic range.

Molecular Characterization of a Reemergent Brugia malayi Parasite in Sri Lanka, Suggestive of a Novel Strain

Sri Lanka achieved elimination status for lymphatic filariasis in 2016; still, the disease remains a potential public health issue. The present study is aimed at identifying a subperiodic Brugia sp. parasite which has reemerged in Sri Lanka after four decades via molecular-based analysis. Polymerase chain reaction performed with pan-filarial primers specific for the internal transcribed spacer region-2 (ITS-2) of the rDNA of Brugia filarial parasites isolated from human, canine, and feline blood samples yielded a 615 bp band establishing the species identity as Brugia malayi. Comparison of the ITS2 sequences of the reemerged B. malayi isolates with GenBank sequences revealed a higher sequence homology with B. pahangi than B. malayi with similar phylogenetic evidence. However, the mean interspecies Kimura-2-parameter pairwise divergence between the generated Brugia sequences with B. malayi and B. pahangi was less than 3%. During the analysis of parsimony sites of the new ITS2 sequences, substitutions at A36T, A296G, T373A, and G482A made the sequences different from both B. pahangi and B. malayi suggesting the possibility of a new genetic variant or a hybrid strain of B. malayi and B. pahangi. Mosquito dissections and xenomonitoring identified M. uniformis and M. annulifera as vectors of this novel strain of B. malayi circulating among cats, dogs, and humans in Sri Lanka.

Newly Emerging Pest in China, Rhynchaenus maculosus (Coleoptera: Curculionidae): Morphology and Molecular Identification with DNA Barcoding

The oak flea weevil, Rhynchaenus maculosus Yang et Zhang 1991, is a newly emerging pest that severely damages oak (genus Quercus) in China. The first R. maculosus outbreak occurred in 2020 and caused spectacular damage to all oak forests in Jilin province, northeast China. The lack of key morphological characters complicates the identification of this native pest, especially in larva and pupa stages. This is problematic because quick and accurate species identification is crucial for early monitoring and intervention during outbreaks. Here, we provided the first detailed morphological description of R. maculosus at four life stages. Additionally, we used DNA barcodes from larva and pupa specimens collected from three remote locations for molecular identification. The average pairwise divergence of all sequences in this study was 0.51%, well below the 2% to 3% (K-2-parameter) threshold set for one species. All sample sequences matched the R. maculosus morphospecies (KX657706.1 and KX657707.1), with 99.23% to 100% (sequence identity, E value: 0.00) matching success. The tree based on barcodes placed the specimens into the Rhynchaenus group, and the phylogenetic relationship between 62 sequences (30 samples and 32 from GeneBank) had high congruence with the morphospecies taxa. The traditional DNA barcodes were successfully transformed into quick response codes with larger coding capacity for information storage. The results showed that DNA barcoding is reliable for R. maculosus identification. The integration of molecular and morphology-based methods contributes to accurate species identification of this newly emerging oak pest.

Existence of Bov-B LINE Retrotransposons in Snake Lineages Reveals Recent Multiple Horizontal Gene Transfers with Copy Number Variation

Transposable elements (TEs) are dynamic elements present in all eukaryotic genomes. They can “jump” and amplify within the genome and promote segmental genome rearrangements on both autosomes and sex chromosomes by disruption of gene structures. The Bovine-B long interspersed nuclear element (Bov-B LINE) is among the most abundant TE-retrotransposon families in vertebrates due to horizontal transfer (HT) among vertebrate lineages. Recent studies have shown multiple HTs or the presence of diverse Bov-B LINE groups in the snake lineage. It is hypothesized that Bov-B LINEs are highly dynamic and that the diversity reflects multiple HTs in snake lineages. Partial sequences of Bov-B LINE from 23 snake species were characterized. Phylogenetic analysis resolved at least two Bov-B LINE groups that might correspond to henophidian and caenophidian snakes; however, the tree topology differed from that based on functional nuclear and mitochondrial gene sequences. Several Bov-B LINEs of snakes showed greater than 80% similarity to sequences obtained from insects, whereas the two Bov-B LINE groups as well as sequences from the same snake species classified in different Bov-B LINE groups showed sequence similarities of less than 80%. Calculation of estimated divergence time and pairwise divergence between all individual Bov-B LINE copies suggest invasion times ranging from 79.19 to 98.8 million years ago in snakes. Accumulation of elements in a lineage-specific fashion ranged from 9 × 10−6% to 5.63 × 10−2% per genome. The genomic proportion of Bov-B LINEs varied among snake species but was not directly associated with genome size or invasion time. No differentiation in Bov-B LINE copy number between males and females was observed in any of the snake species examined. Incongruence in tree topology between Bov-B LINEs and other snake phylogenies may reflect past HT events. Sequence divergence of Bov-B LINEs between copies suggests that recent multiple HTs occurred within the same evolutionary timeframe in the snake lineage. The proportion of Bov-B LINEs varies among species, reflecting species specificity in TE invasion. The rapid speciation of snakes, coinciding with Bov-B LINE invasion in snake genomes, leads us to better understand the effect of Bov-B LINEs on snake genome evolution.

Complete chloroplast genomes of medicinally importantTeucriumspecies and comparative analyses with related species from Lamiaceae

Teucriumis one of the most economically and ecologically important genera in the Lamiaceae family; however, it is currently the least well understood at the plastome level. In the current study, we sequenced the complete chloroplast (cp) genomes ofT. stocksianumsubsp.stenophyllumR.A.King (TSS),T. stocksianumsubsp.stocksianumBoiss. (TS) andT. mascatenseBoiss. (TM) through next-generation sequencing and compared them with the cp genomes of related species in Lamiaceae (Ajuga reptansL.,Caryopteris mongholicaBunge,Lamium albumL.,Lamium galeobdolon(L.) Crantz, andStachys byzantinaK.Koch). The results revealed that the TSS, TS and TM cp genomes have sizes of 150,087, 150,076 and 150,499 bp, respectively. Similarly, the large single-copy (LSC) regions of TSS, TS and TM had sizes of 81,707, 81,682 and 82,075 bp, respectively. The gene contents and orders of these genomes were similar to those of other angiosperm species. However, various differences were observed at the inverted repeat (IR) junctions, and the extent of the IR expansion into ψrps19was 58 bp, 23 bp and 61 bp in TSS, TS and TM, respectively. Similarly, in all genomes, thepbsAgene was present in the LSC at varying distances from the JLA(IRa-LSC) junction. Furthermore, 89, 72, and 92 repeats were identified in the TSS, TM and TS cp genomes, respectively. The highest number of simple sequence repeats was found in TSS (128), followed by TS (127) and TM (121). Pairwise alignments of the TSS cp genome with related cp genomes showed a high degree of synteny. However, relatively lower sequence identity was observed when various coding regions were compared to those of related cp genomes. The average pairwise divergence among the complete cp genomes showed that TSS was more divergent from TM (0.018) than from TS (0.006). The current study provides valuable genomic insight into the genusTeucriumand its subspecies that may be applied to a more comprehensive study.

The genus Rosenvingea (Phaeophyceae: Scytosiphonaceae) in south-west Australia, with the description of Rosenvingea australis sp. nov.

Two species of the brown algal genusRosenvingeaare reported from south-west (SW) Australia, including the widely distributedR. orientalisand the new speciesR. australisHuisman, G.H. BooetS.M. Boo, sp. nov. Molecular phylogenies of mitochondrialcox3 and plastidpsaA unequivocally align the SW AustralianR. orientaliswith specimens from Vietnam and the species is morphologically consistent throughout its Australian range. Australian specimens of the new speciesR. australisjoin with a specimen from New Caledonia and these resolve as a sister species toR. intricata, with levels of pairwise divergence (4.2–4.9% incox3 and 3.9–4.0% inpsaA) comparable to those between other scytosiphonacean species. The new species can be distinguished morphologically by its branch dimensions and the arrangement and size of plurangia, but further studies including molecular analyses of a full range of species and possible morphological variants are needed.

Rediscovery of Rhacophorus yaoshanensis and Theloderma kwangsiensis at their type localities after five decades

Rhacophorus yaoshanensis Liu & Hu, 1962 and Theloderma kwangsiensis Liu & Hu, 1962 were described by Liu & Hu (1962) based on two specimens and one specimen, respectively, from the Dayaoshan Ranges, Guangxi, China. Since these two species were described, no additional specimens have been collected from their type localities, presenting an issue for phylogenetic studies of the genera. Five decades later, we have rediscovered R. yaoshanensis and T. kwangsiensis from their type localities. In this paper, we re-describe the two species and conduct a preliminary assessment of their phylogenetic relationships using two mitochondrial DNA genes (12S and 16S rRNA). The results indicate with high support that R. yaoshanensis is closely related to Rhacophorus pinglongensis. Theloderma kwangsiensis is nested within Theloderma corticale, with only 0.0–0.6% pairwise divergence, a level typical of intraspecific variation. Based on both molecular and morphological analyses, we further confirm that T. kwangsiensis is a synonym of T. corticale. Shiwandashan National Nature Reserve, Guangxi Province, China, is a new record for T. corticale.

Genomic and phylogenetic characterization of viruses included in the Manzanilla and Oropouche species complexes of the genus Orthobunyavirus, family Bunyaviridae

A thorough characterization of the genetic diversity of viruses present in vector and vertebrate host populations is essential for the early detection of and response to emerging pathogenic viruses, yet genetic characterization of many important viral groups remains incomplete. The Simbu serogroup of the genus Orthobunyavirus, family Bunyaviridae, is an example. The Simbu serogroup currently consists of a highly diverse group of related arboviruses that infect both humans and economically important livestock species. Here, we report complete genome sequences for 11 viruses within this group, with a focus on the large and poorly characterized Manzanilla and Oropouche species complexes. Phylogenetic and pairwise divergence analyses indicated the presence of high levels of genetic diversity within these two species complexes, on a par with that seen among the five other species complexes in the Simbu serogroup. Based on previously reported divergence thresholds between species, the data suggested that these two complexes should actually be divided into at least five species. Together these five species formed a distinct phylogenetic clade apart from the rest of the Simbu serogroup. Pairwise sequence divergences among viruses of this clade and viruses in other Simbu serogroup species complexes were similar to levels of divergence among the other orthobunyavirus serogroups. The genetic data also suggested relatively high levels of natural reassortment, with three potential reassortment events present, including two well-supported events involving viruses known to infect humans.

Biogeography of butterflies in the Australian monsoon tropics

The biogeography of butterflies within the monsoon tropical biome of northern Australia is reviewed in terms of patterns of species richness, endemism and area relationships. Available data indicate that the region supports a relatively rich fauna, comprising 265 species (~62% of the total Australian fauna), but endemism is low (6%). No genera are endemic to the monsoon tropics, but two (Neohesperilla, Nesolycaena) are characteristic components, embracing a total of seven species in the region, of which five are endemic. Three ecological specialists (Neohesperilla senta, Elodina walkeri, Candalides delospila), each associated with different vegetation types, appear to be characteristic elements of the monsoon tropics. Of 67 range-restricted species in the monsoon tropics, 15 (mostly associated with savanna) are endemic to the region, while 52 (mostly associated with rainforest) are non-endemic, occurring also in south-east Asia and/or mainland New Guinea. A pronounced attenuation in species richness from Cape York Peninsula across the Top End to the Kimberley is evident. Within the monsoon tropics, Cape York Peninsula stands out as an area of exceptional biodiversity, with 95% of the butterflies (251 species; 7 endemic species, 31 endemic subspecies/geographical forms) recorded from the entire region, compared with the Top End (123 species; 3 endemic species, 17 endemic subspecies/geographical forms). In contrast, the Kimberley has a comparatively depauperate fauna (85 species; 1 endemic species, 0 endemic subspecies) without strong Indonesian affinities, and contains only two range-restricted species. A sister-area relationship between Cape York Peninsula and the Top End–Kimberley is evident in one clade, Acrodipsas hirtipes (northern Cape York Peninsula) + A. decima (Top End), with a pairwise divergence of ~1% based on mtDNA, and is suspected in another, Nesolycaena medicea (southern Cape York Peninsula) and N. urumelia (Top End) + N. caesia (Kimberley); a further five species show similar sister-area relationships across the Carpentarian Gap but at the level of subspecies or geographical form. Three general and complementary hypotheses are proposed to explain patterns of geographical differentiation of butterflies in the monsoon tropics: (1) the Carpentarian Gap is a biogeographical filter, functioning as a barrier for some species but as a bridge for others; (2) divergence among taxa between Cape York Peninsula and the Top End–Kimberley has occurred fairly recently (Quaternary), probably through vicariance; and (3) the Bonaparte Gap, with the exception of Nesolycaena, is not a vicariant barrier for butterflies in the Top End and Kimberley.