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Rapid in-situ detection kit (RisK): Development of loop-mediated isothermal amplification (LAMP) assay for the rapid identification of selected invasive alien fish in Malaysian freshwaters

Vythalingam LM, Hossain MAM, Bhassu S

Mol Cell Probes, 2021 02;55:101683.
PMID: 33259896 DOI: 10.1016/j.mcp.2020.101683

Invasive alien fish species have become a silent treat towards the ecosystem especially the native fish population in Malaysia. There has been a need to develop rapid identification methods that can aid management teams in identifying fish species that are not native to our ecosystem. Current visual identification methods are highly tedious and require time, delaying action towards curbing the invasion. The LAMP assay successfully identified six popular invasive fish species in Malaysia. None of the LAMP assays showed false positives and the Limit of Detection of the LAMP primers were highly sensitive and could detect DNA samples up to 1 × 10-15 ng/μl. The LAMP primers designed were highly specific to the target species and did not amplify non target species. DNA sequencing was done to ensure the accuracy of LAMP assay results. This study demonstrates that LAMP is a suitable tool in species identification efforts of invasive fish species in Malaysia.

Matched MeSH terms: Introduced Species*
Fulltext Genetic evidence of multiple invasions and a small number of founders of Asian Palmyra palm (Borassus flabellifer) in Thailand

Pipatchartlearnwong K, Swatdipong A, Vuttipongchaikij S, Apisitwanich S

BMC Genet, 2017 10 12;18(1):88.
PMID: 29025415 DOI: 10.1186/s12863-017-0554-y

BACKGROUND: Borassus flabellifer or Asian Palmyra palm is an important crop for local economies in the South and Southeast Asia for its fruit and palm sugar production. Archeological and historical evidence indicated the presence of this species in Southeast Asia dating back at least 1500 years. B. flabellifer is believed to be originated in Africa, spread to South Asia and introduced into Southeast Asia through commercial routes and dissemination of cultures, however, the nature of its invasion and settlement in Thailand is unclear.
RESULTS: Here, we analyzed genetic data of 230 B. flabellifer accessions across Thailand using 17 EST-SSR and 12 gSSR polymorphic markers. Clustering analysis revealed that the population consisted of two genetic clusters (STRUCTURE K = 2). Cluster I is found mainly in southern Thailand, while Cluster II is found mainly in the northeastern. Those found in the central are of an extensive mix between the two. These two clusters are in moderate differentiation (F ST = 0.066 and N M = 3.532) and have low genetic diversity (HO = 0.371 and 0.416; AR = 2.99 and 3.19, for the cluster I and II respectively). The minimum numbers of founders for each genetic group varies from 3 to 4 individuals, based on simulation using different allele frequency assumptions. These numbers coincide with that B. flabellifer is dioecious, and a number of seeds had to be simultaneously introduced for obtaining both male and female founders.
CONCLUSIONS: From these data and geographical and historical evidence, we hypothesize that there were at least two different invasive events of B. flabellifer in Thailand. B. flabellifer was likely brought through the Straits of Malacca to be propagated in the southern Thailand as one of the invasive events before spreading to the central Thailand. The second event likely occurred in Khmer Empire, currently Cambodia, before spreading to the northeastern Thailand.

Matched MeSH terms: Introduced Species*
Notes on the occurrence of the tropical eel Anguilla bicolor bicolor in Peninsular Malaysia, Malaysia

Arai T, Chino N, Zulkifli SZ, Ismail A

J Fish Biol, 2012 Mar;80(3):692-7.
PMID: 22380562 DOI: 10.1111/j.1095-8649.2011.03154.x

Previous studies indicated that a tropical freshwater eel Anguilla bicolor bicolor occurs in Africa, India, Sri Lanka, Bangladesh, Myanmar, Indonesia and Australia, but an intensive survey has indicated an extended distribution range for the species into Peninsular Malaysia. Thus, A. b. bicolor is a native subspecies of Malaysia.

Matched MeSH terms: Introduced Species
Fulltext Response of marine copepods to a changing tropical environment: winners, losers and implications

Chew LL, Chong VC

PeerJ, 2016;4:e2052.
PMID: 27257540 DOI: 10.7717/peerj.2052

Background. Climate change concurrent with anthropogenic disturbances can initiate serial changes that reverberate up the food chain with repercussions for fisheries. To date, there is no information available concerning the combined effects of global warming and human impacts on tropical marine food webs. While temperate copepods respond differently to warming and environmental stressors, the extent to which tropical copepods can adapt to rising temperature of already warm waters remains unknown. We hypothesize that sea warming and other anthropogenic disturbances over the long term will have the greatest impact on the copepod community in nearshore waters where their effects are accentuated, and therefore vulnerable and resilient species could be identified. Methods. Zooplankton samples were collected during two time periods (1985-86 and 2014-15) interposed by marked anthropogenic disturbances, and at the same five stations located progressively from inshore to offshore in Klang Strait, Malaysia, following the asymmetrical before-after-control-impact (BACI) design. Copepods were identified to species, and results were interpreted by univariate (ANOVA) and multivariate (PERMANOVA, PCO) analyses of the computed species abundance and diversity measures. Results. Copepod total abundance was not significantly different among stations but higher after disturbance than before disturbance. However, changes in the abundance of particular species and the community structure between time periods were dramatic. Coastal large-bodied calanoid species (e.g., Acartia spinicauda, Calanopia thompsoni, Pseudodiaptomus bowmani and Tortanus forcipatus) were the most vulnerable group to disturbance. This however favored the opportunistic species (e.g., Oithona simplex, O. attenuata, Hemicyclops sp., Pseudomacrochiron sp. and Microsetella norvegica). Small-bodied copepods (e.g., Paracalanus sp., Parvocalanus crassirostris and Euterpina acutifrons) were unaffected. Centropages tenuiremis was likely an introduced species. There was no significant loss in species richness of copepods despite the dramatic changes in community structure. Discussion. Sea warming and other human-induced effects such as eutrophication, acidification and coastal habitat degradation are likely the main factors that have altered copepod community structure. The large-bodied estuarine and coastal calanoid copepods are surmised to be vulnerable to eutrophication and hypoxia, while both resilient and opportunistic species are largely unaffected by, or adaptable to, degraded coastal environments and observed sea surface temperature (SST) rise. It is forecasted that SST rise with unmitigated anthropogenic impacts will further reduce large-bodied copepod species the favoured food for fish larvae with dire consequences for coastal fish production.

Matched MeSH terms: Introduced Species
Reproductive viability of paradoxically masculinised Gambusia holbrooki generated following diethylstilbestrol (DES) treatment

Patil JG, Norazmi-Lokman NH, Kwan TN

Comp Biochem Physiol B Biochem Mol Biol, 2020 07 22;248-249:110468.
PMID: 32710933 DOI: 10.1016/j.cbpb.2020.110468

Hormonal sex reversal can produce monosex fish stocks and provide insights into their gamity and reproductive physiology. However, paradoxical effects have been reported in several fish species that remain largely ignored as anomalies, particularly those of masculinisation. As a first step, this study examined reproductive viability of paradoxically masculinised Gambusia holbrooki produced following oral administration (20-100 mg/kg feed) of a feminizing hormone diethylstilbestrol (DES). Contrary to expectation, all treatment groups produced 100% male populations. Survival, mating behaviour, gamete production, breeding output as well as expression of anti-Mullerian hormone (amh), ovarian (cyp19a1a) and brain (cyp19a1b) aromatase of masculinised fish were also examined. Survival (≤ 54.1 ± 7.3%) at termination of DES treatment was significantly lower compared with controls (88.6 ± 4.3%) but remained unaffected post treatment. Gonopodium thrusting frequency (33 ± 9.8 per 10 min) was not significantly different to untreated males just as sperm abundance (3.9 ± 1.5 × 108/male) and their motility (88.6 ± 29.1%). Importantly, paradoxically masculinised fish mated with virgin females and produced clutch sizes (22 ± 4) and progeny survival (87.0 ± %) that were comparable to that of untreated males. Masculinised testes showed high amh and low cyp19a1a expression, a pattern resembling those of untreated males. Production of paradoxically sex-reversed males with a capability to produce viable offspring has not been reported previously in this or other fish species. The outcomes support a feed-back regulation of oestrogenic pathways in this viviparous fish and could be useful for ecological applications such as controlling invasive fish populations.

Matched MeSH terms: Introduced Species
The complete mitogenome of the invasive spiny-cheek crayfish Orconectes limosus (Rafinesque, 1817) (Crustacea: Decapoda: Cambaridae)

Gan HM, Gan HY, Lee YP, Grandjean F, Austin CM

Mitochondrial DNA A DNA Mapp Seq Anal, 2016 09;27(5):3181-3.
PMID: 25648916 DOI: 10.3109/19401736.2015.1007326

The invasive freshwater crayfish Orconectes limosus mitogenome was recovered by genome skimming. The mitogenome is 16,223 base pairs in length consisting of 13 protein-coding genes, 2 ribosomal subunit genes, 22 transfer RNAs, and a non-coding AT-rich region. The O. limosus mitogenome has an AT bias of 71.37% and base composition of 39.8% for T, 10.3% for C, 31.5% for A, and 18.4% for G. The mitogene order is identical to two other genera of northern hemisphere crayfish that have been sequenced for this organelle.

Matched MeSH terms: Introduced Species
Fulltext Wild pigs (Sus scrofa) mediate large-scale edge effects in a lowland tropical rainforest in Peninsular Malaysia

Fujinuma J, Harrison RD

PLoS One, 2012;7(5):e37321.
PMID: 22615977 DOI: 10.1371/journal.pone.0037321

Edge-effects greatly extend the area of tropical forests degraded through human activities. At Pasoh, Peninsular Malaysia, it has been suggested that soil disturbance by highly abundant wild pigs (Sus scrofa), which feed in adjacent Oil Palm plantations, may have mediated the invasion of Clidemia hirta (Melastomataceae) into the diverse tropical lowland rain forest. To investigate this hypothesis, we established three 1 km transects from the forest/Oil Palm plantation boundary into the forest interior. We recorded the distribution of soil disturbance by wild pigs, C. hirta abundance, and environmental variables. These data were analyzed using a hierarchical Bayesian model that incorporated spatial auto-correlation in the environmental variables. As predicted, soil disturbance by wild pigs declined with distance from forest edge and C. hirta abundance was correlated with the level of soil disturbance. Importantly there was no effect of distance on C. hirta abundance, after controlling for the effect of soil disturbance. Clidemia hirta abundance was also correlated with the presence of canopy openings, but there was no significant association between the occurrence of canopy openings and distance from the edge. Increased levels of soil disturbance and C. hirta abundance were still detectable approximately 1 km from the edge, demonstrating the potential for exceptionally large-scale animal mediated edge effects.

Matched MeSH terms: Introduced Species
Fulltext Feral Cat Globetrotters: genetic traces of historical human-mediated dispersal

Koch K, Algar D, Schwenk K

Ecol Evol, 2016 08;6(15):5321-32.
PMID: 27551385 DOI: 10.1002/ece3.2261

Endemic species on islands are highly susceptible to local extinction, in particular if they are exposed to invasive species. Invasive predators, such as feral cats, have been introduced to islands around the world, causing major losses in local biodiversity. In order to control and manage invasive species successfully, information about source populations and level of gene flow is essential. Here, we investigate the origin of feral cats of Hawaiian and Australian islands to verify their European ancestry and a potential pattern of isolation by distance. We analyzed the genetic structure and diversity of feral cats from eleven islands as well as samples from Malaysia and Europe using mitochondrial DNA (ND5 and ND6 regions) and microsatellite DNA data. Our results suggest an overall European origin of Hawaiian cats with no pattern of isolation by distance between Australian, Malaysian, and Hawaiian populations. Instead, we found low levels of genetic differentiation between samples from Tasman Island, Lana'i, Kaho'olawe, Cocos (Keeling) Island, and Asia. As these populations are separated by up to 10,000 kilometers, we assume an extensive passive dispersal event along global maritime trade routes in the beginning of the 19th century, connecting Australian, Asian, and Hawaiian islands. Thus, islands populations, which are characterized by low levels of current gene flow, represent valuable sources of information on historical, human-mediated global dispersal patterns of feral cats.

Matched MeSH terms: Introduced Species
Fulltext Pollination implications of the diverse diet of tropical nectar-feeding bats roosting in an urban cave

Lim VC, Ramli R, Bhassu S, Wilson JJ

PeerJ, 2018;6:e4572.
PMID: 29607265 DOI: 10.7717/peerj.4572

Background: Intense landscaping often alters the plant composition in urban areas. Knowing which plant species that pollinators are visiting in urban areas is necessary for understanding how landscaping impacts biodiversity and associated ecosystem services. The cave nectar bat,Eonycteris spelaea, is an important pollinator for many plants and is often recorded in human-dominated habitats. Previous studies of the diet ofE. spelaearelied on morphological identification of pollen grains found in faeces and on the body of bats and by necessity disregarded other forms of digested plant material present in the faeces (i.e., plant juice and remnants). The main objective of this study was to examine the diet of the nectarivorous bat,E. spelaea,roosting in an urban cave at Batu Caves, Peninsular Malaysia by identifying the plant material present in the faeces of bats using DNA metabarcoding.
Methods: Faeces were collected under the roost ofE. spelaeaonce a week from December 2015 to March 2016. Plant DNA was extracted from the faeces, Polymerase chain reaction (PCR) amplified atITS2andrbcLregions and mass sequenced. The resultant plant operational taxonomic units were searched against NCBI GenBank for identification.
Results: A total of 55 species of plants were detected from faeces ofE. spelaeaincludingArtocarpus heterophyllus, Duabanga grandifloraandMusaspp. which are likely to be important food resources for the cave nectar bat.
Discussion: Many native plant species that had not been reported in previous dietary studies ofE. spelaeawere detected in this study includingBauhinia strychnoideaandUrophyllum leucophlaeum, suggesting thatE. spelaearemains a crucial pollinator for these plants even in highly disturbed habitats. The detection of many introduced plant species in the bat faeces indicates thatE. spelaeaare exploiting them, particularlyXanthostemon chrysanthus,as food resources in urban area. Commercial food crops were detected from all of the faecal samples, suggesting thatE. spelaeafeed predominantly on the crops particularly jackfruit and banana and play a significant role in pollination of economically important plants. Ferns and figs were also detected in the faeces ofE. spelaeasuggesting future research avenues to determine whether the 'specialised nectarivorous'E. spelaeafeed opportunistically on other parts of plants.

Matched MeSH terms: Introduced Species
Fulltext Cryptic diversity: Two morphologically similar species of invasive apple snail in Peninsular Malaysia

Rama Rao S, Liew TS, Yow YY, Ratnayeke S

PLoS One, 2018;13(5):e0196582.
PMID: 29734361 DOI: 10.1371/journal.pone.0196582

Invasive snails in the genus Pomacea have spread across Southeast Asia including Peninsular Malaysia. Their effects on natural and agricultural wetlands are appreciable, but species-specific effects are less clear because of morphological similarity among the species. Our objective was to establish diagnostic characteristics of Pomacea species in Malaysia using genetic and morphological criteria. The mitochondrial COI gene of 52 adult snails from eight localities in Peninsular Malaysia was amplified, sequenced, and analysed to verify species and phylogenetic relationships. Shells were compared using geometric morphometric and covariance analyses. Two monophyletic taxa, P. canaliculata and P. maculata, occurred in our samples. The mean ratio of shell height: aperture height (P = 0.042) and shell height: shell width (P = 0.007) was smaller in P. maculata. P. maculata co-occurred with P. canaliculata in five localities, but samples from three localities contained only P. canaliculata. This study is the first to confirm the presence of two of the most invasive species of Pomacea in Peninsular Malaysia using a molecular technique. P. canaliculata appears to be the more widespread species. Despite statistical differences, both quantitative and qualitative morphological characteristics demonstrated much interspecific overlap and intraspecific variability; thus, shell morphology alone cannot reliably verify species identity. Molecular techniques for distinguishing between these two highly invasive Pomacea species are needed to understand their specific ecological niches and to develop effective protocols for their management.

Matched MeSH terms: Introduced Species
Fulltext A standardized dataset for conservation prioritization of songbirds to support CITES

Juergens J, Bruslund S, Staerk J, Oegelund Nielsen R, Shepherd CR, Leupen B, et al.

Data Brief, 2021 Jun;36:107093.
PMID: 34041313 DOI: 10.1016/j.dib.2021.107093

In this article we present a standardized dataset on 6659 songbirds (Passeriformes) highlighting information relevant to species conservation prioritization with a main focus to support the Convention on International Trade in Endangered Species of Wild Fauna and Flora (CITES). Data were collected from both scientific and grey literature as well as several online databases. The data are structured into six knowledge categories: Conventions and Treaties, Human Use, Extinction Risk, Management Opportunities, Biological Information, and Intrinsic Values. The Conventions and Treaties category includes the listings for two international conventions, CITES and the Convention on the Conservation of Migratory Species of Wild Animals (CMS), as well as EU listings for the EU Wildlife Trade Regulations and the EU Birds Directive. The Human Use category contains information on both regulated trade collected from the CITES Trade Database and the United States' Law Enforcement Management Information System (LEMIS), and highly aggregated data on seizures which we obtained from TRAFFIC, the United Nations Office on Drugs and Crime (UNODC) and two data sources on traditional medicine. We also present, for the first time, the complete Songbirds in Trade Database (SiTDB), a trade database curated by taxon expert S. Bruslund based on expert knowledge, literature review, market surveys and sale announcements. Data on the types of human use, including traditional medicine are also provided. The knowledge area on Extinction Risk contains data on the species' IUCN Red List status, the Alliance for Zero Extinction Trigger Species status, site and population at the site, the species' IUCN Climate Change Vulnerability Assessment, and the listing of priority species at the Asian Songbird Crisis Summit. In the Management Opportunities category, we gathered data on ex-situ management from Species360 zoo holdings as well as species management plans from the European and North American Zoo Associations (EAZA and AZA, respectively). Biological Information includes data on body mass, clutch size, diet, availability of data from the IUCN Red List on habitat systems, extent of occurrence, generation length, migration pattern, distribution, and biological data from the Demographic Species Knowledge Index, number of occurrences recorded by the Global Biodiversity Information Facility (GBIF) as well as genomic data from the Bird 10 000K Genomes (B10K) project, Vertebrate Genome Project (VGP) and GenBank. Information on invasive species is also part of this knowledge area. The Intrinsic Value category refers to two measures of the species' intrinsic value, namely Ecological and Evolutionary Distinctiveness. In order to make these knowledge areas comparable, we standardized data following the taxonomy of the Handbook of the Birds of the World and Birdlife (Version 4, 2019). The data enable a broad spectrum of analyses and will be useful to scientists for further research and to policymakers, zoos and other conservation stakeholders for future prioritization decisions.

Matched MeSH terms: Introduced Species
Fulltext Emerging Infectious Disease Implications of Invasive Mammalian Species: The Greater White-Toothed Shrew (Crocidura russula) Is Associated With a Novel Serovar of Pathogenic Leptospira in Ireland

Nally JE, Arent Z, Bayles DO, Hornsby RL, Gilmore C, Regan S, et al.

PLoS Negl Trop Dis, 2016 12;10(12):e0005174.
PMID: 27935961 DOI: 10.1371/journal.pntd.0005174

The greater white-toothed shrew (Crocidura russula) is an invasive mammalian species that was first recorded in Ireland in 2007. It currently occupies an area of approximately 7,600 km2 on the island. C. russula is normally distributed in Northern Africa and Western Europe, and was previously absent from the British Isles. Whilst invasive species can have dramatic and rapid impacts on faunal and floral communities, they may also be carriers of pathogens facilitating disease transmission in potentially naive populations. Pathogenic leptospires are endemic in Ireland and a significant cause of human and animal disease. From 18 trapped C. russula, 3 isolates of Leptospira were cultured. However, typing of these isolates by standard serological reference methods was negative, and suggested an, as yet, unidentified serovar. Sequence analysis of 16S ribosomal RNA and secY indicated that these novel isolates belong to Leptospira alstonii, a unique pathogenic species of which only 7 isolates have been described to date. Earlier isolations were limited geographically to China, Japan and Malaysia, and this leptospiral species had not previously been cultured from mammals. Restriction enzyme analysis (REA) further confirms the novelty of these strains since no similar patterns were observed with a reference database of leptospires. As with other pathogenic Leptospira species, these isolates contain lipL32 and do not grow in the presence of 8-azagunaine; however no evidence of disease was apparent after experimental infection of hamsters. These isolates are genetically related to L. alstonii but have a novel REA pattern; they represent a new serovar which we designate as serovar Room22. This study demonstrates that invasive mammalian species act as bridge vectors of novel zoonotic pathogens such as Leptospira.

Matched MeSH terms: Introduced Species

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