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Fulltext Widespread ancient whole-genome duplications in Malpighiales coincide with Eocene global climatic upheaval

Cai L, Xi Z, Amorim AM, Sugumaran M, Rest JS, Liu L, et al.

New Phytol, 2019 Jan;221(1):565-576.
PMID: 30030969 DOI: 10.1111/nph.15357

Whole-genome duplications (WGDs) are widespread and prevalent in vascular plants and frequently coincide with major episodes of global and climatic upheaval, including the mass extinction at the Cretaceous-Tertiary boundary (c. 65 Ma) and during more recent periods of global aridification in the Miocene (c. 10-5 Ma). Here, we explore WGDs in the diverse flowering plant clade Malpighiales. Using transcriptomes and complete genomes from 42 species, we applied a multipronged phylogenomic pipeline to identify, locate, and determine the age of WGDs in Malpighiales using three means of inference: distributions of synonymous substitutions per synonymous site (Ks ) among paralogs, phylogenomic (gene tree) reconciliation, and a likelihood-based gene-count method. We conservatively identify 22 ancient WGDs, widely distributed across Malpighiales subclades. Importantly, these events are clustered around the Eocene-Paleocene transition (c. 54 Ma), during which time the planet was warmer and wetter than any period in the Cenozoic. These results establish that the Eocene Climatic Optimum likely represents a previously unrecognized period of prolific WGDs in plants, and lends further support to the hypothesis that polyploidization promotes adaptation and enhances plant survival during episodes of global change, especially for tropical organisms like Malpighiales, which have tight thermal tolerances.

Matched MeSH terms: Phylogeny*
Fusarium andiyazi, a Pathogenic Species Associated with Rice Bakanae Disease in Malaysia

Husna A, Miah MA, Zakaria L, Nor NMIM

Curr Microbiol, 2024 Aug 16;81(10):308.
PMID: 39150554 DOI: 10.1007/s00284-024-03823-5

Rice is the main staple food crops for the Malaysian population. Rice is also susceptible to bakanae diseases caused by some Fusarium species and reducing yield, and quality of rice also profit. In this study, several rice fields were surveyed to collect Fusarium isolates associated with bakanae disease. The morphological features of Fusarium andiyazi isolates found on infected rice plants were identified in this investigation. For biological species identification, MAT-1 (Mating type idiomorphs) bearing isolates were crossed with MAT-2 isolates. Crossing was succeeded between cross of two different mating type bearing field isolates. Consequently, there is a possibility of exchange of genetic material within the F. andiyazi population in Malaysia. The identity of the isolates was further determined up to the species level by comparing DNA sequences and phylogenetic analysis of two genes. The phylogenetic analyses of the joined dataset of translation elongation factor 1-alpha (TEF1-α) and RNA polymerase subunit II (RPB2) revealed that all the isolates were F. andiyazi. In pathogenicity tests, F. andiyazi were found to be pathogenic on the susceptible rice cultivars MR211 and MR220. Inoculated rice seedling produced typical bakanae symptom like elongation, thin and yellow leaves. F. andiyazi was further confirmed as pathogenic species by Ultra High-Performance Liquid Chromatography (UPLC) detection of Gibberellic acid (GA3) and Fusaric acid. In this study, F. andiyazi strains have been identified as the responsible pathogen for causing rice bakanae disease in Malaysia and it is the first report of F. andiyazi, as a pathogenic species on rice in Malaysia.

Matched MeSH terms: Phylogeny*
Phylogenetics of Asian Small-Clawed Otters (Aonyx cinereus) in West Sumatra

Tjong DH, Roesma DI, Aadrean, Agustina NT, Maharani S, Azzahra I

Pak J Biol Sci, 2024 Jun;27(7):373-379.
PMID: 39206471 DOI: 10.3923/pjbs.2024.373.379

Background and Objective: The presence of Asian small-clawed otters (Aonyx cinereus) in West Sumatra has been reported from ecological data in the form of footprints and feces, while its genetic information has not been reported yet. This genetic information needs to be reported along with the determination of A. cinereus as a vulnerable species and is experiencing population decline by the International Union for Conservation of Nature (IUCN). This study aimed to determine the phylogenetic relationship of A. cinereus found in West Sumatra with other regions. Materials and Methods: The samples used were A. cinereus stool collected from several wetland locations in West Sumatra. Aonyx cinereus DNA was extracted from stool samples following the QIAamp Fast DNA Stool Mini Kit protocol (Qiagen). Amplification was performed using the CO1 gene. The IQTree was used to provide phylogenetic information on A. cinereus and MEGA 7 was used to determine the uncorrected genetic distance of A. cinereus. Results: Aonyx cinereus clustered to form three sub-clusters namely A. cinereus Sundaland, Laos lineage and unknown lineage. Aonyx cinereus Sundaland consists of A. cinereus West Sumatra and A. cinereus Sarawak, Malaysia which are closely related with a genetic distance of 0.68%. Moreover, compared to A. cinereus from unknown lineage (including Captive Copenhagen Zoo) and Laos lineage, A. cinereus of West Sumatra had a genetic distance of 0.68-1.20 and 4.18%, respectively. Conclusion: Wetland conversion and the role of humans have influenced the obstacle to connectivity among populations that cause genetic variation.

Matched MeSH terms: Phylogeny*
Fulltext Molecular phylogeny and genetic diversity of Fusarium oxysporum from various hosts in Malaysia

Mohd-Hafifi AB, Mohamed Nor NMI, Zakaria L, Mohd MH

Sci Rep, 2024 Nov 29;14(1):29708.
PMID: 39613784 DOI: 10.1038/s41598-024-78195-8

Fusarium oxysporum is a cosmopolitan fungus, consisting of both pathogenic and non-pathogenic members and known to be the causative agent of several diseases on various host plants. In Malaysia, most studies have focused on pathogenic F. oxysporum isolates because of their implications for agricultural production, but less attention has been given to non-pathogenic isolates. The aim of this study was to determine the phylogenetic relationship, genetic diversity, pathogenicity and host range of F. oxysporum in Malaysia. A total of 133 isolates of F. oxysporum were isolated from symptomatic plants of Abelmoschus esculentus, Solanum melongena, Solanum tuberosum, Cucumis sativus, Solanum lycopersicum, Cucumis melo, Musa paradisiaca var. awak, Hymenocallis littoralis, Asparagus officinalis, and Sansevieria trifasciata and non-agricultural soils in Malaysia. Comparison of nucleotide sequences of translation elongation factor 1-alpha (tef1-α) and mitochondrial small subunit (mtSSU) showed that the isolates were 98-100% similar to F. oxysporum from GenBank, thus, confirming the fungal identity. Besides, Malaysian isolates of F. oxysporum exhibited polyphyletic evolutionary origin, wide host range, and genetically diverse by grouping into 20 VCGs and 17 IGS haplotypes. This finding is beneficial for the purpose of quarantine, monitoring and disease management in the agricultural settings in Malaysia.

Matched MeSH terms: Phylogeny*
Reliability of wing morphometrics for species identification of human-biting black flies (Diptera: Simuliidae) in Thailand

Aupalee K, Srisuka W, Limsopatham K, Sanit S, Takaoka H, Saeung A

Parasit Vectors, 2024 Dec 18;17(1):508.
PMID: 39695748 DOI: 10.1186/s13071-024-06597-8

BACKGROUND: Fast and reliable species identification of black flies is essential for research proposes and effective vector control. Besides traditional identification based on morphology, which is usually supplemented with molecular methods, geometric morphometrics (GM) has emerged as a promising tool for identification. Despite its potential, no specific GM techniques have been established for the identification of black fly species.
METHODS: Adult female black flies collected using human bait, as well as those reared from pupae, were used in this study. Here, landmark-based GM analysis of wings was assessed for the first time to identify human-biting black fly species in Thailand, comparing this approach with the standard morphological identification method and DNA barcoding based on the mitochondrial cytochrome c oxidase subunit I (COI) gene. To explore genetic relationships between species, maximum likelihood (ML) and neighbor-joining (NJ) phylogenetic trees were built. Additionally, three different methods of species delimitation, i.e., assemble species by automatic partitioning (ASAP), generalized mixed yule coalescent (GMYC), and single Poisson tree processes (PTP), were utilized to identify the morphologically defined species. The effectiveness of a COI barcode in identifying black fly species was further examined through the best match (BM) and best close match (BCM) methods.
RESULTS: Seven black fly species, namely Simulium tenebrosum Takaoka, Srisuka & Saeung, 2018 (complex), S. doipuiense Takaoka & Choochote, 2005 (complex), S. nigrogilvum Summers, 1911, S. nodosum Puri, 1933, S. asakoae Takaoka & Davies, 1995, S. chamlongi Takaoka & Suzuki, 1984, and S. umphangense Takaoka, Srisuka & Saeung, 2017 were morphologically identified. Compared with the standard method, the GM analysis based on wing shape showed high success in separating species, achieving an overall accuracy rate of 88.54%. On the other hand, DNA barcoding surpassed wing GM for species identification with a correct identification rate of 98.57%. Species delimitation analyses confirmed the validity of most nominal species, with an exception for S. tenebrosum complex and S. doipuiense complex, being delimited as a single species. Moreover, the analyses unveiled hidden diversity within S. asakoae, indicating the possible existence of up to four putative species.
CONCLUSIONS: This study highlights the potential of wing GM as a promising and reliable complementary tool for species identification of human-biting black flies in Thailand.

Matched MeSH terms: Phylogeny*
Breeding sites, migration paths and phylogenetic relationships of mosquitoes in seven cities in northern and southern China

Su J, Zhao JY, Li YF, Lu YJ

Trop Biomed, 2024 Dec 01;41(4):471-480.
PMID: 39876505 DOI: 10.47665/tb.41.4.008

Mosquito-borne diseases have wreaked havoc on human health, with consequences dramatically increasing in recent years. The incidence of mosquito-borne diseases is closely linked to the locations that are chosen for urban development. The aim of this study was to provide characteristics of mosquito breeding sites in northern and southern China and to document the most important arbovirus vectors found in the study area, the evidence generated here is critical for early prevention and control inter ventions. This research involved a random selection of various sites across four provinces, spanning both the northern and southern regions of China. The dwellings and accessible water storage containers in these sites were investigated to detect the presence of immature mosquitoes. Samples were then collected, mosquitoes were nurtured to adulthood, and the species that were present were identified. A total of 1 249 samples were collected during this survey of the mosquito breeding sites. A total of 80 samples were processed using the Chelex method to extract mosquito DNA from all the samples. The ITS2 gene fragment was then amplified by PCR and sequenced. A subsequent BLAST comparison allowed the identification of the mosquito species, and MEGA11 software was used for phylogenetic analysis. The results showed that there were four species of mosquitoes, including Aedes albopictus, Culex quinquefasciatus, Lutzia fuscanus and Armigeres subalbatus. The primary mosquito breeding grounds in the four provinces of China consisted of storm drains, discarded containers, garbage bins, and areas with standing water. Still-water environments, such as rice fields were the primary breeding locations in the southern cities. In contrast, in the northern regions, most breeding occurred at construction sites, and in similar water-prone areas. The most prevalent mosquitoes in the four provinces of China were of the genus Aedes, with a significant number originating from Fujian Province, China. This information sheds light on the migration patterns of mosquitoes and significantly enhances community-based protection measures and mobilization efforts.

Matched MeSH terms: Phylogeny*
Genomic characterization and identification of multiple drug resistance genes in clinical isolates of Acinetobacter baumannii through whole genome sequencing

Habibi N, Mustafa AS, Nasser K, Al-Obaid I, Alfouzan W, Uddin S, et al.

Mol Biol Rep, 2025 Feb 15;52(1):233.
PMID: 39954144 DOI: 10.1007/s11033-025-10353-1

BACKGROUND: Acinetobacter baumannii is a notorious nosocomial pathogen universally in healthcare settings. Its natural competent characteristics for genetic recombination are responsible for acquired antibiotic resistance and render it untreatable through commonly used antibiotics. Hence, characterizing the A. baumannii genomes for multidrug resistance carriage is of paramount importance. The study aimed to characterize the whole genome of clinical isolates of A. baumannii to identify specifically the types of antibiotic resistance genes, drug classes and mobile genetic elements. We also aimed to determine the significant multi-locus sequence tags (MLSTs). The phylogeny of the isolates was established with other clinical strains distributed globally.
METHODS AND RESULTS: Fifteen clinical isolates (isolated from tracheal secretion, urine and bronchoalveolar lavage) were subjected to whole genome sequencing. Raw sequences were assembled using SPAdes and species were identified using KmerFinder 3.2. The assembled genomes were annotated using the Prokka v1.14.6. Resfinder 4.6.0 was used to determine antibiotic resistance genes. The sequences were aligned against seven housekeeping genes aka sequence tags (STs) available within the MLST database (v 2.0.9). MobileGeneticElement finder (v1.0.3) were used for profiling mobile genetic elements associated with the antibiotic resistance genes. The genomes of nosocomial A. baumannii were assembled with an average N50 of 23,480 and GC content of 38%. There were approximately 3700 CDs, 53 tRNA and 3 rRNA. About 80% of the isolates were ST2 type. The genomes possessed antibiotic resistance genes (n = 24) belonging to 17 drug classes. The predicted phenotype was multidrug resistant. Among the mobile genetic elements, 12 insertion sequences and 2 composite transposons were also found. The mode of antibiotic resistance was mostly through antibiotic inactivation in all the isolates.
CONCLUSIONS: The results imply the occurrence of multidrug resistant genes in clinical isolates of A. baumannii strains in the healthcare settings of Kuwait. A more comprehensive survey should be undertaken for antimicrobial resistance monitoring on a regular basis for surveillance, contact tracing, and potential mitigation in clinical settings.

Matched MeSH terms: Phylogeny*
A genome-based phylogeny for Mollusca is concordant with fossils and morphology

Chen Z, Baeza JA, Chen C, Gonzalez MT, González VL, Greve C, et al.

Science, 2025 Feb 28;387(6737):1001-1007.
PMID: 40014700 DOI: 10.1126/science.ads0215

Extreme morphological disparity within Mollusca has long confounded efforts to reconstruct a stable backbone phylogeny for the phylum. Familiar molluscan groups-gastropods, bivalves, and cephalopods-each represent a diverse radiation with myriad morphological, ecological, and behavioral adaptations. The phylum further encompasses many more unfamiliar experiments in animal body-plan evolution. In this work, we reconstructed the phylogeny for living Mollusca on the basis of metazoan BUSCO (Benchmarking Universal Single-Copy Orthologs) genes extracted from 77 (13 new) genomes, including multiple members of all eight classes with two high-quality genome assemblies for monoplacophorans. Our analyses confirm a phylogeny proposed from morphology and show widespread genomic variation. The flexibility of the molluscan genome likely explains both historic challenges with their genomes and their evolutionary success.

Matched MeSH terms: Phylogeny*
Revalidation of Enteromius karkensis (Gilchrist and Thompson 1913) (Cypriniformes: Smiliogastrinae) from the southern temperate freshwater ecoregion, South Africa

Martin MB, Chakona A, Kadye WT, Scheepers M

J Fish Biol, 2025 Mar;106(3):741-759.
PMID: 39537578 DOI: 10.1111/jfb.15987

The chubbyhead barbs, a distinct group of fishes endemic to southern Africa, currently include eight valid species. Historically, Enteromius anoplus was the most widespread freshwater fish in South Africa due to synonymizations in the 1960s. It occurred in nearly every river system except coastal systems in the Cape Fold Ecoregion and the lower Orange River. However, a recent revision utilizing molecular and morphological analyses has led to significant taxonomic updates. Enteromius anoplus is restricted to the Gouritz River system, whereas Enteromius cernuus and Enteromius oraniensis have been revalidated and respectively confined to the Olifants and Orange River systems. Additionally, a new species Enteromius mandelai was described, with its range currently considered to encompass several river systems in the Eastern Cape. Despite these advances, the taxonomic status of fish previously assigned to E. anoplus from KwaZulu-Natal remained uncertain. In this study, an integrative approach, combining genetic analysis, morphological characteristics, and geographic data, was employed to resurrect Enteromius karkensis as a distinct species from E. anoplus. Enteromius karkensis is deeply genetically differentiated (3.99%-8.07% p-distance) from its congeners within the chubbyhead group. Morphologically, E. karkensis is easily distinguishable from its counterparts due to possession of a terminal mouth (vs. inferior in E. amatolicus), one pair of maxillary barbels (vs. two conspicuous pairs in E. motebensis, E. treurensis, and E. gurneyi), and a complete lateral line (vs. incomplete in E. anoplus and E. oraniensis). Furthermore, E. karkensis is differentiated from E. mandelai and E. cernuus by its long maxillary barbels that extend beyond the midpoint of the orbit. These findings highlight a consistent pattern from previous studies that show many freshwater fishes in South Africa have narrow geographic ranges. This emphasizes the importance of targeted conservation and management efforts, and our understanding of the biogeographic and evolutionary history of freshwater fishes in southern Africa.

Matched MeSH terms: Phylogeny*
Current knowledge of taxonomy, physiology and chemical ecology about Bactrocera dorsalis and its related species with comments to Wu et al. (2020)

Hee AK, Wee SL, Ono H, Nishida R, Tan KH

Mol Phylogenet Evol, 2021 03;156:107019.
PMID: 33248203 DOI: 10.1016/j.ympev.2020.107019
Matched MeSH terms: Phylogeny
Linking functional traits to multiscale statistics of leaf venation networks

Blonder B, Both S, Jodra M, Xu H, Fricker M, Matos IS, et al.

New Phytol, 2020 12;228(6):1796-1810.
PMID: 32712991 DOI: 10.1111/nph.16830

Leaf venation networks evolved along several functional axes, including resource transport, damage resistance, mechanical strength, and construction cost. Because functions may depend on architectural features at different scales, network architecture may vary across spatial scales to satisfy functional tradeoffs. We develop a framework for quantifying network architecture with multiscale statistics describing elongation ratios, circularity ratios, vein density, and minimum spanning tree ratios. We quantify vein networks for leaves of 260 southeast Asian tree species in samples of up to 2 cm2 , pairing multiscale statistics with traits representing axes of resource transport, damage resistance, mechanical strength, and cost. We show that these multiscale statistics clearly differentiate species' architecture and delineate a phenotype space that shifts at larger scales; functional linkages vary with scale and are weak, with vein density, minimum spanning tree ratio, and circularity ratio linked to mechanical strength (measured by force to punch) and elongation ratio and circularity ratio linked to damage resistance (measured by tannins); and phylogenetic conservatism of network architecture is low but scale-dependent. This work provides tools to quantify the function and evolution of venation networks. Future studies including primary and secondary veins may uncover additional insights.

Matched MeSH terms: Phylogeny
Fulltext Contribution to the Pteridophyte Flora of Langkawi Archipelago, Peninsular Malaysia

Maideen H, Damanhuri A

Trop Life Sci Res, 2015 Dec;26(2):111-9.
PMID: 26868714 MyJurnal

The pteridophyte flora of Langkawi Archipelago consists of 130 species, 1 subspecies and 12 varieties in 68 genera and 27 families. This value represents 22.1% of the 647 taxa at the species level and below reported for Peninsular Malaysia. Of the 143 recorded taxa of pteridophytes at the species level and below, 8 species in 2 genera and 2 families are lycophytes and the other 135 taxa in 66 genera and 25 families are monilophytes or ferns.

Matched MeSH terms: Phylogeny
A new set of microsatellite markers for Phoxinus lumaireul senso lato, Phoxinus marsilii and Phoxinus krkae for population and molecular taxonomic studies

Vucić M, Jelić M, Klobučar G, Jelić D, Gan HM, Austin C, et al.

J Fish Biol, 2022 Nov;101(5):1225-1234.
PMID: 36054289 DOI: 10.1111/jfb.15194

Minnows of the genus Phoxinus are common and an often highly abundant fish species in Palearctic freshwater habitats. Phoxinus species have a complex evolutionary history, phylogenetic relationships are not well understood and there are a number of unresolved taxonomic problems. There are currently 23 different mitochondrial genetic lineages identified in the genus Phoxinus, 13 of which are recognized as valid species. The taxonomic status of these lineages requires resolution, including the degree to which they can interbreed. Suitable nuclear molecular markers for studies of population divergence and interbreeding between morphotypes and mitochondrial lineages are lacking for Phoxinus species. Therefore, the authors developed a set of microsatellite markers using genomic information from Phoxinus lumaireul and tested their suitability for this and two related species, Phoxinus krkae and Phoxinus marsilii. Out of 16 microsatellite candidate loci isolated, 12 were found to be in Hardy-Weinberg equilibrium when tested on two P. lumaireul senso lato populations. Seven loci amplified across the three species, enabling the study of intraspecific genetic diversity and population structure within P. marsilii and P. krkae. The markers were able to clearly resolve differences among the three tested species, including the recently described P. krkae, and are therefore suitable for the detection of introgression and hybridization among populations consisting of mixtures of two or more of P. lumaireul s. l., P. marsilii and P. krkae.

Matched MeSH terms: Phylogeny
Six marine thecate Heterocapsa (Dinophyceae) from Malaysia, including the description of three novel species and their cytotoxicity potential

Hanifah AH, Teng ST, Law IK, Abdullah N, Chiba SUA, Lum WM, et al.

Harmful Algae, 2022 Dec;120:102338.
PMID: 36470602 DOI: 10.1016/j.hal.2022.102338

Thirty-four strains of Heterocapsa were established from Malaysian waters and their morphologies were examined by light, scanning, and transmission electron microscopy. Three species, H. bohaiensis, H. huensis, and H. rotundata, and three new species, H. borneoensis sp. nov., H. limii sp. nov., and H. iwatakii sp. nov. were described in this study. The three species were differentiated morphologically by unique characteristics of cell size, shape, displacement of the cingulum, shape and position of nucleus, the number and position of pyrenoids, and body scale ultrastructure. The species delimitations were robustly supported by the molecular data. A light-microscopy-based key to species of Heterocapsa is established, with two major groups, i.e., species with a single pyrenoid, and species with multiple pyrenoids. Bioassays were conducted by exposing Artemia nauplii to Heterocapsa densities of 1-5 × 105 cells mL-1, and treatments exposed to H. borneoensis showed naupliar mortality, while no naupliar death was observed in the treatments exposed to cells of H. bohaiensis, H. huensis, H. limii, and H. iwatakii. Naupliar death was observed during the initial 24 h for both tested H. borneoensis strains, and mortality rates increased up to 50% after 72-h exposure. This study documented for the first time the diversity and cytotoxic potency of Heterocapsa species from Malaysian waters.

Matched MeSH terms: Phylogeny
Fulltext The biogeography of bent-toed geckos, Cyrtodactylus (Squamata: Gekkonidae)

Grismer LL, Poyarkov NA, Quah ESH, Grismer JL, Wood PL

PeerJ, 2022;10:e13153.
PMID: 35341041 DOI: 10.7717/peerj.13153

The gekkonid genus Cyrtodactylus is the third largest vertebrate genus on the planet with well over 300 species that range across at least eight biogeographic regions from South Asia to Melanesia. The ecological and morphological plasticity within the genus, has contributed to its ability to disperse across ephemeral seaways, river systems, basins, land bridges, and mountain ranges-followed by in situ diversification within specific geographic areas. Ancestral ranges were reconstructed on a mitochondrial phylogeny with 346 described and undescribed species from which it was inferred that Cyrtodactylus evolved in a proto-Himalaya region during the early Eocene. From there, it dispersed to what is currently Indoburma and Indochina during the mid-Eocene-the latter becoming the first major center of origin for the remainder of the genus that seeded dispersals to the Indian subcontinent, Papua, and Sundaland. Sundaland became a second major center of radiation during the Oligocene and gave rise to a large number of species that radiated further within Sundaland and dispersed to Wallacea, the Philippines, and back to Indochina. One Papuan lineage dispersed west to recolonize and radiate in Sundaland. Currently, Indochina and Sundaland still harbor the vast majority of species of Cyrtodactylus.

Matched MeSH terms: Phylogeny
Fulltext DNA Barcoding, Phylogenetic Analysis and Secondary Structure Predictions of Nepenthes ampullaria, Nepenthes gracilis and Nepenthes rafflesiana

Saidon NA, Wagiran A, Samad AFA, Mohd Salleh F, Mohamed F, Jani J, et al.

Genes (Basel), 2023 Mar 11;14(3).
PMID: 36980969 DOI: 10.3390/genes14030697

Nepentheceae, the most prominent carnivorous family in the Caryophyllales order, comprises the Nepenthes genus, which has modified leaf trap characteristics. Although most Nepenthes species have unique morphologies, their vegetative stages are identical, making identification based on morphology difficult. DNA barcoding is seen as a potential tool for plant identification, with small DNA segments amplified for species identification. In this study, three barcode loci; ribulose-bisphosphate carboxylase (rbcL), intergenic spacer 1 (ITS1) and intergenic spacer 2 (ITS2) and the usefulness of the ITS1 and ITS2 secondary structure for the molecular identification of Nepenthes species were investigated. An analysis of barcodes was conducted using BLASTn, pairwise genetic distance and diversity, followed by secondary structure prediction. The findings reveal that PCR and sequencing were both 100% successful. The present study showed the successful amplification of all targeted DNA barcodes at different sizes. Among the three barcodes, rbcL was the least efficient as a DNA barcode compared to ITS1 and ITS2. The ITS1 nucleotide analysis revealed that the ITS1 barcode had more variations compared to ITS2. The mean genetic distance (K2P) between them was higher for interspecies compared to intraspecies. The results showed that the DNA barcoding gap existed among Nepenthes species, and differences in the secondary structure distinguish the Nepenthes. The secondary structure generated in this study was found to successfully discriminate between the Nepenthes species, leading to enhanced resolutions.

Matched MeSH terms: Phylogeny
Thecal plate morphology, molecular phylogeny, and toxin analyses reveal two novel species of Alexandrium (Dinophyceae) and their potential for toxin production

Abdullah N, Teng ST, Hanifah AH, Law IK, Tan TH, Krock B, et al.

Harmful Algae, 2023 Aug;127:102475.
PMID: 37544675 DOI: 10.1016/j.hal.2023.102475

This study describes two novel species of marine dinophytes in the genus Alexandrium. Morphological characteristics and phylogenetic analyses support the placement of the new taxa, herein designated as Alexandrium limii sp. nov. and A. ogatae sp. nov. Alexandrium limii, a species closely related to A. taylorii, is distinguished by having a shorter 2'/4' suture length, narrower plates 1' and 6'', with larger length: width ratios, and by the position of the ventral pore (Vp). Alexandrium ogatae is distinguishable with its metasert plate 1' having almost parallel lateral margins, and by lacking a Vp. Production of paralytic shellfish toxins (PSTs), cycloimines, and goniodomins (GDs) in clonal cultures of A. ogatae, A. limii, and A. taylorii were examined analytically and the results showed that all strains contained GDs, with GDA as major variants (6-14 pg cell-1) for all strains except the Japanese strain of A. limii, which exclusively had a desmethyl variant of GDA (1.4-7.3 pg cell-1). None of the strains contained detectable levels of PSTs and cycloimines.

Matched MeSH terms: Phylogeny
A new species of the rare monotypic genus Cyrtinoclerus Chapin from Borneo, with notes on Meprinogenus Kolibáč (Coleoptera: Thanerocleridae)

Kolibáč J

Zootaxa, 2023 Apr 27;5271(3):569-578.
PMID: 37518109 DOI: 10.11646/zootaxa.5271.3.9

Cyrtinoclerus sabahensis sp. nov. of the less diverse cleroid family Thanerocleridae is described from Borneo. The unique specimen was found in the Malaysian state of Sabah and represents the first collecting record of the genus in one hundred years. The new species is assigned to the hitherto monotypic genus Cyrtinoclerus Chapin, 1924, whose single species is known from a single specimen from Basilan, Philippines, with no subsequently collected specimens known to date. Cyrtinoclerus is distinct in its unique synapomorphies, namely the tarsi with formula 5-5-5 but tarsomeres 4 reduced in size, elytron depressed in basal third with distinct bulge, and seriate punctation of elytra. The genus is re-examined and again classified within Thanerocleridae. A systematic status of Cyrtinoclerus and its relative Meprinogenus Kolibáč, 1992, also known only from two just one-hundred-year-old specimens, is discussed and possible synonymy of the latter genus suggested. The family Thanerocleridae now comprises 38 extant species in eleven genera and four extinct Cretaceous genera and species found in Burmese and Charentese ambers. A phylogenetic analysis of all fifteen extinct and extant genera of Thanerocleridae based on 36 morphological characters is presented and updated key to the tribe Thaneroclerini provided.

Matched MeSH terms: Phylogeny
Solving the taxonomic identity of Hipposideros cineraceus sensu lato (Chiroptera: Hipposideridae) in the Thai-Malay Peninsula, with the description of a new species

Wongwaiyut P, Karapan S, Saekong P, Francis CM, Guillén-Servent A, Senawi J, et al.

Zootaxa, 2023 May 03;5277(3):401-442.
PMID: 37518310 DOI: 10.11646/zootaxa.5277.3.1

A new species of small Hipposideros in the bicolor group is described based on specimens from Thailand and Malaysia. It can be distinguished from other small Hipposideros in Southeast Asia by a combination of external, craniodental, and bacular morphology, as well as echolocation call frequency. The new species has a distinct rounded swelling on the internarial septum of the noseleaf, with a forearm length of 35.3-42.6 mm, greatest skull length of 15.94-17.90 mm, and a call frequency of maximum energy of 132.3-144.0 kHz. Although clearly different in morphology, the new species forms a sister clade with H. kunzi and H. bicolor in the phylogenetic trees based on mitochondrial DNA. In addition, this study reports echolocation and genetic data, with a confirmed record of H. einnaythu from Thailand for the first time. The new species most closely resembles H. einnaythu. However, it differs in the details of the noseleaf and craniodental morphology, and it has a genetic distance of 9.6% and 10.4% based on mitochondrial COI and ND2, respectively. It is currently documented from five localities: two in peninsular Thailand, at Hala Forest in Yala Province, and Phru To Daeng Swamp Forest in Narathiwat Province, one from peninsular Malaysia at Krau Wildlife Reserve in Pahang, and another two in Sabah, Malaysian Borneo at Gunung Kinabalu, and near Madai Caves. However, it is likely that many previous records of "H. cineraceus" from Borneo refer to this species. Most records of the species are from lowland evergreen rainforest, though one record from Sabah was at 1800m. The roosting sites for this new species are currently unknown. Future research with a combination of data such as genetics, echolocation and morphology would be necessary to further determine the species geographic distribution in Southeast Asia.

Matched MeSH terms: Phylogeny
Molecular characterization and phylogenetic analysis of avian influenza H3N8 virus isolated from imported waterfowl in Malaysia

Leow BL, Shohaimi SA, Mohd Yusop FF, Sidik MR, Mohd Saeid FH

Trop Biomed, 2023 Jun 01;40(2):220-235.
PMID: 37650410 DOI: 10.47665/tb.40.2.014

Wild aquatic birds are natural reservoirs of influenza A viruses and H3 subtype is one of the most prevalent subtypes in waterfowl. Two H3N8 viruses of low pathogenic avian influenza (LPAI) were isolated via egg inoculation technique from the fecal swab specimens from imported barnacle goose and paradise shelduck in Veterinary Research Institute Ipoh, Malaysia. The full length of eight gene segments of the two viruses were amplified and sequenced with specific primers. The sequences were molecularly characterized, and the sequence identity were assessed with other published sequences. The two viruses are identical and they possess the same amino acid sequences for all the eight gene segments. The viruses were highly similar to the H3 virus from Netherlands and N8 virus from Belgium respectively. Phylogenetic analysis revealed that all the eight gene segments were grouped in the Eurasian lineage, and genetic reassortment may occur between the internal genes of the H3 viruses and other AI subtypes. Though four amino acid substitutions were identified in the hemagglutinin gene, the viruses retained most of the avian-type receptor binding preference. Few amino acid substitutions were observed in all internal genes. Most of the neuraminidase inhibitors and adamantine resistance related mutation were not seen in the viruses. The replicative capacity, cross species transmissibility, and potential zoonotic risk of the viruses are worth further investigation. As H3 virus poses potential threats to both human and animals, and with the increase in the international trade of birds; strict quarantine practice at the entry point and good laboratory diagnostic capabilities is crucial to prevent the introduction of new AI virus into our country.

Matched MeSH terms: Phylogeny

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