This paper reports a new weevil genus Devernodes gen. n. established for five new species from Southeast Asia: D. alkippe sp. n. (China: Mt. Emei), D. asteria sp. n. (Vietnam: Tam Dao), D. chthonia sp. n. (Vietnam: Tam Dao; the type species), D. drimo sp. n. (Malaysia: Pasoh Forest Reserve) and D. methone sp. n. (Malaysia: Tanah Rata). All Devernodes are wingless and inhabit the forest leaf litter. Adult Devernodes share a combination of two head characters unique among weevils in Asia: antenna with apparently unsegmented club and 6-segmented antennal funicle, as well as strong constriction separating the eye-bearing rostrum from the head capsule. To test monophyly and investigate phylogenetic relationships of Devernodes, Maximum Likelihood phylogenetic analysis was undertaken using parts of mitochondrial (COI) and nuclear ribosomal (28S) genes, as well as the nuclear internal transcribed spacer (ITS2) from 14 Devernodes and 55 outgroup Curculionidae specimens. Results strongly corroborated monophyly of Devernodes and did not suggest its realistic sister-group. The new genus is assigned to the molytine tribe Lymantini (not represented in the DNA analysis) based on two potential synapomorphies: head markedly constricted behind eyes and presence of undivided female hemisternites IX (= "merged coxite and stylus"). Thus interpreted, Devernodes is the twelfth nominal genus of Lymantini and the first record of the tribe outside of the Americas. All original data (localities, DNA sequences, specimen images) are available online in public datasets dx.doi.org/10.5883/DS-DEVERNO1 and dx.doi.org/10.5883/DS-DEVERNO2.
North America is currently home to a number of grey wolf (Canis lupus) and wolf-like canid populations, including the coyote (Canis latrans) and the taxonomically controversial red, Eastern timber and Great Lakes wolves. We explored their population structure and regional gene flow using a dataset of 40 full genome sequences that represent the extant diversity of North American wolves and wolf-like canid populations. This included 15 new genomes (13 North American grey wolves, 1 red wolf and 1 Eastern timber/Great Lakes wolf), ranging from 0.4 to 15x coverage. In addition to providing full genome support for the previously proposed coyote-wolf admixture origin for the taxonomically controversial red, Eastern timber and Great Lakes wolves, the discriminatory power offered by our dataset suggests all North American grey wolves, including the Mexican form, are monophyletic, and thus share a common ancestor to the exclusion of all other wolves. Furthermore, we identify three distinct populations in the high arctic, one being a previously unidentified "Polar wolf" population endemic to Ellesmere Island and Greenland. Genetic diversity analyses reveal particularly high inbreeding and low heterozygosity in these Polar wolves, consistent with long-term isolation from the other North American wolves.
The island of Borneo lies within one of the most biodiverse regions in the world. Despite this, its documented gekkonid diversity is not commensurate with other areas of Southeast Asia. The megadiverse genus Cyrtodactylus is especially underrepresented. Limestone-karst ecosystems, in particular, harbor many endemic Cyrtodactylus species, but only one karst-dwelling species is currently recognized from Borneo. This paper adds two additional karst-dwelling Cyrtodactylus species-C. muluensis sp. nov. and C. limajalur sp. nov.-from Sarawak, Malaysia. Cyrtodactylus muluensis sp. nov. is endemic to Gunung Mulu and is distinguished from its congeners by having a precloacal groove, 31-38 ventral scales, a maximum SVL of at least 88 mm, enlarged subcaudals, 19-20 subdigital lamellae, and a banded dorsal body pattern. Cyrtodactylus limajalur sp. nov. is endemic to the Serian region and is distinguished from its congeners by having 33-42 ventral scales, enlarged subcaudals, a precloacal pit, a maximum SVL of at least 94 mm, 5-6 enlarged femoral scales, 19-22 subdigital lamellae, and five distinct bands on the dorsum. Both species are phylogenetically distinct and deeply divergent from all other congeners. The description of two new karst-dwelling species highlights the need to conserve karst habitats and the endemic species they harbor.
A new species of Ansonia is described from the Shan Plateau of Myanmar based on an integrative taxonomic analysis that differentiates it from all other congeners. Molecular phylogenetic analyses based on the mitochondrial genes 12S and 16S rRNA and tRNA-val recover A. kyaiktiyoensis sp. nov. as the sister species to A. inthanon from Thailand but differs from it and other congeners by at least a 5.0% sequence divergence. It is further differentiated by the following combination of morphological characters: (1) maximum SVL 24 mm in males and females; (2) first finger shorter than second; (3) absence of interorbital and tarsal ridges; (4) presence of light-coloured interscapular spot; (5) presence of yellow rictal tubercle; (6) absence of wide, light-coloured patch below eye; (7) presence of large, discrete, bright-yellow submandibular spots along the underside of lower jaw; (8) iris yellow-gold; (9) presence of markings on the snout consisting of streaks below the eye to the lip, and on the canthus rostralis to the nostril; (10) dorsum grey-brown with orange-beige spots, a dark-brown X-shaped marking on the back surrounding the interscapular spot, and dark-coloured markings on rump; (11) fore- and hind limbs with orange-beige cross-bars; and (12) venter light-gray with yellow spotting, especially near flanks and underside of hind limbs. Ansonia kyaiktiyoensis sp. nov. is the westernmost known record for the genus and the only species west of the Salween Basin. Its discovery echoes the increasing number of herpetological discoveries being made in upland regions fringing the Ayeyarwady and Salween Basins.
This study was conducted to characterize the selected marine fish species using partial sequence of mtDNA 12S and 16S rRNA gene. PCR amplification of 12S and 16S rRNA generated PCR amplicons at 350 and 440 bp lengths, respectively. Sequence analysis was performed using BioEdit software. Phylogenetic tree was constructed using MEGA software. Two reference species have been used namely Gobio gobio (AB239596 and EF112528) and Pentapodus caninus (DQ533268 and DQ532933). Based on the result obtained, mtDNA 12S and 16S rRNA were found to be useful as molecular markers for fish species identification. These markers will provide correct identification of fish species when considered along with morphological characteristics.
The Tioman Island of Malaysia experienced acute muscular sarcocystosis outbreaks from 2011 to 2014. So far, a previous study based on the 18S rRNA gene sequencing has reported S. singaporensis, S. nesbitti and Sarcocystis sp. YLL-2013 in water samples acquired from the island, thus confirming the waterborne nature of this emerging parasitic disease. This study aimed to improve the detection methods for Sarcocystis, in order to have a clearer picture of the true diversity of Sarcocystis species in Tioman. A new primer set (28S R7F-28S R8 Deg R) was designed to amplify the 28S rRNA gene of Sarcocystis. Subsequently, Sarcocystidae was detected in 65.6% (21/32) of water samples and 28% (7/25) of soil samples acquired between 2014 and 2015 from Tioman. Next-generation sequencing (NGS) on 18 of the positive samples was then performed using amplicons generated from the same primer set. This yielded 53 potentially unique Sarcocystidae sequences (290 bp), of which nine of the most abundant, prevalent and unique sequences were named herein. In contrast, NGS of the 18S rRNA gene V9 hypervariable region of 10 selected samples detected only two Sarcocystis species (160 bp). S. mantioni was the most ubiquitous sequence found in this study.
The isolation of 66 streptomycetes from rhizosphere soil of chili plants was done for their inhibitory activities against three different dominant species of Colletotrichum namely C. acutatum, C. gloeosporioides and C. capsici. Twenty one streptomycetes strains were active against at least one of the Colletotrichum species. In addition, ten strains that inhibited the in vitro growth of Colletotrichum species showed chitinase activity. Strain P42, which displayed the highest inhibitory activity against all three anthracnose fungi species and high chitinase activity was tested as biological control agent in a greenhouse study. The strain successfully controlled chili anthracnose disease by significantly reducing the disease severity. Phylogenetic analysis of the 16S rRNA gene sequences showed that strain P42 belongs to the Streptomyces rochei clade. The results of the current study showed that rhizosphere-derived soil of chili plants is an important source of bioactive streptomycetes which are antagonistic against Colletotrichum.
Phylogenetic inference refers to the reconstruction of evolutionary relationships among various species that is usually
presented in the form of a tree. This study constructs the phylogenetic tree by using a novel distance-based method known
as Modified one step M-estimator (MOM) method. The branches of the phylogenetic tree constructed were then evaluated
to see their reliability. The performance of the reliability was then compared between the p-value of multiscale bootstrap
(AU value) and bootstrap p-value (BP value). The aim of this study was to compare the performance between the AU value
and BP value for assessing phylogenetic tree of RNA polymerase. The results have shown that multiscale bootstrap analysis
can detect high sampling errors but not in bootstrap analysis. To overcome this problem, the multiscale bootstrap analysis
has reduced the sampling error by increasing the number of replications. The clusters were indicated as significant if AU
values or BP values were 95% or higher. From the analysis, the results showed that the BP and AU values differ at 11th
and 15th branch of the phylogenetic tree. The BP values at both branches were 72 and 85%, respectively, thereby making
the cluster not significant but by looking at the AU values, the two branches were more than 95% and the clusters were
significant. This was due to the biasness in calculation of the probability of bootstrap analysis, therefore, the multiscale
bootstrap analysis has improved the calculation of the probability value compared to the bootstrap analysis.
Objectives: Isolation of Leptospira by culture represents a definitive growth and confirmation of the disease, yet it is hampered with its nature of slow growth. With slight modification of culture method, the study aims to isolate and characterize Leptospira spp. from patients with acute febrile illness. Methods: A total of 109 blood samples were collected from patients with acute febrile illness that presented at the Emergency Department of Hospital Universiti Sains Malaysia, Malaysia. Clinical samples were subjected to Leptospira IgM Rapid test, microscopic agglutination test (MAT), isolation by culture method, and direct real-time PCR test. For leptospiral isolation, the samples (whole blood and deposit from spun plasma) were cultured into modified Ellinghausen McCullough Johnson Harris (EMJH) media with and without 5'-fluorouracil (5-FU). In every culture positive sample, partial 16S rRNA gene sequencing was performed for molecular identification of the isolates. Phylogenetic analysis was carried out to determine the genetic relatedness among the isolates. An inhibition of 5-FU study was performed on Leptospirainterrogans serovar Canicola with different concentrations to compare the growth detection of the tested Leptospira with or without 5-FU within 7 days of incubation. Results: Leptospirosis was diagnosed in 14.7% of patients with acute febrile illness. Two Leptospira spp. (n = 2/109, 1.85%) were successfully isolated from whole blood and deposit from spun plasma samples. B004 and B208 samples were positive at day 11 and day 7, respectively, in EMJH media without addition of 5-FU. Sample B004 was identified as Leptospira interrogans and B208 as Leptospira weilli. Phylogenetic analysis confirmed that both of them were within pathogenic group and they were not related. The 5-FU inhibition study revealed that additional of 5-FU at final concentration of 200 µg/mL to EMJH media demonstrated an inhibitory effect on the growth of the tested strain Conclusion: Isolation of Leptospira spp. using EMJH media without addition of 5'-fluorouracil resulted in a better outcome. Two pathogenic Leptospira isolates were successfully cultivated from patients with acute febrile illness that were genetically not related.
A total of 170 bambara groundnut (Vigna subterranea) accessions were evaluated using both simple sequence repeat (SSR) and single nucleotide polymorphism (SNP) markers generated using genotyping-by-sequencing (GbS), of which 56 accessions were collected from West and East Java. Principal coordinate analysis (PCoA), population structure, and cluster analysis suggest that the East Java accessions could be a result of the introduction of selected West Java accessions. In addition, the current Indonesian accessions were likely introduced from Southern Africa, which would have produced a very marked founding effect such that these accessions present only a fraction of the genetic variability that exists within this species.
We investigated the spatial and temporal patterns of Cautires diversification on the Malay Peninsula and Sumatra to understand if the narrow and frequently dry Malacca Strait separates different faunas. Moreover, we analyzed the origin of Cautires in Malayan and Sumatran mountains. We sampled 18 localities and present the mtDNA-based phylogeny of 76 species represented by 388 individuals. The phylogenetic tree was dated using mtDNA evolution rates and the ancestral ranges were estimated using the maximum likelihood approach. The phylogeny identified multiple lineages on the Malay Peninsula since the Upper Eocene (35 million years ago, mya) and a delayed evolution of diversity in Sumatra since the Upper Oligocene (26 mya). A limited number of colonization events across the Malacca Strait was identified up to the Pliocene and more intensive faunal exchange since the Pleistocene. The early colonization events were commonly followed by in situ diversification. As a result, the Malacca Strait now separates two faunas with a high species-level turnover. The montane fauna diversified in a limited space and seldom took part in colonization events across the Strait. Besides isolation by open sea or a savannah corridor, mimetic patterns could decrease the colonization capacity of Cautires. The Malay fauna is phylogenetically more diverse and has a higher value if conservation priorities should be defined.
Western Southeast Asia is hosting one of the world's most diverse faunas, and one of the reasons for this huge diversity is the complex geologic past of the area, increasing the frequency of isolation and expansion events over evolutionary time scale. As an example case, the present study reveals the phylogeny and biogeographic history of the Paracanthocobitis zonalternans species complex, small benthic freshwater fish (Teleostei: Nemacheilidae) that are commonly occurring across western Southeast Asia (from central Myanmar through western and southern Thailand to northern Malaysia). The group is particularly interesting since it occurs in three biogeographic subdivisions (Indian, Indochinese, Malay/Sundaic) and across all of the major biogeographic barriers in the region. Basing on mitochondrial and nuclear sequence data of 93 samples from about 50 localities we found six major clades, most with exclusive geographic distribution. Divergence time dated the origin of the P. zonalternans species complex to early Miocene (17.8 MYA) and a biogeographic analysis identified the Tenasserim region as the ancestral region. From this region the fish spread during periods of lowered global sea level, particularly during late Miocene (11-8 MYA) northwards into all Burmese river basins and southwards into south Thailand and northern Malaysia. Besides lowered global sea level periods, local stream capture events allowed the complex to expand, e.g. into the Mae Klong basin. Strong fragmentations during periods with elevated sea level during the Pliocene and Pleistocene repeatedly restricted populations to refuges and shaped the observed major lineages. Our results document a higher diversity within the P. zonalternans species complex than formerly believed and a strong impact of global sea level on its evolutionary history. Low sea levels promoted dispersal and elevated sea levels fragmentation events. A very similar impact of sea level changes can be expected in all stationary fauna (freshwater and terrestrial) in all non-mountainous coastal regions worldwide.
The intra- and inter-specific variation of Acetes shrimps were evaluated based on samples collected from in-shore catches and off-shore trawling around the west coast of Peninsular Malaysia. Species captured were identified as Acetes indicus, A. serrulatus, A. japonicus and A. sibogae. A region of the mitochondrial cytochrome c oxidase subunit I (COI) gene comprising 552 base pairs (bp) was amplified from 159 Acetes specimens. The sequence alignment analysis generated phylogenetic trees which depicted the four major clades that were consistent with the species identified morphologically. These four species varied considerably for haplotype and nucleotide diversity, with A. indicus and A. serrulatus showing different demographic histories. Furthermore, the observation of two clades in the A. indicus and A. sibogae lineages, with relatively high levels of intraspecific divergence, suggests that cryptic diversity is possibly present in these two taxa. This study has contributed to the knowledge of the distribution patterns and molecular phylogenetics of four Acetes spp. in the Straits of Malacca.
The whipworm Trichuris muris is known to be associated with various rodent species in the northern hemisphere, but the species identity of whipworm infecting rodents in the Oriental region remains largely unknown. We collected Trichuris of Muridae rodents in mainland and insular Southeast Asia between 2008 and 2015 and used molecular and morphological approaches to identify the systematic position of new specimens. We discovered two new species that were clearly distinct from T. muris, both in terms of molecular phylogenetic clustering and morphological features, with one species found in Thailand and another one in Borneo. We named the new species from Thailand as Trichuris cossoni and the species from Borneo as Trichuris arrizabalagai. Molecular phylogeny using internal transcribed spacer region (ITS1-5.8S-ITS2) showed a divergence between T. arrizabalagai n. sp., T. cossoni n. sp. and T. muris. Our findings of phylogeographically distinct Trichuris species despite some globally distributed host species requires further research into the distribution of different species, previously assumed to belong to T. muris, which has particular relevance for using these species as laboratory model organisms.
This study utilized genetic and morphometric approaches to assess the molecular and morphometric differentiation among commercially important species of mud crab. Molecular investigations were derived from 542 bp mitochondrial DNA COI on 249 individuals within genus Scylla from nine states in Malaysia represents four marine regions; South China Sea, Sulu Sea, Straits of Singapore and Straits of Malacca. Four specimens were obtained from Indonesia to give a robust analysis in this study. For species delimitation, Automatic Barcode Gap Discovery (ABGD) method on a web interface was employed. Analysis on phylogenetics was implemented utilizing Neighbour joining (NJ) and Maximum Parsimony (MP) methods. The inter- and intraspecies genetic distances (Ds ) was computed using Kimura 2-parameter distance and executed in MEGA version 5.05. All samples were genetically and morphologically identified and clustered into four distinct species. Among the species, S. olivacea was the most abundant (n = 111), on the other hand the occurrence of S. paramamosain in Malaysia was very low (n = 29). No single individual of S. serrata from Malaysia was recorded in this study. Both genetic distance and phylogenetic approaches exhibited a correlative monophyletic association among all specimens analysed. This present study is crucial as it reports the reassessment of all species within genus Scylla in Malaysia, eventually could be employed as a reference source for subsequent research mainly on mariculture and other conservation efforts for the species.
The study of microbial communities from extreme environments is a fascinating topic. With every study, biologists and ecologists reveal interesting facts and questions that dispel the old belief that these are inhospitable environments. In this work, we assess the microbial diversity of three hot springs from Neuquén, Argentina, using high-throughput amplicon sequencing. We predicted a distinct metabolic profile in the acidic and the circumneutral samples, with the first ones being dominated by chemolithotrophs and the second ones by chemoheterotrophs. Then, we collected data of the microbial communities of hot springs around the world in an effort to comprehend the roles of pH and temperature as shaping factors. Interestingly, there was a covariation between both parameters and the phylogenetic distance between communities; however, neither of them could explain much of the microbial profile in an ordination model. Moreover, there was no correlation between alpha diversity and these parameters. Therefore, the microbial communities' profile seemed to have complex shaping factors beyond pH and temperature. Lastly, we looked for taxa associated with different environmental conditions. Several such taxa were found. For example, Hydrogenobaculum was frequently present in acidic springs, as was the Sulfolobaceae family; on the other hand, Candidatus Hydrothermae phylum was strongly associated with circumneutral conditions. Interestingly, some singularities related to sites featuring certain taxa were also observed.
Globally, norovirus (NoV) has become one of the important causes of acute gastroenteritis (AGE) in children. It is responsible for death of children younger than 5 years in developing countries. Although there is limited information and the rate of child mortality caused by diarrhea is low in Malaysia, the burden of diarrhea is high, especially in Sabah. NoV GI, GII and GIV genogroups are known to infect humans, and GII.4 is the predominant genotype distributed worldwide. Better understanding of the etiology of NoV will help to inform policies for prevention and control. The aim of this study was to determine the burden and genotype distribution of NoV in children younger than 5 years with AGE who attended health-care facilities in Sabah, Malaysia. Diarrhea stool samples were collected from 299 children with AGE and NoV was detected by amplifying the capsid and RNA-dependent RNA polymerase gene and reverse transcription-polymerase chain reaction (RT-PCR) analysis. Nucleotide sequencing of the amplicons was used for genotypes and phylogenetic analyses . NoV-positive stool samples were found in 17.7% (53/299) among which 13/53 (24.5%), 38/53 (71.7%), and 2/53 (3.8%) identified as NoV GI, GII and combination of GI and GII, respectively. The most common genotypes were GII.3 [P12] (80%) followed by GII.6 [P7] (13.3%), and GII.17 [P17] (6.7%). In the phylogenetic tree, all Sabahan NoV samples were shown to share ancestry with their respective genotype from predominantly East Asian countries and to some extent Australia and Europe. However, the Sabahan strains formed independent clusters with significant bootstrap values, indicating a clonal spread after the strains had entered Sabah.
Morphology-based taxonomy of freshwater fish is effective when there are representative specimens covering large regions. However, in Sundaland, where the presence of cryptic species is high, the technique has its limitations. This is compounded by uncritical descriptions of holotypes in old literature. We demonstrate the problem using Barbodes binotatus first described from an ink drawing. Several species in the Barbodes genus of Sundaland exhibit morphological similarity to B. binotatus. We applied new DNA sequences of 16S, cytochrome c oxidase subunit I (COI), cytochrome b (Cytb) and recombination-activating gene 1 (RAG1), and pigmentation markers to clarify species complex boundaries in the Malay Peninsula, namely B. aff. binotatus "Malay Peninsula", Barbodes cf. banksi and Barbodes rhombeus. Results suggest B. binotatus-like specimens in the Malay Peninsula are B. rhombeus based on a threshold of 3% COI genetic divergence. B. aff. binotatus recorded in Sumatra, Borneo and the Philippines are likely valid but undescribed species. However, if the 2% COI threshold is applied, some populations in the northern Malay Peninsula would qualify as new and undescribed species. The implications of the 2% threshold and the likelihood of "grey zone" incipient populations are discussed. We further found a rapid visual method, not reported previously, to delineate B. aff. binotatus and B. cf. banksi, but it requires further validation. Additionally, we offer fresh perspectives by discussing the roles of biological species concept, morphological species concept, genetic species concept and mate recognition concept in the B. binotatus complex. Our findings reinforce the standpoint that species delineation is not entirely a binary process, but there is a spectrum to consider, especially in biogeography intersection regions.
A broad-scale comparative phylogeographic and phylogenetic study of pennah croakers, mainly Pennahia anea, P. macrocephalus, and P. ovata was conducted to elucidate the mechanisms that may have driven the diversification of marine organisms in Southeast Asian waters. A total of 316 individuals from the three species, and an additional eight and six individuals of P. argentata and P. pawak were employed in this study. Two genetically divergent lineages each of P. argentata and P. anea (lineages L1 and L2) were respectively detected from the analyses based on mitochondrial cytochrome b gene data. Historical biogeography analysis with a multi-gene dataset revealed that Pennahia species most likely originated in the South China Sea and expanded into the eastern Indian Ocean, East China Sea, and northwestern Pacific Ocean through three separate range expansions. The main diversifications of Pennahia species occurred during Miocene and Pliocene periods, and the occurrences of lineage divergences within P. anea and P. argentata were during the Pleistocene, likely as a consequence of cyclical glaciations. The population expansions that occurred after the sea level rise might be the reason for the population homogeneity observed in P. macrocephalus and most P. anea L2 South China Sea populations. The structure observed between the two populations of P. ovata, and the restricted distributions of P. anea lineage L1 and P. ovata in the eastern Indian Ocean, might have been hampered by the northward flowing ocean current at the Malacca Strait and by the distribution of coral reefs or rocky bottoms. While our results support S. Ekman's center-of-origin hypothesis taking place in the South China Sea, the Malacca Strait serving as the center of overlap is a supplementary postulation for explaining the present-day high diversity of pennah croakers centered in these waters.
Dengue viral attacks have been reported in various parts of India in recent years. In this paper we report on our studies of the characterisation and evolutionary aspects of gene sequences of the envelope glycoprotein of the prevalent Indian dengue virus type 1. Comparison with sequences from other countries shows that the envelope genes identified in India are closely related to strains from Malaysia. From the evolutionary point of view the envelope gene sequences of this dengue virus of India for past few years show that a marked mutational shift in the nucleotide sequences of the envelope gene have taken place from around the year 2000. Also, phylogenetic relationship with other three sera of dengue virus reported in India from 2005 shows that the dengue virus 1 is more closely related to dengue viruses 3 and 4 and relatively distantly to dengue virus 2.