scholarly journals DNA-based taxonomy of a mangrove-associated community of fishes in Southeast Asia

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Danial Hariz Zainal Abidin ◽  
Siti Azizah Mohd. Nor ◽  
Sébastien Lavoué ◽  
Masazurah A. Rahim ◽  
Noorul Azliana Jamaludin ◽  
...  
Keyword(s):  
Peninsular Malaysia ◽  
Tropical Fish ◽  
Fish Diversity ◽  
Molecular Evidence ◽  
Mangrove Forests ◽  
Morphological Examination ◽  
Operational Taxonomic Units ◽  
Reference Collection ◽  
Morphological Species ◽  
Merbok Estuary

AbstractThe Merbok Estuary comprises one of the largest remaining mangrove forests in Peninsular Malaysia. Its value is significant as it provides important services to local and global communities. It also offers a unique opportunity to study the structure and functioning of mangrove ecosystems. However, its biodiversity is still partially inventoried, limiting its research value. A recent checklist based on morphological examination, reported 138 fish species residing, frequenting or subject to entering the Merbok Estuary. In this work, we reassessed the fish diversity of the Merbok Estuary by DNA barcoding 350 specimens assignable to 134 species initially identified based on morphology. Our results consistently revealed the presence of 139 Molecular Operational Taxonomic Units (MOTUs). 123 of them are congruent with morphology-based species delimitation (one species = one MOTU). In two cases, two morphological species share the same MOTU (two species = one MOTU), while we unveiled cryptic diversity (i.e. COI-based genetic variability > 2%) within seven other species (one species = two MOTUs), calling for further taxonomic investigations. This study provides a comprehensive core-list of fish taxa in Merbok Estuary, demonstrating the advantages of combining morphological and molecular evidence to describe diverse but still poorly studied tropical fish communities. It also delivers a large DNA reference collection for brackish fishes occurring in this region which will facilitate further biodiversity-oriented research studies and management activities.

scholarly journals Assessing fish diversity of Merbok Estuary and adjacent marine waters by DNA taxonomy: towards building comprehensive DNA barcode reference library

2021 ◽  
Author(s):  
Danial Hariz Zainal Abidin ◽  
Siti Azizah Mohd. Nor ◽  
Sébastien Lavoué ◽  
Masazurah A. Rahim ◽  
Noorul Azliana Jamaludin ◽  
...  
Keyword(s):  
Dna Barcode ◽  
Peninsular Malaysia ◽  
Tropical Fish ◽  
Fish Diversity ◽  
Molecular Evidence ◽  
Mangrove Forests ◽  
Morphological Examination ◽  
Dna Taxonomy ◽  
Reference Collection ◽  
Merbok Estuary

Abstract The Merbok Estuary comprises one of the largest remaining mangrove forests in Peninsular Malaysia. Its value is significant as it provides both direct and indirect services to local and global communities. It also offers a unique opportunity to study the structure and functioning of mangrove ecosystems. However, its biodiversity is still partially described, limiting its research value. Recent inventories based on morphological examination, documented 138 fish species residing, frequenting or subject to entering the Merbok Estuary. Using a molecular approach, we assessed the fish diversity of the Merbok Estuary and its adjacent waters in DNA barcoding 350 specimens assignable to 135 species initially identified based on morphology. Our results revealed the presence of 140 MOTUs, 130 of them are congruent with morphology-based species delimitation. In two cases, barcodes did not permit to differentiate between two morphotypes while they unveiled cryptic diversity within six other species, calling for further taxonomic investigations. This study provides a comprehensive core-list of fish taxa in Merbok Estuary, demonstrating the advantages of combining morphological and molecular evidence to describe diverse but still poorly studied tropical fish communities. It also delivers a large DNA reference collection for brackish fishes occurring in this region which will facilitate further biodiversity-oriented research studies and management activities.

Genetic Diversity of Pediculus humanus capitis (Phthiraptera: Pediculidae) in Peninsular Malaysia and Molecular Detection of Its Potential Associated Pathogens

2019 ◽  
Vol 57 (3) ◽  
pp. 915-926
Author(s):  
Aida Syafinaz Mokhtar ◽  
Yee Ling Lau ◽  
John-James Wilson ◽  
Noraishah Mydin Abdul-Aziz
Keyword(s):  
Genetic Diversity ◽  
Dna Barcoding ◽  
Pathogenic Bacteria ◽  
Peninsular Malaysia ◽  
Molecular Evidence ◽  
Head Lice ◽  
Pediculus Humanus Capitis ◽  
Accurate Identification ◽  
Pediculosis Capitis ◽  
Pediculus Humanus

Abstract Pediculosis capitis caused by Pediculus humanus capitis (De Geer) is endemic all over the world, and children are mostly affected, particularly those living in overcrowded institutions. Several studies have shown that P. h. capitis carried human pathogenic bacteria, suggesting the potential role of head lice in the transmission of pathogens to humans. In this study, we determined the genetic diversity of head lice collected from welfare homes sheltering underprivileged children by using DNA barcoding and demonstrated the presence of Acinetobacter spp., Serratia marcescens, and Staphylococcus aureus in head lice, which have never been investigated before in Malaysia. Cox1 DNA barcoding identified the head lice, P. h. capitis collected from welfare homes across two geographical areas of Peninsular Malaysia as belonging to clades A, B, and D. Acinetobacter bacteria: Acinetobacter guillouiae, Acinetobacter junii, Acinetobacter baumannii, and Acinetobacter nosocomialis were detected in head lice belonging to clades A and also D. In addition, DNA from S. marcescens and S. aureus were also detected in both clades A and D. To our knowledge, this is the first report on the genetic diversity of head lice in Malaysia through DNA barcoding, as well as the first to provide molecular evidence on the type of bacteria occurring in head lice in Malaysia. It is anticipated that the DNA barcoding technique used in this study will be able to provide rapid and accurate identification of arthropods, in particular, medically important ectoparasites.

Mitochondrial sequence data clarify species concepts in the Cyclocephala mafaffa species complex (Coleoptera: Scarabaeidae: Dynastinae: Cyclocephalini)

Zootaxa ◽  
2020 ◽  
Vol 4772 (1) ◽  
pp. 89-110
Author(s):  
MATTHEW R. MOORE ◽  
STEFANI M. HARRISON ◽  
RONALD D. CAVE ◽  
MARC A. BRANHAM
Keyword(s):  
Species Complex ◽  
Gap Analysis ◽  
Sequence Data ◽  
Species Concepts ◽  
Neighbor Joining ◽  
The West ◽  
Research Attention ◽  
Operational Taxonomic Units ◽  
Floral Visitation ◽  
Morphological Species

The speciose genus Cyclocephala Dejean (Coleoptera: Scarabaeidae: Dynastinae: Cyclocephalini) has attracted research attention due to their diversity, agroeconomic importance, and floral visitation habits. Uniquely among Cyclocephala species, C. mafaffa Burmeister and C. deceptor (Casey), two nearly identical species, are diagnosed by a pronotal character: beaded or not beaded basal pronotal margin. We evaluated these morphological species hypotheses with a phylogenetic analysis of 12S and COI, neighbor-joining analysis, and several single-locus species delimitation procedures (automatic barcode gap analysis and three Poisson tree processes analyses). Together, these analyses supported the species concepts for C. deceptor and C. mafaffa. Delimitation procedures supported several distinct molecular operational taxonomic units among these taxa. We consider the separation of C. deceptor and C. mafaffa to be valid. We conservatively synonymize the West Indian subspecies C. mafaffa grandis Burmeister under C. mafaffa and offer a discussion on subspecific concepts in Cyclocephalini. We designate the lectotype of Stigmalia deficiens Casey. Implications of this study for other geographically widespread cyclocephalines or species with variable pronotal morphology are discussed. 

scholarly journals Contrasting effects of mangroves and armoured shorelines on fish assemblages in tropical estuarine seascapes

2019 ◽  
Vol 76 (4) ◽  
pp. 1052-1061 ◽  
Author(s):  
Christopher J Henderson ◽  
Ben L Gilby ◽  
Thomas A Schlacher ◽  
Rod M Connolly ◽  
Marcus Sheaves ◽  
...  
Keyword(s):  
Fish Assemblages ◽  
Urban Expansion ◽  
Ecological Impacts ◽  
Spatial Context ◽  
Fish Diversity ◽  
Mangrove Forests ◽  
Habitat Types ◽  
Tropical Estuarine ◽  
Eastern Australia ◽  
Close Proximity

Abstract Coastal seascapes are composed of a diversity of habitats that are linked in space and time by the movement of organisms. The context and configuration of coastal ecosystems shapes many important properties of animal assemblages, but potential seascape effects of natural and artificial habitats on nearby habitats are typically considered in isolation. We test whether, and how, the seascape context of natural and urban habitats modified fish assemblages across estuaries. Fish were sampled with underwater videos in five habitat types (mangroves, rock bars, log snags, unvegetated sediments, armoured shorelines) in 17 estuaries in eastern Australia. Different habitats supported distinct fish assemblages, but the spatial context of mangroves and armoured shorelines had pervasive ecological effects that extended across entire estuaries. In most estuarine habitats, fish diversity and abundance was greatest when they were in close proximity of mangroves, and decreased due to the proximity of armoured shorelines. Many cities are centred on estuaries, and urban expansion is often associated with the fragmentation of mangrove forests. Our findings emphasize that these transformations of urban estuarine landscapes are likely to propagate to broader ecological impacts detectable in multiple habitats beyond mangrove forests.

Molecular phylogenetic analyses and morphological variation point to taxonomic problems among four genera of parasitoid doryctine wasps (Hymenoptera : Braconidae)

2015 ◽  
Vol 29 (6) ◽  
pp. 591 ◽  
Author(s):  
Marco Gebiola ◽  
Antonio P. Garonna ◽  
Umberto Bernardo ◽  
Sergey A. Belokobylskij
Keyword(s):  
Phylogenetic Analyses ◽  
Morphological Characters ◽  
Molecular Data ◽  
Molecular Evidence ◽  
A Posteriori ◽  
Morphological Examination ◽  
Ongoing Effort ◽  
The Status ◽  
Molecular Phylogenetic

Doryctinae (Hymenoptera : Braconidae) is a large and diverse subfamily of parasitic wasps that has received much attention recently, with new species and genera described and phylogenies based on morphological and/or molecular data that have improved higher-level classification and species delimitation. However, the status of several genera is still unresolved, if not controversial. Here we focus on two related groups of such genera, Dendrosoter Wesmael–Caenopachys Foerster and Ecphylus Foerster–Sycosoter Picard & Lichtenstein. We integrated morphological and molecular (COI and 28S–D2 genes) evidence to highlight, by phylogenetic analyses (maximum likelihood and Bayesian) and a posteriori morphological examination, previously overlooked variation, which is here illustrated and discussed. Monophyly of Dendrosoter and Caenopachys and the presence of synapomorphic morphological characters support synonymy of Caenopachys under Dendrosoter. Low genetic differentiation and high variability for putatively diagnostic morphological characters found in both C. hartigii (Ratzeburg) and C. caenopachoides (Ruschka) supports synonymy of D. caenopachoides under D. hartigii, syn. nov. Morphological and molecular evidence together also indicate independent generic status for Sycosoter, stat. rev., which is here resurrected. This work represents a further advancement in the framework of the ongoing effort to improve systematics and classification of the subfamily Doryctinae.

Systematics of Eutropis rugifera (Stoliczka, 1870) (Squamata: Scincidae) including the redescription of the holotype

Zootaxa ◽  
2017 ◽  
Vol 4272 (1) ◽  
pp. 103 ◽  
Author(s):  
A.A. THASUN AMARASINGHE ◽  
NIKOLAY A. POYARKOV JR. ◽  
PATRICK D. CAMPBELL ◽  
SANDY LEO ◽  
JATNA SUPRIATNA ◽  
...  
Keyword(s):  
Species Complex ◽  
Taxonomic Status ◽  
The Philippines ◽  
Peninsular Malaysia ◽  
Nicobar Island ◽  
Single Specimen ◽  
Morphological Examination ◽  
Widespread Species ◽  
Voucher Specimens ◽  
Biogeographic Regions

Eutropis rugifera has long been identified as a widespread species complex distributed in Nicobar, Peninsular Malaysia, Greater Sundaic Islands, Bali, Sulawesi and the Philippines. This skink was described by Stoliczka in 1870 from Nicobar Island based on a single specimen (holotype by monotypy). Later, Peters (1871), Bartlett (1895) and Werner (1896) described three more species which were morphologically similar to Euprepes percarinatus (from Java), Mabuia rubricollis (Borneo) and M. quinquecarinata (Sumatra) respectively, which are currently considered junior objective synonyms of Eutropis rugifera. We examined all the available synonym types and voucher specimens of Eutropis rugifera deposited at several museums. A morphological examination of the types of this species and mtDNA analysis (584 bp of 16S rRNA) of the samples from different biogeographic regions revealed that Eutropis rugifera from Nicobar Island, Bali Island, and Bawean Island are composed of a monophyletic species. However, the taxonomic status of the above population requires further clarification, and the population in Bawean Island may represent a cryptic species. Finally, we provide a complete redescription of E. rugifera based on its holotype.

scholarly journals Short communication: A new record of Etlingera megalocheilos (Griff.) A.D. Poulsen (Zingiberaceae) in Sulawesi, Indonesia

2018 ◽  
Vol 19 (4) ◽  
pp. 1227-1235 ◽  
Author(s):  
TRIMANTO TRIMANTO ◽  
LIA HAPSARI
Keyword(s):  
New Record ◽  
Short Communication ◽  
Morphological Characters ◽  
Peninsular Malaysia ◽  
Corolla Lobe ◽  
High Potential ◽  
Botanic Garden ◽  
Morphological Examination ◽  
Central Sulawesi

Trimanto, Hapsari L. 2018. Short communication: A new record of Etlingera megalocheilos (Griff.) A.D. Poulsen(Zingiberaceae) in Sulawesi, Indonesia. Biodiversitas 19: 1227-1235. A through morphological examination has been conducted to aliving specimen of Zingiberaceae collection of Purwodadi Botanic Garden, East Java which was collected from Pangi Binangga NatureReserve, Central Sulawesi. The result showed that the characters of the species match very well with the description of Etlingeramegalocheilos. The distribution of E. megalocheilos was previously reported to occur only in Sundaland includes Peninsular Malaysia,Singapore, Sumatra, Java, and Borneo. Thus, E. megalocheilos is a newly recorded species in Sulawesi; and confirmed that itsdistribution record now has expanded to Wallacea. The key morphological characters of E. megalocheilos are labellum hourglassshaped,dull red or red to orange-red with the yellow margin, the anther is not covered by the corolla lobe, and have slightly angledfilament. Detailed descriptions, photographs, and notes of the species are presented in this paper. Due to its high potential medicinalproperties, further bioprospecting studies are necessary to conduct.

scholarly journals Molecular Evidence of Sarcocystis Species Infecting Reptiles in Peninsular Malaysia

2019 ◽  
Author(s):  
Nahdatul Fatihah MOHD FADIL ◽  
Tengku Idzzan Nadzirah TENGKU-IDRIS ◽  
Shahhaziq SHAHARI ◽  
Mun Yik FONG ◽  
Yee Ling LAU
Keyword(s):  
18S Rdna ◽  
Pcr Amplification ◽  
Peninsular Malaysia ◽  
Molecular Evidence ◽  
Sarcocystis Species ◽  
Lizard Species ◽  
Fecal Samples ◽  
Rdna Sequences ◽  
Three Samples ◽  
Host Life

Background: The genus Sarcocystis consists of intracellular coccidian protozoan parasites with the ability to invade muscle tissue and mature into sarcocysts, causing the zoonotic disease sarcocystosis. These parasites have an obligatory two-host life cycle, which correlates with prey-predator relationship. The distribution and prevalence of Sarcocystis in reptiles remains unclear, despite several previous reports. The aim of this study was to identify the genetic assemblage of the species of Sarcocystis infecting Malaysian snakes and lizards by screening stool samples.    Methods: Overall, 54 fecal samples of various snake species and four fecal samples of several lizard species in Malaysia were taken within the course of August 2015 to January 2016 from Seremban, Melaka, Tioman Island, Pahang, Klang and Langkawi Wildlife Park located in Malaysia. The samples were examined for Sarcocystis through PCR amplification of the 18S rDNA sequence at the Department of Parasitology, University of Malaya Results: Fourteen snake fecal samples were positive via PCR; however, only eight samples (14%) were found positive for Sarcocystis species, whereas four were positive for other genera and the identity of another three samples was unable to be determined. Further phylogenetic analysis of the 18S rDNA sequences revealed that the snakes were infected with either S. singaporensis, S. lacertae, or undefined Sarcocystis species closely related to either S. singaporensis or S. zuoi. Sarcocystis nesbitti infection was not identified in any of the infected snakes. Conclusion: This is the first report of identification of S. lacertae in the black-headed cat snake.

scholarly journals Ichthyofauna of Sungai Merbok Mangrove Forest Reserve, northwest Peninsular Malaysia, and its adjacent marine waters

Check List ◽  
2021 ◽  
Vol 17 (2) ◽  
pp. 601-631
Author(s):  
Danial Hariz Zainal Abidin ◽  
Sébastien Lavoué ◽  
Norli Fauzani Mohd Abu Hassan Alshari ◽  
Siti Azizah Mohd. Nor ◽  
Masazurah A. Rahim ◽  
...  
Keyword(s):  
Mangrove Forest ◽  
River Estuary ◽  
Alpha Diversity ◽  
Taxonomic Diversity ◽  
Peninsular Malaysia ◽  
Fish Diversity ◽  
Marine Waters ◽  
Forest Patch ◽  
Forest Reserve ◽  
Aquatic Biodiversity

Sungai Merbok Mangrove Forest Reserve, encompassing the Merbok river estuary, was established as a permanent forest reserve in 1951 and is the second-largest intact mangrove forest patch in Peninsular Malaysia. Despite its importance, few studies have been conducted to assess its aquatic biodiversity. In this study, we surveyed the fish diversity of the Merbok river estuary, and its adjacent marine waters. We recorded 138 fish species belonging to two classes, 18 orders, 47 families, and 94 genera. The richest order is Perciformes, with 32 recorded species, represents 23% of the alpha diversity, followed by Carangiformes with 21 recorded species or 14% of the diversity. Low taxonomic diversity overlaps with previous inventories and indicates that the inventory is still incomplete. All specimens examined are catalogued and deposited in a local museum collection. The fish checklist presented here represents a step forward in the conservation of fish diversity in the Merbok river estuary.

scholarly journals Review of the mudflat varunid crab genus Metaplax (Crustacea, Brachyura, Varunidae) from East Asia and northern Vietnam

ZooKeys ◽  
2019 ◽  
Vol 877 ◽  
pp. 1-29
Author(s):  
Hsi-Te Shih ◽  
Jhih-Wei Hsu ◽  
Kingsley J. H. Wong ◽  
Ngan Kee Ng
Keyword(s):  
Molecular Evidence ◽  
Intertidal Mudflat ◽  
Cytochrome Oxidase Subunit ◽  
Morphological Examination ◽  
Mitochondrial Cytochrome Oxidase Subunit ◽  
Northern Vietnam ◽  
Taxonomic Confusion ◽  
De Man ◽  
Considerable Range ◽  
Mitochondrial Cytochrome Oxidase

Intertidal mudflat crabs of the genus Metaplax H. Milne Edwards, 1852 (Crustacea: Brachyura: Varunidae) from China, Taiwan, and northern Vietnam are taxonomically revised by morphological and molecular evidence. These crabs show sexual dimorphism and morphological variation of a considerable range in the infraorbital ridge, one of the primary features previously used for species identification. In this study, four species were identified from the region: M. elegans De Man, 1888; M. longipes Stimpson, 1858; M. sheni Gordon, 1930; and M. tredecim Tweedie, 1950. Based on the results of the morphological examination, and as confirmed by molecular evidence from mitochondrial cytochrome oxidase subunit I (COI), taxonomic confusion surrounding M. longipes was resolved, and M. takahasii Sakai, 1939, is considered a junior synonym of M. longipes. The geographical distribution of Metaplax longipes extends along the shores of China, north to Jiangsu, whereas the Southeast Asian M. tredecim was newly recorded from northern Vietnam and Hong Kong.

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