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Unexpected diversity of sandflies (Diptera: Psychodidae) in tourist caves in Northern Thailand

Sukantamala J, Sing KW, Jaturas N, Polseela R, Wilson JJ

Mitochondrial DNA A DNA Mapp Seq Anal, 2017 11;28(6):949-955.
PMID: 27759464 DOI: 10.1080/24701394.2016.1214728

Certain species of Phlebotomine sandflies (Diptera: Psychodidae) are vectors of the protozoa which causes leishmaniasis. Sandflies are found breeding in enclosed places like caves. Thailand is a popular tourist destination, including for ecotourism activities like caving, which increases the risk of contact between tourists and sandflies. Surveillance of sandflies is important for monitoring this risk but identification of species based on morphology is challenged by phenotypic plasticity and cryptic diversity. DNA barcodes have been used for the identification of sandflies in Thailand. We collected sandflies using CDC light trap from four tourist caves in Northern Thailand. Female sandflies were provisionally sorted into 13 morphospecies and 19 unidentified specimens. DNA was extracted from the thorax and legs of sandflies and the DNA barcode region of cytochrome c oxidase I mtDNA amplified and sequenced. The specimens were sorted into 22 molecular operational taxonomic units (MOTU) based on the 145 DNA barcodes, which is significantly more than the morphospecies. Several of the taxa thought to be present in multiple caves, based on morphospecies sorting, split into cave-specific MOTU which likely represent cryptic species. Several MOTU reported in an earlier study from Wihan Cave, Thailand, were also found in these caves. This supports the use of DNA barcodes to investigate species diversity of sandflies and their useful role in surveillance of sandflies in Thailand.

Matched MeSH terms: Genes, Mitochondrial*
Two new Bent-toed Geckos of the Cyrtodactylus pulchellus complex from Peninsular Malaysia and multiple instances of convergent adaptation to limestone forest ecosystems

Grismer LL, Wood PL, Anuar S, Grismer MS, Quah ES, Murdoch ML, et al.

Zootaxa, 2016 Apr 25;4105(5):401-29.
PMID: 27394789 DOI: 10.11646/zootaxa.4105.5.1

A new species of limestone cave-adapted gecko of the Cyrtodactylus pulchellus complex, C. hidupselamanya sp. nov., is described from an isolated karst formation at Felda Chiku 7, Kelantan, Peninsular Malaysia. This formation is scheduled to be completely quarried for its mineral content. From what we know about the life history of C. hidupselamanya sp. nov., this will result in its extinction. A new limestone forest-adapted species, C. lenggongensis sp. nov., from the Lenggong Valley, Perak was previously considered to be conspecific with C. bintangrendah but a re-evaluation of morphological, color pattern, molecular, and habitat preference indicates that it too is a unique lineage worthy of specific recognition. Fortunately C. lenggongensis sp. nov. is not facing extinction because its habitat is protected by the UNESCO Archaeological Heritage of the Lenggong Valley due to the archaeological significance of that region. Both new species can be distinguished from all other species of Cyrtodactylus based on molecular evidence from the mitochondrial gene ND2 and its flanking tRNAs as well as having unique combinations of morphological and color pattern characteristics. Using a time-calibrated BEAST analysis we inferred that the evolution of a limestone habitat preference and its apparently attendant morphological and color pattern adaptations evolved independently at least four times in the C. pulchellus complex between 26.1 and 0.78 mya.

Matched MeSH terms: Genes, Mitochondrial
Timeframes of speciation, reticulation, and hybridization in the bulldog bat explained through phylogenetic analyses of all genetic transmission elements

Khan FA, Phillips CD, Baker RJ

Syst Biol, 2014 Jan 1;63(1):96-110.
PMID: 24149076 DOI: 10.1093/sysbio/syt062

Phylogenetic comparisons of the different mammalian genetic transmission elements (mtDNA, X-, Y-, and autosomal DNA) is a powerful approach for understanding the process of speciation in nature. Through such comparisons the unique inheritance pathways of each genetic element and gender-biased processes can link genomic structure to the evolutionary process, especially among lineages which have recently diversified, in which genetic isolation may be incomplete. Bulldog bats of the genus Noctilio are an exemplar lineage, being a young clade, widely distributed, and exhibiting unique feeding ecologies. In addition, currently recognized species are paraphyletic with respect to the mtDNA gene tree and contain morphologically identifiable clades that exhibit mtDNA divergences as great as among many species. To test taxonomic hypotheses and understand the contribution of hybridization to the extant distribution of genetic diversity in Noctilio, we used phylogenetic, coalescent stochastic modeling, and divergence time estimates using sequence data from cytochrome-b, cytochrome c oxidase-I, zinc finger Y, and zinc finger X, as well as evolutionary reconstructions based on amplified fragment length polymorphisms (AFLPs) data. No evidence of ongoing hybridization between the two currently recognized species was identified. However, signatures of an ancient mtDNA capture were recovered in which an mtDNA lineage of one species was captured early in the noctilionid radiation. Among subspecific mtDNA clades, which were generally coincident with morphology and statistically definable as species, signatures of ongoing hybridization were observed in sex chromosome sequences and AFLP. Divergence dating of genetic elements corroborates the diversification of extant Noctilio beginning about 3 Ma, with ongoing hybridization between mitochondrial lineages separated by 2.5 myr. The timeframe of species' divergence within Noctilio supports the hypothesis that shifts in the dietary strategies of gleaning insects (N. albiventris) or fish (N. leporinus) are among the most rapid instances of dietary evolution observed in mammals. This study illustrates the complex evolutionary dynamics shaping gene pools in nature, how comparisons of genetic elements can serve for understanding species boundaries, and the complex considerations for accurate taxonomic assignment.

Matched MeSH terms: Genes, Mitochondrial/genetics
The transfer of two clades of Malaysian Sphenomorphus Fitzinger (Squamata: Scincidae) into the genus Tytthoscincus Linkem, Diesmos, & Brown and the description of a new Malaysian swamp-dwelling species

Grismer LL, Muin MA, Wood PL, Anuar S, Linkem CW

Zootaxa, 2016 Mar 15;4092(2):231-42.
PMID: 27394452 DOI: 10.11646/zootaxa.4092.2.6

Phylogenetic analyses based on the mitochondrial gene ND2 and its flanking tRNAs indicate the diminutive upland and insular species Sphenomorphus bukitensis, S. butleri, S. langkawiensis, S. perhentianensis, and S. temengorensis form a monophyletic group that is phylogenetically embedded within the Southeast Asian genus Tytthoscincus. The analyses also indicate that a new swamp-dwelling skink from the Bukit Panchor State Park, Pulau Pinang, Peninsular Malaysia is the sister species to the swamp-dwelling species S. sibuensis from Pulau Sibu, Johor and Singapore and that these two are also embedded in the genus Tytthoscincus. By transferring the two Peninsular Malaysian clades of Sphenomorphus into the genus Tytthoscincus, the monophyly of the latter is maintained. The new species T. panchorensis sp. nov. can be distinguished from all other species of Tytthoscincus by having a unique combination of morphological and color pattern characteristics.

Matched MeSH terms: Genes, Mitochondrial
The nearly complete mitogenome of the Southeast Asian firefly Pteroptyx tener (Coleoptera: Lampyridae)

Cheng S, Mat-Isa MN, Sapian IS, Ishak SF

Mol Biol Rep, 2021 Feb;48(2):1281-1290.
PMID: 33582950 DOI: 10.1007/s11033-021-06189-0

The estuarine firefly, Pteroptyx tener, aggregates in the thousands in mangrove trees lining tidal rivers in Southeast Asia where they engage one another in a nocturnal, pre-mating ritual of synchronised courtship flashes. Unfortunately, populations of the species by virtue of being restricted to isolated estuarine rivers systems in the region, are at risk of genetic isolation. Because of this concern we undertook the task of sequencing and characterising the mitochondrial DNA genome of P. tener, as the first step towards helping us to characterise and better understand their genetic diversity. We sequenced and assembled the mitochondrial DNA genome of P. tener from two male and female specimens from the district of Kuala Selangor in Peninsular Malaysia and announce the molecules in this publication. We also reconstructed the phylogenetic trees of all available lampyrids mitogenomes and suggest the need to re-examine our current understanding of their classification which have largely been based on morphological data and the cox1 gene. Separately, our analysis of codon usage patterns among lampyrid mitogenomes showed that the codon usage in a majority of the protein-coding genes were non-neutral. Codon usage patterns between mitogenome sequences of P. tener were, however, largely neutral. Our findings demonstrate the usefulness of mitochondrial genes/mitogenomes for analysing both inter- and intra- specific variation in the Lampyridae to aid in species discovery in this highly variable genus; and elucidate the phylogenetic relationships of Pteroptyx spp. from the region.

Matched MeSH terms: Genes, Mitochondrial/genetics
The mitogenome of Pangasius sutchi (Teleostei, Siluriformes: Pangasiidae)

Zhao H, Kong X, Zhou C

Mitochondrial DNA, 2014 Oct;25(5):342-4.
PMID: 23795847 DOI: 10.3109/19401736.2013.800492

The Pangasius sutchi is an important ornamental and economic fish in Southeast Asia e.g. Thailand, Malaysia and China. The complete mitochondrial genome sequence of P. sutchi has been sequenced, which contains 22 tRNA genes, 13 protein-coding genes, 2 rRNA genes and a non-coding control region with the total length of 16,522 bp. The gene order and composition are similar to most of other vertebrates. Just like most other vertebrates, the bias of G and C was found in different region/genes statistics results. Most of the genes are encoded on heavy strand, except for eight tRNA and ND6 genes. The mitogenome sequence of P. sutchi would contribute to better understand population genetics, evolution of this lineage.

Matched MeSH terms: Genes, Mitochondrial
The male and female complete mitochondrial genome sequences of the Endangered freshwater mussel Potomida littoralis (Cuvier, 1798) (Bivalvia: Unionidae)

Froufe E, Gan HM, Lee YP, Carneiro J, Varandas S, Teixeira A, et al.

Mitochondrial DNA A DNA Mapp Seq Anal, 2016 09;27(5):3571-2.
PMID: 27158872 DOI: 10.3109/19401736.2015.1074223

Freshwater mussels of the family Unionidae exhibit a particular form of mitochondria inheritance called double uniparental inheritance (DUI), in which the mitochondria are inherited by both male and female parents. The (M)ale and (F)emale mitogenomes are highly divergent within species. In the present study, we determine and describe the complete M and F mitogenomes of the Endangered freshwater mussel Potomida littoralis (Cuvier, 1798). The complete M and F mitogenomes sequences are 16 451 bp and 15 787 bp in length, respectively. Both F and M have the same gene content: 13 protein-coding genes (PCGs), 22 transfer RNA (trn) and 2 ribosomal RNA (rrn) genes. Bayesian analyses based on the concatenated nucleotide sequences of 12 PCGs and 2 rrn genes of both genomes, including mitogenome sequences available from related species, were performed. Male and Female lineages are monophyletic within the family, but reveal distinct phylogenetic relationships.

Matched MeSH terms: Genes, Mitochondrial
The genus Scirtothrips (Thysanoptera: Thripidae) in Malaysia, with four new species and comments on Biltothrips, a related genus

Ng YF, Mound LA, Azidah AA

Zootaxa, 2014;3856(2):253-66.
PMID: 25284657 DOI: 10.11646/zootaxa.3856.2.6

Species of the genus Scirtothrips are studied from Malaysia for the first time. Six species of this genus are here recorded from Malaysia: S. dobroskyi is newly recorded, and four new species: S. lantanae sp.n., S. lixinae sp.n., S. hitam sp.n. and S. malayensis sp.n. are described together with an illustrated identification key. Relationships were examined between S. dorsalis and the closely related S. hitam sp.n., based on the mitochondrial gene COI, and a redescription of the widespread pest species, dorsalis, is provided. Biltothrips minutus (Bhatti) is reported from Malaysia for the first time, and illustrations provided to distinguish this genus from Scirtothrips.

Matched MeSH terms: Genes, Mitochondrial
Fulltext The first mitochondrial genome data of an old world fruit bat, Cynopterus sphinx from Malaysia

Jahari PNS, Mohd Azman S, Munian K, Zakaria NA, Omar MSS, Richter SR, et al.

Mitochondrial DNA B Resour, 2021 Jan 12;6(1):53-55.
PMID: 33521264 DOI: 10.1080/23802359.2020.1846472

We assembled the complete mitogenome of Cynopterus sphinx (Vahl, 1797) of the family Pteropodidae originating from Malaysia. The total mitogenome size was 16,710bp which consists of 37 genes (13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes and one control region). A phylogenetic and BLASTn result showed the mitogenome sequence in this study varies by nearly 7% (93.48% similarity) from the same species in Cambodia. The next closest match of BLASTn was at 92% similarity to the C. brachyotis. This suggests the species-complex in Cynopterus sp. has given rise to the genetic variability.

Matched MeSH terms: Genes, Mitochondrial
Fulltext The employment of q-PCR using specific primer targeting on mitochondrial cytochrome-b gene for identification of wild boar meat in meatball samples

Aina GQ, Erwanto Y, Hossain M, Johan MR, Ali ME, Rohman A

J Adv Vet Anim Res, 2019 Sep;6(3):300-307.
PMID: 31583226 DOI: 10.5455/javar.2019.f348

Objective: The objective of this study was to employ real-time or quantitative polymerase chain reaction (q-PCR) using novel species specific primer (SSP) targeting on mitochondrial cytochrome-b of wild boar species (CYTBWB2-wb) gene for the identification of non-halal meat of wild boar meat (WBM) in meatball products.
Materials and Methods: The novel SSP of CYTBWB2-wb was designed by our group using PRIMERQUEST and NCBI software. DNA was extracted using propanol-chloroform-isoamyl alcohol method. The designed SSP was further subjected for validation protocols using DNA isolated from fresh meat and from meatball, which include specificity test, determination of efficiency, limit of detection and repeatability, and application of developed method for analysis of commercially meatball samples.
Results: The results showed that CYTBWB2-wb was specific to wild boar species against other animal species with optimized annealing temperature of 59°C. The efficiency of q-PCR obtained was 91.9% which is acceptable according to the Codex Allimentarius Commission (2010). DNA, with as low as 5 pg/μl, could be detected using q-PCR with primer of CYTBWB2-wb. The developed method was also used for DNA analysis extracted from meatball samples commercially available.
Conclusion: q-PCR using CYTBWB2-wb primers targeting on mitochondrial cytochrome-b gene (forward: CGG TTC CCT CTT AGG CAT TT; Reverse: GGA TGA ACA GGC AGA TGA AGA) can be fruitfully used for the analysis of WBM in commercial meatball samples.

Matched MeSH terms: Genes, Mitochondrial
The discovery and description of a new species of Bent-toed Gecko of the Cyrtodactylus pulchellus complex (Squamata: Gekkonidae) from the Langkawi Archipelago, Kedah, Peninsular Malaysia

Quah ESH, Grismer LL, Wood PLJ, Mohd Sah SA

Zootaxa, 2019 Sep 09;4668(1):zootaxa.4668.1.3.
PMID: 31716638 DOI: 10.11646/zootaxa.4668.1.3

A new species of limestone karst-adapted gecko of the Cyrtodactylus pulchellus complex, C. dayangbuntingensis sp. nov., is described from Dayang Bunting Island of the Langkawi Archipelago off the northwest coast of Peninsular Malaysia. It is the third species of the group to be described from the archipelago after C. langkawiensis and C. macrotuberculatus. The new species can be distinguished from all other species of Cyrtodactylus based on molecular evidence from the mitochondrial gene ND2 and its flanking tRNAs as well as having unique combinations of morphological and color pattern characteristics. This discovery underscores the need for continued surveys of the many islands in the archipelago to properly ascertain its true herpetological diversity.

Matched MeSH terms: Genes, Mitochondrial
The complete mitogenome of the soldier crab Mictyris longicarpus (Latreille, 1806) (Crustacea: Decapoda: Mictyridae)

Tan MH, Gan HM, Lee YP, Austin CM

Mitochondrial DNA A DNA Mapp Seq Anal, 2016 05;27(3):2121-2.
PMID: 25423510 DOI: 10.3109/19401736.2014.982585

The Mictyris longicarpus (soldier crab) complete mitochondrial genome sequence is reported making it the first for the family Mictyridae and the second for the superfamily Ocypodoidea. The mitogenome is 15,548 base pairs made up of 13 protein-coding genes, 2 ribosomal subunit genes, 22 transfer RNAs and a non-coding AT-rich region. The soldier crab mitogenome gene order is characteristic of brachyuran crabs with a base composition of 36.58% for T, 19.15% for C, 32.43% for A and 11.83% for G, with an AT bias of 69.01%.

Matched MeSH terms: Genes, Mitochondrial
The complete mitogenome of the river blackfish, Gadopsis marmoratus (Richardson, 1848) (Teleostei: Percichthyidae)

Gan HM, Tan MH, Lee YP, Austin CM

Mitochondrial DNA A DNA Mapp Seq Anal, 2016 05;27(3):2030-1.
PMID: 25329292 DOI: 10.3109/19401736.2014.974174

The mitogenome of the Australian freshwater blackfish, Gadopsis marmoratus was recovered coverage by genome skimming using the MiSeq sequencer (GenBank Accession Number: NC_024436). The blackfish mitogenome has 16,407 base pairs made up of 13 protein-coding genes, 2 ribosomal subunit genes, 22 transfer RNAs, and a 819 bp non-coding AT-rich region. This is the 5th mitogenome sequence to be reported for the family Percichthyidae.

Matched MeSH terms: Genes, Mitochondrial
The complete mitogenome of the porcelain crab Petrolisthes haswelli Miers, 1884 (Crustacea: Decapoda: Anomura)

Tan MH, Gan HM, Lee YP, Austin CM

Mitochondrial DNA A DNA Mapp Seq Anal, 2016 11;27(6):3983-3984.
PMID: 25541305

The mitochondrial genome sequence of the porcellanid crab, Petrolisthes haswelli is provided, making it the second for the family Porcellanidae and the third for the superfamily Galatheoidea. Petrolisthes haswelli has a mitogenome of 15,348 bp consisting of 13 protein-coding genes, two ribosomal subunit genes, 22 transfer RNAs and a non-coding AT-rich region. The base composition of the P. haswelli mitogenome is 35.66% for T, 18.65% for C, 34.35% for A and 11.34% for G, with an AT bias of 70.01%. The mitogenome gene order is identical to the mitogenome of Neopetrolisthes maculatus, the only other species of the family with a sequenced mitogenome.

Matched MeSH terms: Genes, Mitochondrial*
The complete mitogenome of the giant clam Tridacna squamosa (Heterodonta: Bivalvia: Tridacnidae)

Gan HM, Gan HY, Tan MH, Penny SS, Willan RC, Austin CM

Mitochondrial DNA A DNA Mapp Seq Anal, 2016 09;27(5):3220-1.
PMID: 25648928 DOI: 10.3109/19401736.2015.1007355

The complete mitochondrial genome of the commercially and ecologically important and internationally vulnerable giant clam Tridacna squamosa was recovered by genome skimming using the MiSeq platform. The T. squamosa mitogenome has 20,930 base pairs (62.35% A+T content) and is made up of 12 protein-coding genes, 2 ribosomal subunit genes, 24 transfer RNAs, and a 2594 bp non-coding AT-rich region. The mitogenome has a relatively large insertion in the atp6 gene. This is the first mitogenome to be sequenced from the genus Tridacna, and the family Tridacnidae and represents a new gene order.

Matched MeSH terms: Genes, Mitochondrial
The complete mitogenome of the ghost crab Ocypode ceratophthalmus (Pallas, 1772) (Crustacea: Decapoda: Ocypodidae)

Tan MH, Gan HM, Lee YP, Austin CM

Mitochondrial DNA A DNA Mapp Seq Anal, 2016 05;27(3):2123-4.
PMID: 25423512 DOI: 10.3109/19401736.2014.982587

The mitochondrial genome sequence of the ghost crab, Ocypode ceratophthalmus, is documented (GenBank accession number: LN611669) in this article. This is the first mitogenome for the family Ocypodidae and the second for the order Ocypodoidea. Ocypode ceratophthalmus has a mitogenome of 15,564 base pairs consisting of 13 protein-coding genes, two ribosomal subunit genes, 22 transfer RNAs and a non-coding AT-rich region. The base composition of the O. ceratophthalmus mitogenome is 35.78% for T, 19.36% for C, 33.73% for A and 11.13% for G, with an AT bias of 69.51% and the gene order is the typical arrangement for brachyuran crabs.

Matched MeSH terms: Genes, Mitochondrial
The complete mitogenome of the endangered white-clawed freshwater crayfish Austropotamobius pallipes (Lereboullet, 1858) (Crustacea: Decapoda: Astacidae)

Grandjean F, Tan MH, Gan HY, Gan HM, Austin CM

Mitochondrial DNA A DNA Mapp Seq Anal, 2016 09;27(5):3329-30.
PMID: 25738217 DOI: 10.3109/19401736.2015.1018207

The Austropotamobius pallipes complete mitogenome has been recovered using Next-Gen sequencing. Our sample of A. pallipes has a mitogenome of 15,679 base pairs (68.44% A + T content) made up of 13 protein-coding genes, 2 ribosomal subunit genes, 22 transfer RNAs, and a 877 bp non-coding AT-rich region. This is the first mitogenome sequenced for a crayfish from the family Astacidae and the 4(th) for northern hemisphere genera.

Matched MeSH terms: Genes, Mitochondrial
The complete mitogenome of the New Zealand freshwater crayfish Paranephrops planifrons White 1842 (Crustacea: Decapoda: Parastacidae)

Lee YP, Gan HM, Tan MH, Lys I, Page R, Dias Wanigasekera B, et al.

Mitochondrial DNA A DNA Mapp Seq Anal, 2016 09;27(5):3333-4.
PMID: 25707411 DOI: 10.3109/19401736.2015.1018209

The mitogenome of Paranephrops planifrons, was obtained by next generation sequencing. This crayfish has a mitochondrial genome of 16,174 base pairs with 13 protein-coding genes, 2 ribosomal subunit genes, 22 transfer RNAs (tRNA), and a non-coding AT-rich region of 771 bp. The P. planifrons nucleotide composition is: 33.63% for T, 21.92% for C, 34.46% for A, and 9.98% for G and has a 68.09% AT bias. While the mitogenome gene order for this species is consistent with aspects of the highly distinctive parastacid crayfish mitogenome gene arrangement, it has a novel gene order involving the rearrangements of a protein coding and several tRNA genes.

Matched MeSH terms: Genes, Mitochondrial
The complete mitogenome of the Macquarie perch, Macquaria australasica Cuvier, 1830 (Teleostei: Percichthyidae)

Gan HM, Tan MH, Austin CM

Mitochondrial DNA A DNA Mapp Seq Anal, 2016;27(1):383-4.
PMID: 24617484 DOI: 10.3109/19401736.2014.895996

The complete mitochondrial genome of the conservationally significant Macquarie perch (Macquaria australasica) was obtained from low-coverage shotgun sequencing using the MiSeq sequencer. The M. australasica mitogenome has 16,496 base pairs (55% A + T content) made up of 13 protein-coding genes, 2 ribosomal subunit genes, 22 transfer RNAs, and a 819 bp non-coding AT-rich region. This is the first mitogenome sequence for the genus Macquaria, and the third to be reported for the family Percichthyidae.

Matched MeSH terms: Genes, Mitochondrial
The complete mitogenome of the Australian tadpole shrimp Triops australiensis (Spencer & Hall, 1895) (Crustacea: Branchiopoda: Notostraca)

Gan HM, Tan MH, Lee YP, Austin CM

Mitochondrial DNA A DNA Mapp Seq Anal, 2016 05;27(3):2028-9.
PMID: 25329290 DOI: 10.3109/19401736.2014.974173

The mitochondrial genome sequence of the Australian tadpole shrimp, Triops australiensis is presented (GenBank Accession Number: NC_024439) and compared with other Triops species. Triops australiensis has a mitochondrial genome of 15,125 base pairs consisting of 13 protein-coding genes, 2 ribosomal subunit genes, 22 transfer RNAs, and a non-coding AT-rich region. The T. australiensis mitogenome is composed of 36.4% A, 16.1% C, 12.3% G and 35.1% T. The mitogenome gene order conforms to the primitive arrangement for Branchiopod crustaceans, which is also conserved within the Pancrustacean.

Matched MeSH terms: Genes, Mitochondrial

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