Displaying publications 81 - 100 of 573 in total

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  1. Proteomic analysis of Moroccan cobra Naja haje legionis venom using tandem mass spectrometry
    Malih I, Ahmad rusmili MR, Tee TY, Saile R, Ghalim N, Othman I
    J Proteomics, 2014 Jan 16;96:240-52.
    PMID: 24269350 DOI: 10.1016/j.jprot.2013.11.012
    The proteome of the venom of Naja haje legionis, the only medically important elapid species in Morocco, has been elucidated by using a combination of proteomic techniques that includes size exclusion chromatography, reverse-phase HPLC, Tricine/SDS-Page, tryptic digestion, Q-TOF tandem mass spectrometry and database search. The sequence analysis of venom fractions revealed a highly complex venom proteome which counts a total of 76 proteins identified from database that can be assigned into 9 proteins families. We report the identification of: cobra venom factor (CVF), l-amino-acid oxidases (LAAO), acetylcholinesterase (AChE), snake venom metalloproteinases (SVMP), cysteine rich secretory proteins (CRISP), venom nerve growth factor (vNGF), phospholipases A2 (PLA2), vespryns, kunitz-type inhibitor, short neurotoxins, long neurotoxins, weak neurotoxins, neurotoxin like proteins, muscarinic toxins, cardiotoxins and cytotoxins. Comparison of these proteins showed high sequence homology with proteins from other African and Asian cobras. Further works are needed to assess the contribution of individual toxins in venom toxicity.
    Matched MeSH terms: Species Specificity
  2. Description of two new species of Dermacentor Koch, 1844 (Acari: Ixodidae) from Oriental Asia
    Apanaskevich DA, Apanaskevich MA
    Syst Parasitol, 2016 Feb;93(2):159-71.
    PMID: 26790680 DOI: 10.1007/s11230-015-9614-8
    Dermacentor tamokensis n. sp. and Dermacentor pseudocompactus n. sp. (Acari: Ixodidae) are described based on adults ex wild boar and vegetation from China, India, Malaysia, and Vietnam and males ex wild boar from Nepal, respectively. Adults of D. tamokensis n. sp. are similar to those of D. taiwanensis Sugimoto, 1935 and D. atrosignatus Neumann, 1906 but can be distinguished by the colour pattern of the conscutum and scutum, the size and density of punctations on the pseudoscutum and scutum, the width of the cornua, and the shape of female genital structures. Males of D. pseudocompactus n. sp. are most similar to those of D. compactus Neumann, 1901 but can be distinguished by the colour pattern, sculpture and punctations of the conscutum, and the shape and length of the coxal spurs.
    Matched MeSH terms: Species Specificity
  3. Leaf and twig traits predict habitat adaptation and demographic strategies in tropical freshwater swamp forest trees
    Lam WN, Huang J, Tay AHT, Sim HJ, Chan PJ, Lim KE, et al.
    New Phytol, 2024 Aug;243(3):881-893.
    PMID: 38840520 DOI: 10.1111/nph.19876
    Differences in demographic and environmental niches facilitate plant species coexistence in tropical forests. However, the adaptations that enable species to achieve higher demographic rates (e.g. growth or survival) or occupy unique environmental niches (e.g. waterlogged conditions) remain poorly understood. Anatomical traits may better predict plant environmental and demographic strategies because they are direct measurements of structures involved in these adaptations. We collected 18 leaf and twig traits from 29 tree species in a tropical freshwater swamp forest in Singapore. We estimated demographic parameters of the 29 species from growth and survival models, and degree of association toward swamp habitats. We examined pairwise trait-trait, trait-demography and trait-environment links while controlling for phylogeny. Leaf and twig anatomical traits were better predictors of all demographic parameters than other commonly measured leaf and wood traits. Plants with wider vessels had faster growth rates but lower survival rates. Leaf and spongy mesophyll thickness predicted swamp association. These findings demonstrate the utility of anatomical traits as indicators of plant hydraulic strategies and their links to growth-mortality trade-offs and waterlogging stress tolerance that underlie species coexistence mechanisms in tropical forest trees.
    Matched MeSH terms: Species Specificity
  4. Morphological identification and phylogenetic analysis of Eimeria coypi and Eimeria fluviatilis (Apicomplexa: Eimeriidae) isolated from nutrias (Myocastor coypus [Rodentia]) in Japan
    Ouchi S, Koda R, Ishizuka Y, Ikemoto S, Sakata M, Iwaide S, et al.
    Syst Parasitol, 2025 Jan 28;102(1):18.
    PMID: 39873855 DOI: 10.1007/s11230-025-10216-0
    The nutria (Myocastor coypus) is a semiaquatic rodent that originally inhabited South America. However, the animals have spread to different continents as alien species, and their numbers are quickly increasing, especially in North America, Europe, and Eastern Asia including Japan. Although nutrias have been suggested to serve as reservoirs for pathogens, including parasites, there have been few reports on this subject. In the present study, we surveyed the gastrointestinal parasites in nutrias living in Japan to better understand their prevalence in nutrias. We collected 72 samples of intestinal contents or feces from nutrias in Osaka and Okayama Prefectures. We found that 49 (68.1 %) samples were positive for Eimeria parasites, and two types of oocysts were identified: ellipsoidal (Type A) and subspherical (Type B) oocysts. In addition, Strongyloides myopotami was detected in 44 samples, and Capillaria spp. and Fasciola spp. were detected in one and three samples, respectively. Based on the morphologies of the detected Eimeria oocysts, Types A and B were identified to be E. coypi and E. fluviatilis, respectively. Phylogenetic analyses after PCR and sequencing targeting the cytochrome c oxidase subunit I gene placed the sequences of E. fluviatilis (Type B) as a cluster between the sequences of Eimeria derived from rodents. The sequences of the three subgenotypes of E. coypi (Type A) were included in the cluster containing the sequences of Eimeria spp. from rodents of multiple species, which is referred to as the Apionodes supercluster, and is separate from other clades. It has been suggested that Eimeria spp. from rodents in this cluster can quickly adapt to infect different hosts. Although further analyses are needed to construct more detailed phylogenetic trees, our results revealed the genetical positions of Eimeria spp. in nutrias. In addition, our results may be helpful when considering host specificity as well as host switching by the pathogen.
    Matched MeSH terms: Species Specificity
  5. Isolation, characterization and antigenic cross-reactivities of the major hemorrhagin from Cryptelytrops purpureomaculatus venom
    Fung SY, Tan NH
    Indian J Exp Biol, 2013 Dec;51(12):1063-9.
    PMID: 24579371
    The major hemorrhagin from C. purpureomaculatus (mangrove pit viper) venom was purified to homogeneity and termed Maculatoxin. Maculatoxin has a molecular weight of 38 kDa as determined by SDS-PAGE. It is an acidic protein (pI= 4.2) and exhibited proteolytic and hemorrhagic activities (MHD10 = 0.84 microg in mice) but was not lethal to mice at a dose of 1 microg/g. The hemorrhagic activity of Maculatoxin was completely inactivated by EDTA and partially inhibited by ATP and citrate. The N-terminal sequence of Maculatoxin (TPEQQRFPPTYIDLGIFVDHGMYAT) shares a significant degree of homology with the metalloprotease domain of other venom hemorrhagins. Indirect ELISA showed anti-Maculatoxin cross reacted with protein components of many snake venoms. In the double-sandwich ELISA, however, anti-Maculatoxin cross-reacted only with venoms of certain species of the Trimeresurus (Asia lance-head viper) complex, and the results support the recent proposed taxonomy changes concerning the Trimeresurus complex.
    Matched MeSH terms: Species Specificity*
  6. DNA barcoding and phylogenetic analysis of Malaysian groupers (Subfamily: Epinephelinae) using mitochondrial Cytochrome c oxidase I (COI) gene
    Aziz NMA, Esa Y, Arshad A
    J Environ Biol, 2016 07;37(4 Spec No):725-33.
    PMID: 28779732
    The present study was carried out to examine the species identification and phylogenetic relationships of groupers in Malaysia using mitochondrial Cytochrome c Oxidase I (COI) gene, commonly known as barcoding gene. A total of 63 individuals comprising 10 species from three genera were collected from the coastal areas of Johor, Kelantan, Pahang, Perak, Selangor and Terengganu. All the individuals were morphologically identified and molecular works involved polymerase chain reaction (PCR) and sequencing of COI barcoding fragment (655 base pairs). Results from the BLAST search showed that 55 sequences could be assigned to 10 grouper species with high percentage identity index (≥95% to 100%), while eight grouper individuals showed discrepancies in their taxonomic identification based on the morphology and the COI barcoding results. The histogram of distances showed that there was a clear-cut barcode gap present in the sequences indicating a clear separation between intraspecific and interspecific distances. The pairwise genetic distances showed lowest pairwise distance between P. leopardus and P. maculatus (4.4%), while the highest pairwise distance was between E. bleekeri and P. maculatus (23.5%), supporting their morphological and habitat similarities and differences. Phylogenetic analysis (Neighbor-Joining) showed the presence of two major clades (1) genus Epinephelus vs (2) genus Plectropomus and Cephalopholis). In conclusion, the present study has managed to show the accuracy of DNA barcoding method for species identification, and utilization of COI gene for phylogenetic study among groupers. ?
    Matched MeSH terms: Species Specificity
  7. Inner shell as variation key of local hard clam Meretrix spp
    Hamli H, Idris MH, Abu Hena MK, Rajaee AH, Arshad A
    J Environ Biol, 2016 07;37(4 Spec No):641-6.
    PMID: 28779722
    The morphology and 12 shell morphometric features proportionate to shell length were analysed between local hard clam; Meretrix lyrata, M. meretrix and M. lusoria from Sarawak, Malaysia. Meretrix spp. was observed to comprise a unique feature of a pallial sinus scar for each species. Analysis of variance revealed significant differences among Meretrix spp. using proportion ratios of SL for SW; LL; AL; LCT; AW; PW and PS (p<0.05). Cluster analysis among morphometric features of M. lyrata, M. meretrix and M. lusoria were discriminated at 98.5% similarities and supported by the principal component analysis. The present study suggests that pallial sinus scar shape, together with interior and exterior morphometric features, were suitable as identification keys for Meretrix spp. Hence, the present study emphasizes on the application of interior, rather than exterior morphology and morphometric features in hard clam identification before further investigation can be performed through genetic identification means.
    Matched MeSH terms: Species Specificity
  8. Fulltext Land snails of Leptopoma Pfeiffer, 1847 in Sabah, Northern Borneo (Caenogastropoda: Cyclophoridae): an analysis of molecular phylogeny and geographical variations in shell form
    Phung CC, Heng PS, Liew TS
    PeerJ, 2017;5:e3981.
    PMID: 29104827 DOI: 10.7717/peerj.3981
    Leptopoma is a species rich genus with approximately 100 species documented. Species-level identification in this group has been based on shell morphology and colouration, as well as some anatomical features based on small sample sizes. However, the implications of the inter- and intra-species variations in shell form to the taxonomy of Leptopoma species and the congruency of its current shell based taxonomy with its molecular phylogeny are still unclear. There are four Leptopoma species found in Sabah, Borneo, and their taxonomy status remains uncertain due to substantial variation in shell forms. This study focuses on the phylogenetic relationships and geographical variation in shell form of three Leptopoma species from Sabah. The phylogenetic relationship of these species was first estimated by performing Maximum Likelihood and Bayesian analysis based on mitochondrial genes (16S rDNA and COI) and nuclear gene (ITS-1). Then, a total of six quantitative shell characters (i.e., shell height, shell width, aperture height, aperture width, shell spire height, and ratio of shell height to width) and three qualitative shell characters (i.e., shell colour patterns, spiral ridges, and dark apertural band) of the specimens were mapped across the phylogenetic tree and tested for phylogenetic signals. Data on shell characters of Leptopoma sericatum and Leptopoma pellucidum from two different locations (i.e., Balambangan Island and Kinabatangan) where both species occurred sympatrically were then obtained to examine the geographical variations in shell form. The molecular phylogenetic analyses suggested that each of the three Leptopoma species was monophyletic and indicated congruence with only one of the shell characters (i.e., shell spiral ridges) in the current morphological-based classification. Although the geographical variation analyses suggested some of the shell characters indicating inter-species differences between the two Leptopoma species, these also pointed to intra-species differences between populations from different locations. This study on Leptopoma species is based on small sample size and the findings appear only applicable to Leptopoma species in Sabah. Nevertheless, we anticipate this study to be a starting point for more detailed investigations to include the other still little-known (ca. 100) Leptopoma species and highlights a need to assess variations in shell characters before they could be used in species classification.
    Matched MeSH terms: Species Specificity
  9. Fulltext Feeding strategies and competition between terrestrial Haemadipsa leeches (Euhirudinea: Arhynchobdellida) in Danum Valley rainforest (Borneo, Sabah)
    Gasiorek P, Rozycka H
    Folia Parasitol., 2017 10 03;64.
    PMID: 28980971 DOI: 10.14411/fp.2017.031
    Haemadipsid leeches are among the most successful terrestrial invertebrates in Bornean rainforests. They are very common ectoparasites of vertebrates, and their abundance has facilitated the conduction of numerous projects in the fields of ecology, zoogeography and taxonomy. We undertook research on two species inhabiting lowland dipterocarp forest, Haemadipsa picta Moore, 1929 and Haemadipsa subagilis (Moore, 1929), in order to address the following questions: (a) is there a difference in leech abundance between trails and off-trails?; (b) is ambush location dependent on specimen size or is species-specific?; (c) is intra- and interspecific competition limited by differences in foraging behaviours or vertical niche partitioning? Our results clearly show that H. picta is more abundant on trails than on off-trails and is vertically dispersed within the understory; the size of a specimen is strongly correlated with plant height. Haemadipsa subagilis was found not to exhibit such patterns. We suggest a possible lowering of interspecific competition between these species as a result of: (i) size-dependent dispersion of H. picta (together with reduction of intraspecific competition); and (ii) habitat specialisation of H. subagilis. Moreover, we provide new observations on their foraging behaviour.
    Matched MeSH terms: Species Specificity
  10. Fulltext Analysis of viral diversity for vaccine target discovery
    Khan AM, Hu Y, Miotto O, Thevasagayam NM, Sukumaran R, Abd Raman HS, et al.
    BMC Med Genomics, 2017 12 21;10(Suppl 4):78.
    PMID: 29322922 DOI: 10.1186/s12920-017-0301-2
    BACKGROUND: Viral vaccine target discovery requires understanding the diversity of both the virus and the human immune system. The readily available and rapidly growing pool of viral sequence data in the public domain enable the identification and characterization of immune targets relevant to adaptive immunity. A systematic bioinformatics approach is necessary to facilitate the analysis of such large datasets for selection of potential candidate vaccine targets.

    RESULTS: This work describes a computational methodology to achieve this analysis, with data of dengue, West Nile, hepatitis A, HIV-1, and influenza A viruses as examples. Our methodology has been implemented as an analytical pipeline that brings significant advancement to the field of reverse vaccinology, enabling systematic screening of known sequence data in nature for identification of vaccine targets. This includes key steps (i) comprehensive and extensive collection of sequence data of viral proteomes (the virome), (ii) data cleaning, (iii) large-scale sequence alignments, (iv) peptide entropy analysis, (v) intra- and inter-species variation analysis of conserved sequences, including human homology analysis, and (vi) functional and immunological relevance analysis.

    CONCLUSION: These steps are combined into the pipeline ensuring that a more refined process, as compared to a simple evolutionary conservation analysis, will facilitate a better selection of vaccine targets and their prioritization for subsequent experimental validation.

    Matched MeSH terms: Species Specificity
  11. Comparison of several lizard Leishmania species and strains in terms of kinetoplast minicircle and maxicircle DNA sequences, nuclear chromosomes, and membrane lipids
    Gomez-Eichelmann MC, Holz G, Beach D, Simpson AM, Simpson L
    Mol Biochem Parasitol, 1988 Jan 15;27(2-3):143-58.
    PMID: 3344003
    Eight strains of a lizard Leishmania species, L. tarentolae, were compared with four other saurian species [L. hoogstrali, L. adleri, L. agamae and Leishmania sp. LizS], with L. major from man and with Trypanosoma platydactyli, a putative lizard trypanosome, in terms of kinetoplast DNA minicircle and maxicircle sequences and in terms of nuclear chromosome patterns on orthogonal gel electrophoresis. The L. tarentolae strains fell into two major groups, one (group A) consisting of the L. tarentolae strains, UC, Krassner and Trager, derived from an Algerian gecko isolate and the other (group B) consisting of five L. tarentolae LEM strains isolated from geckos in southern France. T. platydactyli TPCL2, which was postulated by Wallbanks et al. to represent the lizard form of a French L. tarentolae strain, was closely related to the UC strain and not to the LEM strains, in all respects analyzed. Leishmania sp. LizS from a Mongolian gecko and L. hoogstrali from a Sudanese gecko showed some sequence similarities to the L. tarentolae strains, but the leishmanias said to be L. adleri from a Kenyan lacertid and L. agamae from an Israeli agamid showed no minicircle sequence similarities with lizard Leishmania and in fact were probably the same species. The maxicircle divergent region was larger in the group B strains than in the group A strains, but there were sequences in common with both groups, and not with L. hoogstrali and L. major. Four strains of L. tarentolae, the four other supposed saurian Leishmania species, three mammalian leishmanias, T. platydactyli and four other trypanosomes, T. cyclops (Malaysian macaque), T. conorrhini (Hawaiian reduviid bug), T. cruzi (man) and T. lewisi (feral rat) were analyzed for their contents of sterols and phosphoglyceride fatty acyl groups. T. platydactyli TPCL2 contained a sterol (5-dehydroepisterol), a phosphatidylcholine fatty acyl group (alpha-linolenic acid) and a phosphatidylethanolamine fatty acyl group (dihydrosterculic acid) characteristic of members of the genus Leishmania and not the genus Trypanosoma. The proportions of those lipids in the free sterol and phosphoglyceride fractions of T. platydactyli TPCL2 most closely resembled those seen in the Leishmania strains from Algerian, French, Mongolian and Sudanese geckos.
    Matched MeSH terms: Species Specificity
  12. Fulltext Complete mitochondrial genome of Zeugodacus tau (Insecta: Tephritidae) and differentiation of Z. tau species complex by mitochondrial cytochrome c oxidase subunit I gene
    Yong HS, Song SL, Lim PE, Eamsobhana P
    PLoS One, 2017;12(12):e0189325.
    PMID: 29216281 DOI: 10.1371/journal.pone.0189325
    The tephritid fruit fly Zeugodacus tau (Walker) is a polyphagous fruit pest of economic importance in Asia. Studies based on genetic markers indicate that it forms a species complex. We report here (1) the complete mitogenome of Z. tau from Malaysia and comparison with that of China as well as the mitogenome of other congeners, and (2) the relationship of Z. tau taxa from different geographical regions based on sequences of cytochrome c oxidase subunit I gene. The complete mitogenome of Z. tau had a total length of 15631 bp for the Malaysian specimen (ZT3) and 15835 bp for the China specimen (ZT1), with similar gene order comprising 37 genes (13 protein-coding genes-PCGs, 2 rRNA genes, and 22 tRNA genes) and a non-coding A + T-rich control region (D-loop). Based on 13 PCGs and 15 mt-genes, Z. tau NC_027290 (China) and Z. tau ZT1 (China) formed a sister group in the lineage containing also Z. tau ZT3 (Malaysia). Phylogenetic analysis based on partial sequences of cox1 gene indicates that the taxa from China, Japan, Laos, Malaysia, Bangladesh, India, Sri Lanka, and Z. tau sp. A from Thailand belong to Z. tau sensu stricto. A complete cox1 gene (or 13 PCGs or 15 mt-genes) instead of partial sequence is more appropriate for determining phylogenetic relationship.
    Matched MeSH terms: Species Specificity
  13. New records of 13 species of black flies (Diptera: Simuliidae) from Myanmar
    Takaoka H, Srisuka W, Maleewong W, Saeung A
    Acta Trop, 2018 Feb;178:281-289.
    PMID: 29217382 DOI: 10.1016/j.actatropica.2017.12.009
    A faunistic survey of black flies in Shan State, central Myanmar, was carried out in 2013. A total of 16 species were collected, of which 13 species are newly recorded from Myanmar. Among 13 newly recorded species, S. (S.) chiangmaiense Takaoka & Suzuki varied in the number of pupal gill filaments from eight to 10. This survey increases the number of species of black flies from Myanmar from 8 to 23. They are classified in five subgenera of the genus Simulium: one in Asiosimulium, seven in Gomphostilbia, one in Montisimulium, two in Nevermannia and 12 in Simulium.
    Matched MeSH terms: Species Specificity
  14. Pollinator specialization in the enigmatic Rafflesia cantleyi: A true carrion flower with species-specific and sex-biased blow fly pollinators
    Wee SL, Tan SB, Jürgens A
    Phytochemistry, 2018 Sep;153:120-128.
    PMID: 29906658 DOI: 10.1016/j.phytochem.2018.06.005
    The plants of the enigmatic genus Rafflesia are well known for their gigantic flowers and their floral features such as pungent floral scent and vivid dark color, which mimics the food/brood sites of carrion. However, information on the pollination biology of this plant group remains limited and mostly anecdotal. In the present paper, we studied the floral volatiles of R. cantleyi Solms-Laubach and their role in pollinator attraction. To achieve these aims, the floral scent was collected in situ in the field using a dynamic headspace method followed by chemical analysis via GC-MS. The olfactory preferences of pollinators to the identified chemical compounds, were tested singly and in blends, in flight tunnel bioassays and compared with responses to headspace floral extracts. In addition, flower-visiting calliphorid flies and the local carrion fly community were sampled and identified. Five species of calliphorid flies (subfamilies of Chrysomyinae and Calliphorinae), all females, were found on the flowers, whereas nine species were found in the traps that were baited with tainted meat in the surrounding habitat. However, only flower visitors of one blow fly species, Chrysomya chani Kurahashi, were observed to carry R. cantleyi pollen after visiting male flowers. The floral volatiles emitted by male flowers in full bloom were dominated by two sulphur-containing compounds, dimethyl disulfide (DMDS) and dimethyl trisulfide (DMTS). These were accompanied by other minor compounds such as benzenoids (4), monoterpenoids (4), trace amounts of aliphatic compounds (1), and sesquiterpenes (1). In flight-tunnel bioassays, a female-specific positive response of C. chani flies to individual DMDS, DMTS, and a blend of DMDS and DMTS was evident. Our findings suggest that R. cantleyi biochemically mimics carrion and that relative ratio of oligosulfides in the floral scent play a key role in sex-biased pollinator specialization, attracting only female C. chani carrion flies to the flowers.
    Matched MeSH terms: Species Specificity
  15. Comprehensive multi-locus phylogeny of Old World tree frogs (Anura: Rhacophoridae) reveals taxonomic uncertainties and potential cases of over- and underestimation of species diversity
    Chan KO, Grismer LL, Brown RM
    Mol Phylogenet Evol, 2018 10;127:1010-1019.
    PMID: 30030179 DOI: 10.1016/j.ympev.2018.07.005
    The family Rhacophoridae is one of the most diverse amphibian families in Asia, for which taxonomic understanding is rapidly-expanding, with new species being described steadily, and at increasingly finer genetic resolution. Distance-based methods frequently have been used to justify or at least to bolster the recognition of new species, particularly in complexes of "cryptic" species where obvious morphological differentiation does not accompany speciation. However, there is no universally-accepted threshold to distinguish intra- from interspecific genetic divergence. Moreover, indiscriminant use of divergence thresholds to delimit species can result in over- or underestimation of species diversity. To explore the range of variation in application of divergence scales, and to provide a family-wide assessment of species-level diversity in Old-World treefrogs (family Rhacophoridae), we assembled the most comprehensive multi-locus phylogeny to date, including all 18 genera and approximately 247 described species (∼60% coverage). We then used the Automatic Barcode Gap Discovery (ABGD) method to obtain different species-delimitation schemes over a range of prior intraspecific divergence limits to assess the consistency of divergence thresholds used to demarcate current species boundaries. The species-rich phylogeny was able to identify a number of taxonomic errors, namely the incorrect generic placement of Chiromantis inexpectatus, which we now move to the genus Feihyla, and the specific identity of Rhacophorus bipunctatus from Peninsular Malaysia, which we tentatively reassign to R. rhodopus. The ABGD analysis demonstrated overlap between intra- and interspecific divergence limits: genetic thresholds used in some studies to synonymize taxa have frequently been used in other studies to justify the recognition of new species. This analysis also highlighted numerous groups that could potentially be split or lumped, which we earmark for future examination. Our large-scale and en bloc approach to species-level phylogenetic systematics contributes to the resolution of taxonomic uncertainties, reveals possible new species, and identifies numerous groups that require critical examination. Overall, we demonstrate that the taxonomy and evolutionary history of Old-World tree frogs are far from resolved, stable or adequately characterized at the level of genus, species, and/or population.
    Matched MeSH terms: Species Specificity
  16. Expansion and systematics redefinition of the most threatened freshwater mussel family, the Margaritiferidae
    Lopes-Lima M, Bolotov IN, Do VT, Aldridge DC, Fonseca MM, Gan HM, et al.
    Mol Phylogenet Evol, 2018 10;127:98-118.
    PMID: 29729933 DOI: 10.1016/j.ympev.2018.04.041
    Two Unionida (freshwater mussel) families are present in the Northern Hemisphere; the Margaritiferidae, representing the most threatened of unionid families, and the Unionidae, which include several genera of unresolved taxonomic placement. The recent reassignment of the poorly studied Lamprotula rochechouartii from the Unionidae to the Margaritiferidae motivated a new search for other potential species of margaritiferids from members of Gibbosula and Lamprotula. Based on molecular and morphological analyses conducted on newly collected specimens from Vietnam, we here assign Gibbosula crassa to the Margaritiferidae. Additionally, we reanalyzed all diagnostic characteristics of the Margaritiferidae and examined museum specimens of Lamprotula and Gibbosula. As a result, two additional species are also moved to the Margaritiferidae, i.e. Gibbosula confragosa and Gibbosula polysticta. We performed a robust five marker phylogeny with all available margaritiferid species and discuss the taxonomy within the family. The present phylogeny reveals the division of Margaritiferidae into four ancient clades with distinct morphological, biogeographical and ecological characteristics that justify the division of the Margaritiferidae into two subfamilies (Gibbosulinae and Margaritiferinae) and four genera (Gibbosula, Cumberlandia, Margaritifera, and Pseudunio). The systematics of the Margaritiferidae family is re-defined as well as their distribution, potential origin and main biogeographic patterns.
    Matched MeSH terms: Species Specificity
  17. Diatom Nitzschia navis-varingica (Bacillariophyceae) and its domoic acid production from the mangrove environments of Malaysia
    Tan SN, Teng ST, Lim HC, Kotaki Y, Bates SS, Leaw CP, et al.
    Harmful Algae, 2016 12;60:139-149.
    PMID: 28073557 DOI: 10.1016/j.hal.2016.11.003
    The distribution of the toxic pennate diatom Nitzschia was investigated at four mangrove areas along the coastal brackish waters of Peninsular Malaysia. Eighty-two strains of N. navis-varingica were isolated and established, and their identity confirmed morphologically and molecularly. Frustule morphological characteristics of the strains examined are identical to previously identified N. navis-varingica, but with a sightly higher density of the number of areolae per 1μm (4-7 areolae). Both LSU and ITS rDNAs phylogenetic trees clustered all strains in the N. navis-varingica clade, with high sequence homogeneity in the LSU rDNA (0-0.3%), while the intraspecific divergences in the ITS2 data set reached up to 7.4%. Domoic acid (DA) and its geometrical isomers, isodomoic A (IA) and isodomoic B (IB), were detected in cultures of N. navis-varingica by FMOC-LC-FLD, and subsequently confirmed by LC-MS/MS, with selected ion monitoring (SIM) and multiple reaction monitoring (MRM) runs. DA contents ranged between 0.37 and 11.06pgcell-1. This study demonstrated that the toxigenic euryhaline diatom N. navis-varingica is widely distributed in Malaysian mangrove swamps, suggesting the risk of amnesic shellfish poisoning and the possibility of DA contamination in the mangrove-related fisheries products.
    Matched MeSH terms: Species Specificity
  18. Fulltext Sex and species specific isotopic niche specialisation increases with trophic complexity: evidence from an ephemeral pond ecosystem
    Dalu T, Wasserman RJ, Vink TJ, Weyl OL
    Sci Rep, 2017 02 24;7:43229.
    PMID: 28233858 DOI: 10.1038/srep43229
    It is generally accepted that organisms that naturally exploit an ecosystem facilitate coexistence, at least partially, through resource partitioning. Resource availability is, however, highly variable in space and time and as such the extent of resource partitioning must be somewhat dependent on availability. Here we test aspects of resource partitioning at the inter- and intra-specific level, in relation to resource availability in an atypical aquatic environment using an isotope approach. Using closely related key organisms from an ephemeral pond, we test for differences in isotopic signatures between two species of copepod and between sexes within each species, in relation to heterogeneity of basal food resources over the course of the ponds hydroperiod. We show that basal food resource heterogeneity increases over time initially, and then decreases towards the end of the hydroperiod, reflective of the expected evolution of trophic complexity for these systems. Resource partitioning also varied between species and sexes, over the hydroperiod with intra- and inter-specific specialisation relating to resource availability. Intra-specific specialisation was particularly evident in the omnivorous copepod species. Our findings imply that trophic specialisation at both the intra- and inter-specific level is partly driven by basal food resource availability.
    Matched MeSH terms: Species Specificity
  19. Fulltext Escaping introns in COI through cDNA barcoding of mushrooms: Pleurotus as a test case
    Avin FA, Subha B, Tan YS, Braukmann TWA, Vikineswary S, Hebert PDN
    Ecol Evol, 2017 09;7(17):6972-6980.
    PMID: 28904776 DOI: 10.1002/ece3.3049
    DNA barcoding involves the use of one or more short, standardized DNA fragments for the rapid identification of species. A 648-bp segment near the 5' terminus of the mitochondrial cytochrome c oxidase subunit I (COI) gene has been adopted as the universal DNA barcode for members of the animal kingdom, but its utility in mushrooms is complicated by the frequent occurrence of large introns. As a consequence, ITS has been adopted as the standard DNA barcode marker for mushrooms despite several shortcomings. This study employed newly designed primers coupled with cDNA analysis to examine COI sequence diversity in six species of Pleurotus and compared these results with those for ITS. The ability of the COI gene to discriminate six species of Pleurotus, the commonly cultivated oyster mushroom, was examined by analysis of cDNA. The amplification success, sequence variation within and among species, and the ability to design effective primers was tested. We compared ITS sequences to their COI cDNA counterparts for all isolates. ITS discriminated between all six species, but some sequence results were uninterpretable, because of length variation among ITS copies. By comparison, a complete COI sequences were recovered from all but three individuals of Pleurotus giganteus where only the 5' region was obtained. The COI sequences permitted the resolution of all species when partial data was excluded for P. giganteus. Our results suggest that COI can be a useful barcode marker for mushrooms when cDNA analysis is adopted, permitting identifications in cases where ITS cannot be recovered or where it offers higher resolution when fresh tissue is. The suitability of this approach remains to be confirmed for other mushrooms.
    Matched MeSH terms: Species Specificity
  20. Fulltext To split or not to split? Multilocus phylogeny and molecular species delimitation of southeast Asian toads (family: Bufonidae)
    Chan KO, Grismer LL
    BMC Evol. Biol., 2019 04 25;19(1):95.
    PMID: 31023232 DOI: 10.1186/s12862-019-1422-3
    BACKGROUND: Recent studies have demonstrated that Bayesian species delimitation based on the multispecies coalescent model can produce inaccurate results by misinterpreting population splits as species divergences. An approach based on the genealogical divergence index (gdi) was shown to be a viable alternative, especially for delimiting allopatric populations where gene flow is low. We implemented these analyses to assess species boundaries in Southeast Asian toads, a group that is understudied and characterized by numerous unresolved species complexes.

    RESULTS: Multilocus phylogenetic analyses showed that deep evolutionary relationships including the genera Sigalegalephrynus, Ghatophryne, Parapelophryne, Leptophryne, Pseudobufo, Rentapia, and Phrynoides remain unresolved. Comparison of genetic divergences revealed that intraspecific divergences among allopatric populations of Pelophyrne signata (Borneo vs. Peninsular Malaysia), Ingerophrynus parvus (Peninsular Malaysia vs. Myanmar), and Leptophryne borbonica (Peninsular Malaysia, Java, Borneo, and Sumatra) are consistent with interspecific divergences of other Southeast Asian bufonid taxa. Conversely, interspecific divergences between Pelophryne guentheri/P. api, Ansonia latiffi/A. leptopus, and I. gollum/I. divergens were low (

    Matched MeSH terms: Species Specificity
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