Download Video Black Cat Sub Indonesia
Stefania Gingery
DNA barcoding is a valuable taxonomic tool for rapid and accurate species identification and cryptic species discovery in black flies. Indonesia has 143 nominal species of black flies, but information on their biological aspects, including vectorial capacity and biting habits, remains underreported, in part because of identification problems. The current study represents the first comprehensive DNA barcoding of Indonesian black flies using mitochondrial cytochrome c oxidase subunit I (COI) gene sequences.
Genomic DNA of Indonesian black fly samples were extracted and sequenced, producing 86 COI sequences in total. Two hundred four COI sequences, including 118 GenBank sequences, were analysed. Maximum likelihood (ML) and Bayesian inference (BI) trees were constructed and species delimitation analyses, including ASAP, GMYC and single PTP, were performed to determine whether the species of Indonesian black flies could be delineated. Intra- and interspecific genetic distances were also calculated and the efficacy of COI sequences for species identification was tested.
The findings showed that COI barcoding is a promising taxonomic tool for Indonesian black flies. The DNA barcodes will aid in correct identification and genetic study of Indonesian black flies, which will be helpful in the control and management of potential vector species.
Black flies (Diptera: Simuliidae) are medically important haematophagous insects for humans, domestic animals and wildlife, due to their pestiferous biting habits and vectorial roles in transmitting various parasites. They are the sole vector of the filarial nematode Onchocerca volvulus, which causes river blindness, the second leading infectious cause of blindness in the world [1]. They also transmit other Onchocerca species, Mansonella filarial parasites and Leucocytozoon and Trypanosoma protozoa [2, 3]. In contrast, black flies also function as beneficial organisms in aquatic ecosystems, where the larvae process fine particulate organic matter into larger food pellets, serve as food for other aquatic organisms and act as bioindicators of water quality [4].
Black flies are traditionally identified using morphological keys, such as those by Adler, Currie [11], Crosskey [12], Shelley [13], Takaoka [14], Takaoka and Davies [15], Takaoka and Davies [16] and Takaoka, Sofian-Azirun [17]. Chromosome-based analyses also drive black fly taxonomy and have revealed cryptic diversity in many morphospecies [2]. These two methods, however, are sometimes insufficient for rapid and accurate species identification crucial for biological research and vector control. Morphologically similar species often cannot be differentiated in one or more life stages, and chromosomal identifications are typically applicable only in the larval stage. Both methods also require a higher level of expertise [18, 19].
Although several genetic studies have been conducted on black flies in Indonesia, including S. (N.) feuerborni, S. (S.) nobile and S. (S.) timorense [24, 29, 30], the genetics of other Indonesian black flies is understudied. We, therefore, used the mitochondrial COI gene to delimit species boundaries for 55 species of black flies from Indonesia.
Samples were collected from eight provinces in Indonesia between 2014 and 2017 (Table 1). Aquatic stages of black flies (larvae and pupae) attached to grasses, leaves, twigs, plant roots and rocks were collected by hand using fine forceps. Pupae were individually kept alive in vials until adult emergence. The adults, together with their pupal exuviae and cocoons, were fixed in 80% ethanol for identification at the subgenus, species group or species level. The methods of collection and identification followed those of Adler, Currie [11] and Takaoka [14].
The relationships among 55 nominal species of black flies in 14 previously established species groups in Indonesia are presented for the first time to our knowledge through DNA barcodes based on the mitochondrial COI gene. The accuracy of the COI gene to identify black fly species in Indonesia is > 84%. Most of the species are shown to be monophyletic in their respective species groups and subgenera with a few exceptions. Possible causes of non-monophyly include inadequate phylogenetic signal, imperfect taxonomy, interspecific hybridization, incomplete lineage sorting and gene paralogy [44].
COI-based DNA barcoding is a valuable means of identification of black flies in Indonesia, except for a limited number of taxa, especially nominal species known to be complexes. The separation of these problematic taxa requires other options, such as fast-evolving genes and cytogenetics. Several nominal species were unavailable for in-depth inspection because of limited sampling. For instance, only one sequence was included for the following species, limiting the study of their intraspecific variation: S. (G.) sunapii, S. (G.) rangatense, S. (G.) sumbaense, S. (N.) aureohirtum, S. (S.) fenestratum, S. (S.) nebulicola, S. (S.) baliense and S. (S.) tani. Therefore, more samples should be collected from Indonesia for in-depth studies. Furthermore, no morphological variation was observed in the species that showed high intraspecific divergences; further detailed morphological examinations are thus required to confirm the presence of cryptic diversity. Nevertheless, this research provides a basis for future comprehensive studies on black flies in Indonesia. The deposition of COI sequences into publicly accessible databases also enables the establishment of a novel sequence library for Indonesian black flies. Additionally, the nucleotide database is expected to serve as a reference for species identification and comparative studies of other species of Indonesian black flies that were not included in this study. Overall, our findings establish the groundwork for further utilization of COI barcoding as a rapid and precise method for exploring the diversity of Indonesian black flies.
: Figure. S1. BI tree showing species of black flies from Indonesia in the subgenus Simulium Latreille, Nevermannia Enderlein and Gomphostilbia Enderlein, which was constructed from COI sequences. Posterior probability values of > 0.50 are shown on the branches. Branches with posterior probability values > 0.70 are considered well supported. New sequences generated in the study are in bold. Grey bars indicate the respective operational taxonomic units recognised by the three species delimitation analyses (i.e. ASAP, GMYC and PTP, in order). For GMYC analysis, the three bars labelled with double asterisks (**) represent one taxonomic unit, while the two bars labelled with hashtag (#) symbols represent another taxonomic unit. ASAP: Assemble Species by Automatic Partitioning; GMYC: Generalized Mixed Yule Coalescent; PTP: Poisson Tree Processes
Background: DNA barcoding is a valuable taxonomic tool for rapid and accurate species identification and cryptic species discovery in black flies. Indonesia has 143 nominal species of black flies, but information on their biological aspects, including vectorial capacity and biting habits, remains underreported, in part because of identification problems. The current study represents the first comprehensive DNA barcoding of Indonesian black flies using mitochondrial cytochrome c oxidase subunit I (COI) gene sequences.
Methods: Genomic DNA of Indonesian black fly samples were extracted and sequenced, producing 86 COI sequences in total. Two hundred four COI sequences, including 118 GenBank sequences, were analysed. Maximum likelihood (ML) and Bayesian inference (BI) trees were constructed and species delimitation analyses, including ASAP, GMYC and single PTP, were performed to determine whether the species of Indonesian black flies could be delineated. Intra- and interspecific genetic distances were also calculated and the efficacy of COI sequences for species identification was tested.
Conclusions: The findings showed that COI barcoding is a promising taxonomic tool for Indonesian black flies. The DNA barcodes will aid in correct identification and genetic study of Indonesian black flies, which will be helpful in the control and management of potential vector species.
TAKE A SIP This coffee came to us by a new partner, Co.trade Imports. They sent us a cupping table full of Indonesian coffees, and this one was easily everyone's favorite. We think it's going to take a lot of people by surprise in the best way! Indonesian coffees are sometimes known for having dry, woody, cedar-y undertones, but this coffee is a welcome exception! Super sweet and very fruity, this coffee reminds us of black forest cake when hot. As it begins to cool, the coffee becomes more and more tropical, introducing a delightful kiwi note. When cool, this coffee gets a little wine-y - but not boozy! - reminding us of our post-dinner sips of ruby port.
Black-winged Mynas are prized in the cage bird trade for their striking black and white plumage, lively behaviour and singing ability; today their extreme rarity in the wild adds to their desirability.
African Indonesians are an ethnic group of Indonesians with total or partial ancestry from any of the black racial groups of Africa[1] who were born in or immigrated to Indonesia. The first wave of immigration was in the 19th century, between 1830 and 1872.[2][3]
It is estimated that the trade is worth Indonesian Rupiah 9 Trillion (US$ 900 Million) each year, due to the high prices paid for the more endangered species. In the domestic black market, an orangutan can fetch Rupiah 5 Million (US$ 500), a Sumatran tiger Rp 20 Million (US$2000) and a Javan Owa (gibbon) Rp 3 Million (US$300). The price is much higher in international black market, where a juvenile orangutan can fetch US$45,000.
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