scholarly journals A Nation-wide Phylogenetic and Phylogeographic Investigation of the Endemic New Zealand Oyster Borers, Haustrum scobina and Haustrum albomarginatum

2021 ◽  
Author(s):  
Seamus O'Mahony
Keyword(s):  
New Zealand ◽  
Dna Sequences ◽  
Haplotype Diversity ◽  
Shell Morphology ◽  
Ice Age ◽  
Coi Gene ◽  
Rrna Gene ◽  
Similar Species ◽  
Migration Route ◽  
Outgroup Species

The endemic New Zealand sea snails Haustrum scobina and Haustrum albomarginatum are rocky shore intertidal dogwhelks of the Muricidae family. They have direct developing young and are carnivores. Their radula is used to drill into the shells of their prey, and they are commonly referred to as oyster borers. The taxonomic status of these species is still unresolved and therefore the name Haustrum scobina sensu lato is used.<br><br>The overall goal of this thesis research was to investigate the phylogeny and phylogeography of Haustrum scobina sensu lato using mitochondrial DNA sequences. Comparisons made to phylogeographic studies of ecologically similar species such as Cominella spp. provide an opportunity to identify the common environmental determinates of population migration route, genetic differentiation and speciation whenever similar patterns are found.<br><br>A nation-wide collection of samples was used to generate 277 new sequences from a 610 bp portion of the cytochrome c oxidase subunit I (COI) gene. This enabled the formation of a dataset of 654 DNA sequences, which was comprised of the 277 new sequences, 16 retrieved from a published study that deposited them in GenBank, and 361 from a previous unpublished thesis study. An unexpectedly diverse phylogeny of 58 COI haplotypes from 31 sample sites was recovered. These formed three clusters using K-means clustering by pairwise mutational distance. The in-group species did not form reciprocal monophyly groups, and the expected closest outgroup species (Haustrum haustorium) appeared to be as similar to the in-group clusters as they were to each other. A dataset of 27 DNA sequences from an 827 bp portion of the large sub-unit 28S nuclear rRNA gene was produced with the intention of corroborating the findings from the analyses of the COI dataset. This consisted of 26 new sequences and one sequence from a published study that deposited the sequence on GenBank. The expected taxonomic arrangement of Haustrum scobina sensu lato could not be matched by COI sequences due to incongruence with the 28S phylogeny and shell morphology. <br><br>The 28S dataset and shell morphology indicated there are two species in Haustrum scobina sensu lato. These are most likely Haustrum scobina and Haustrum albomarginatum, but they could not clearly be identified in the COI data. As a result, the phylogeographic certainty was limited when using the COI dataset because of the lack of clarity between the haplotypes of the two putative species. Possible reasons for the complicated COI dataset are discussed. Phylogenetic analysis of both the 28S and COI datasets did not support the expected conclusion that members of Haustrum scobina sensu lato are each other’s closest relatives. Haustrum haustorium was the expected immediate outgroup species but formed a polytomy with the in-group. A decrease in COI haplotype diversity was observed in southern samples when they were compared to the samples collected at northern locations. Taranaki sites shared a haplotype with multiple South Island sites that had no haplotype diversity. This suggested post-glacial re-colonisation of southern sites after displacement by ice-age conditions from these locations, a hypothesis consistent with results from studies of the Cominella genus. Association between Purau Bay in Lyttleton Harbour, Titahi Bay, Port Ahuriri and Kawau Island with no associated haplotypes between these locations suggested human-mediated translocation events. A genetic disjunction was also apparent between the south Wellington/Wairarapa coast and the eastern Wairarapa coast. This pattern was consistent with one study of Cominella maculosa and other studies have attributed similar patterns of other species in the region to recent uplift events affecting coastal community composition. The phylogeny of Haustrum scobina sensu lato will require further investigation before it can be used to more confidently resolve the phylogeographic history of the species.

scholarly journals A Nation-wide Phylogenetic and Phylogeographic Investigation of the Endemic New Zealand Oyster Borers, Haustrum scobina and Haustrum albomarginatum

2021 ◽  
Author(s):  
Seamus O'Mahony
Keyword(s):  
New Zealand ◽  
Dna Sequences ◽  
Haplotype Diversity ◽  
Shell Morphology ◽  
Ice Age ◽  
Coi Gene ◽  
Rrna Gene ◽  
Similar Species ◽  
Migration Route ◽  
Outgroup Species

The endemic New Zealand sea snails Haustrum scobina and Haustrum albomarginatum are rocky shore intertidal dogwhelks of the Muricidae family. They have direct developing young and are carnivores. Their radula is used to drill into the shells of their prey, and they are commonly referred to as oyster borers. The taxonomic status of these species is still unresolved and therefore the name Haustrum scobina sensu lato is used.<br><br>The overall goal of this thesis research was to investigate the phylogeny and phylogeography of Haustrum scobina sensu lato using mitochondrial DNA sequences. Comparisons made to phylogeographic studies of ecologically similar species such as Cominella spp. provide an opportunity to identify the common environmental determinates of population migration route, genetic differentiation and speciation whenever similar patterns are found.<br><br>A nation-wide collection of samples was used to generate 277 new sequences from a 610 bp portion of the cytochrome c oxidase subunit I (COI) gene. This enabled the formation of a dataset of 654 DNA sequences, which was comprised of the 277 new sequences, 16 retrieved from a published study that deposited them in GenBank, and 361 from a previous unpublished thesis study. An unexpectedly diverse phylogeny of 58 COI haplotypes from 31 sample sites was recovered. These formed three clusters using K-means clustering by pairwise mutational distance. The in-group species did not form reciprocal monophyly groups, and the expected closest outgroup species (Haustrum haustorium) appeared to be as similar to the in-group clusters as they were to each other. A dataset of 27 DNA sequences from an 827 bp portion of the large sub-unit 28S nuclear rRNA gene was produced with the intention of corroborating the findings from the analyses of the COI dataset. This consisted of 26 new sequences and one sequence from a published study that deposited the sequence on GenBank. The expected taxonomic arrangement of Haustrum scobina sensu lato could not be matched by COI sequences due to incongruence with the 28S phylogeny and shell morphology. <br><br>The 28S dataset and shell morphology indicated there are two species in Haustrum scobina sensu lato. These are most likely Haustrum scobina and Haustrum albomarginatum, but they could not clearly be identified in the COI data. As a result, the phylogeographic certainty was limited when using the COI dataset because of the lack of clarity between the haplotypes of the two putative species. Possible reasons for the complicated COI dataset are discussed. Phylogenetic analysis of both the 28S and COI datasets did not support the expected conclusion that members of Haustrum scobina sensu lato are each other’s closest relatives. Haustrum haustorium was the expected immediate outgroup species but formed a polytomy with the in-group. A decrease in COI haplotype diversity was observed in southern samples when they were compared to the samples collected at northern locations. Taranaki sites shared a haplotype with multiple South Island sites that had no haplotype diversity. This suggested post-glacial re-colonisation of southern sites after displacement by ice-age conditions from these locations, a hypothesis consistent with results from studies of the Cominella genus. Association between Purau Bay in Lyttleton Harbour, Titahi Bay, Port Ahuriri and Kawau Island with no associated haplotypes between these locations suggested human-mediated translocation events. A genetic disjunction was also apparent between the south Wellington/Wairarapa coast and the eastern Wairarapa coast. This pattern was consistent with one study of Cominella maculosa and other studies have attributed similar patterns of other species in the region to recent uplift events affecting coastal community composition. The phylogeny of Haustrum scobina sensu lato will require further investigation before it can be used to more confidently resolve the phylogeographic history of the species.

scholarly journals Preliminary analysis of New Zealand scampi (Metanephrops challengeri) diet using metabarcoding

2018 ◽  
Author(s):  
Aimee L van der Reis ◽  
Olivier Laroche ◽  
Andrew G Jeffs ◽  
Shane D Lavery
Keyword(s):  
New Zealand ◽  
Preliminary Analysis ◽  
18S Rrna ◽  
18S Rrna Gene ◽  
Coi Gene ◽  
Taxonomic Resolution ◽  
Gut Contents ◽  
Rrna Gene ◽  
Diverse Range ◽  
Dna Metabarcoding

Deep sea lobsters are highly valued for seafood and provide the basis of important commercial fisheries in many parts of the world. Despite their economic significance, relatively little is known about their natural diets. Microscopic analyses of foregut content in some species have suffered from low taxonomic resolution, with many of the dietary items difficult to reliably identify as their tissue is easily digested. DNA metabarcoding has the potential to provide greater taxonomic resolution of the diet of the New Zealand scampi (Metanephrops challengeri) through the identification of gut contents, but a number of methodological concerns need to be overcome first to ensure optimum DNA metabarcoding results. In this study, a range of methodological parameters were tested to determine the optimum protocols for DNA metabarcoding, and provide a first view of M. challengeri diet. Several PCR protocols were tested, using two universal primer pairs targeting the 18S rRNA and COI genes, on DNA extracted from both frozen and ethanol preserved samples for both foregut and hindgut digesta. The selection of appropriate DNA polymerases, buffers and methods for reducing PCR inhibitors (including the use of BSA) were found to be critical. Amplification from frozen or ethanol preserved gut contents appeared similarly dependable, but metabarcoding outcomes indicated that the ethanol samples produced better results from the COI gene. The COI gene was found to be more effective than 18S rRNA gene for identifying large eukaryotic taxa from the digesta, however, it was less successfully amplified. The 18S rRNA gene was more easily amplified, but identified mostly smaller marine organisms such as plankton and parasites. This preliminary analysis of the diet of M. challengeri identified a range of species (13,541 reads identified as diet), which included the ghost shark (Hydrolagus novaezealandiae), silver warehou (Seriolella punctate), tall sea pen (Funiculina quadrangularis) and the salp (Ihlea racovitza), suggesting that they have a varied diet, with a high reliance on scavenging a diverse range of pelagic and benthic species from the seafloor.

Phylogeny of the genus Scathophaga (Diptera: Scathophagidae) inferred from mitochondrial DNA sequences

2001 ◽  
Vol 79 (3) ◽  
pp. 517-524 ◽  
Author(s):  
M V Bernasconi ◽  
J Pawlowski ◽  
C Valsangiacomo ◽  
J -C Piffaretti ◽  
P I Ward
Keyword(s):  
Dna Sequences ◽  
Phylogenetic Trees ◽  
Coi Gene ◽  
Similar Species ◽  
Mitochondrial Cytochrome ◽  
Cyt B ◽  
Protein Coding ◽  
Scathophaga Stercoraria ◽  
Mitochondrial Cytochrome B ◽  
Cyt B Gene

Scathophaga stercoraria has been used for a large number of studies in animal ecology and evolution. Morphological phylogenetic work on the relationships among flies of the family Scathophagidae in general, and the genus Scathophaga in particular, has led to limited or incomplete conclusions. We addressed these relationships by sequencing 810 base pairs (bp) from the mitochondrial cytochrome oxidase subunit I (COI) gene and 738 bp of the mitochondrial cytochrome b (Cyt b) gene in 16 species of Scathophagidae. Phylogenetic analysis of these two protein-coding genes allows us to resolve relatively well the relationships within the genus Scathophaga, using both separate and combined (COI + Cyt b) data. Most of the phylogenetic trees generated by our data support the following relationships: (((S. analis + S. inquinata) + S. lutaria) + S. cineraria + (S. taeniopa + S. suilla + S. incola) + S. furcata + S. tropicalis). The most noteworthy findings are that (i) S. obscura and S. tinctinervis, which were formerly placed in the genus Coniosternum, form a sibling species cluster; (ii) S. taeniopa and S. suilla, which are morphologically very similar species, are clearly distinct taxa; (iii) S. analis, considered a doubtful species in the Catalogue of Palearctic Diptera, could be a synonym of S. inquinata; and (iv) the South American S. tropicalis and the Old World S. stercoraria are not sister-species.

Solution of taxonomic status of Unio mongolicus Middendorff, 1851 (Bivalvia: Unionidae) from the type locality in Transbaikalia and history of its taxonomy

2019 ◽  
Vol 29 (1) ◽  
pp. 55-70
Author(s):  
O. K. Klishko ◽  
M. Lopes-Lima ◽  
E. Froufe ◽  
A. E. Bogan
Keyword(s):  
Taxonomic Status ◽  
Type Specimen ◽  
Shell Morphology ◽  
Type Locality ◽  
Coi Gene ◽  
Mountain Stream ◽  
Past Century ◽  
Amur River Basin ◽  
Similar Species ◽  
History Of

Unio mongolicus Middendorff, 1851 (Bivalvia: Unionidae) was described from Gorbitza mountain stream (in the east of Trans-Baikal Territory, Russia) and the taxonomy has changed over the past century and a half. A specimen of Middendorffinaia mongolica from the Gorbitza stream collected 160 years later is a match with the type illustration of Unio mongolicus from the type locality. Comparison of the shell morphology of the type specimen of U. mongolicus with the modern specimen collected from this location, combined with our analyses of molecular, anatomical and conchological data of M. cf. mongolica species from rivers of the Upper Amur River Basin and the far eastern Russia, revealed that these taxa all belong to a single polymorphic species. The molecular analysis of the COI gene fragment of mtDNA of examined Comparatory Species assigned to Middendorffinaia Moskvicheva et Starobogatov, 1973 confirmed they are only intraspecific forms of M. mongolica. Morphological and genetic distances between M. mongolica and Nodularia douglasiae (Griffith et Pidgeon, 1833) confirmed their assignment to two independent genera. Based on conchological characteristics and anatomical features, the differences between morphologically similar species M. mongolica, N. douglasiae and Unio crassus Retzius, 1788 were determined. History of the taxonomic changes for Unio mongolicus is discussed.

scholarly journals Preliminary analysis of New Zealand scampi (Metanephrops challengeri) diet using metabarcoding

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e5641 ◽  
Author(s):  
Aimee L. van der Reis ◽  
Olivier Laroche ◽  
Andrew G. Jeffs ◽  
Shane D. Lavery
Keyword(s):  
New Zealand ◽  
Preliminary Analysis ◽  
18S Rrna ◽  
18S Rrna Gene ◽  
Coi Gene ◽  
Taxonomic Resolution ◽  
Gut Contents ◽  
Rrna Gene ◽  
Diverse Range ◽  
Dna Metabarcoding

Deep sea lobsters are highly valued for seafood and provide the basis of important commercial fisheries in many parts of the world. Despite their economic significance, relatively little is known about their natural diets. Microscopic analyses of foregut content in some species have suffered from low taxonomic resolution, with many of the dietary items difficult to reliably identify as their tissue is easily digested. DNA metabarcoding has the potential to provide greater taxonomic resolution of the diet of the New Zealand scampi (Metanephrops challengeri) through the identification of gut contents, but a number of methodological concerns need to be overcome first to ensure optimum DNA metabarcoding results. In this study, a range of methodological parameters were tested to determine the optimum protocols for DNA metabarcoding, and provide a first view ofM.challengeridiet. Several PCR protocols were tested, using two universal primer pairs targeting the 18S rRNA and COI genes, on DNA extracted from both frozen and ethanol preserved samples for both foregut and hindgut digesta. The selection of appropriate DNA polymerases, buffers and methods for reducing PCR inhibitors (including the use of BSA) were found to be critical. Amplification from frozen or ethanol preserved gut contents appeared similarly dependable. The COI gene was found to be more effective than 18S rRNA gene for identifying large eukaryotic taxa from the digesta; however, it was less successfully amplified. The 18S rRNA gene was more easily amplified, but identified mostly smaller marine organisms such as plankton and parasites. This preliminary analysis of the diet ofM.challengeriidentified a range of species (13,541 reads identified as diet), which included the ghost shark (Hydrolagus novaezealandiae), silver warehou (Seriolella punctata), tall sea pen (Funiculina quadrangularis) and the salp (Ihlea racovitzai), suggesting that they have a varied diet, with a high reliance on scavenging a diverse range of pelagic and benthic species from the seafloor.

scholarly journals A new Eumerus hoverfly (Diptera: Syrphidae) from Namibia and South Africa, with notes on similar species

Zootaxa ◽  
2020 ◽  
Vol 4890 (4) ◽  
pp. 493-508
Author(s):  
ANTONIO RICARTE ◽  
MARTIN HAUSER ◽  
SCOTT KINNEE ◽  
Mª ÁNGELES MARCOS-GARCÍA
Keyword(s):  
South Africa ◽  
New Species ◽  
Dna Sequences ◽  
Coi Gene ◽  
Medium Size ◽  
Similar Species ◽  
African Species ◽  
Afrotropical Region ◽  
National Botanic Garden ◽  
A New Species

Within the pollinator family Syrphidae, Eumerus Meigen, 1822 is a diverse genus with over 70 species recorded in the Afrotropical Region. A new species is described here from Namibia and South Africa. Adults are small to medium size flies, with spur-like expansions in the metatarsomeres 2 and 3. DNA sequences of the Cytochrome c oxidase subunit I (COI) gene were obtained from Namibian specimens. This is only the second Eumerus species documented from Namibia, where it was recorded from The National Botanic Garden, Windhoek. The new species is compared with similar species such as Eumerus vestitus Bezzi, 1912, for which a lectotype is designated. In addition, a new and preliminary morphological concept of the Eumerus obliquus group is proposed and a key to its African species is provided. 

scholarly journals Preliminary analysis of New Zealand scampi (Metanephrops challengeri) diet using metabarcoding

2018 ◽  
Author(s):  
Aimee L van der Reis ◽  
Olivier Laroche ◽  
Andrew G Jeffs ◽  
Shane D Lavery
Keyword(s):  
New Zealand ◽  
Preliminary Analysis ◽  
18S Rrna ◽  
18S Rrna Gene ◽  
Coi Gene ◽  
Taxonomic Resolution ◽  
Gut Contents ◽  
Rrna Gene ◽  
Diverse Range ◽  
Dna Metabarcoding

Deep sea lobsters are highly valued for seafood and provide the basis of important commercial fisheries in many parts of the world. Despite their economic significance, relatively little is known about their natural diets. Microscopic analyses of foregut content in some species have suffered from low taxonomic resolution, with many of the dietary items difficult to reliably identify as their tissue is easily digested. DNA metabarcoding has the potential to provide greater taxonomic resolution of foregut and hindgut contents of the New Zealand (NZ) scampi (Metanephrops challengeri), but a number of methodological concerns need to first be overcome to ensure optimum DNA metabarcoding results. In this study, a range of methodological parameters were trialled to determine the optimum protocols for DNA metabarcoding, and provide a first view of the NZ scampi diet. Several PCR protocols were trialled, using two universal primer pairs targeting the 18S rRNA and COI genes, on DNA extracted from frozen and ethanol preserved samples of both foregut and hindgut digesta. The selection of appropriate DNA polymerases, buffers and methods for reducing PCR inhibitors (including use of BSA) were found to be critical. Amplification from frozen or ethanol preserved gut contents appeared similarly dependable, but metabarcoding results showed that ethanol samples resulted in better results from the COI gene. The COI gene was found to be more effective than 18S rRNA gene for identifying large eukaryotic taxa from the digesta, however, it was less successfully amplified. The 18S rRNA gene was more easily amplified, but identified mostly smaller marine organisms such as plankton and parasites. This preliminary analysis of the diet of the NZ scampi identified a range of species, which included the ghost shark (Hydrolagus novaezealandiae), silver warehou (Seriolella punctate), tall sea pen (Funiculina quadrangularis ) and salp (Ihlea racovitza), suggesting that they have a varied diet, with a high reliance on scavenging a diverse range of pelagic and benthic species from the seafloor.

scholarly journals Phylogeography of the oyster borer (Haustrum scobina)

2021 ◽  
Author(s):  
◽  
Sebastian Logan
Keyword(s):  
New Zealand ◽  
Dna Sequences ◽  
Population Genetic ◽  
Isolation By Distance ◽  
Haplotype Diversity ◽  
Genetic Connectivity ◽  
Long Distance Dispersal ◽  
Genetic Structuring ◽  
Long Distance ◽  
Ecological Processes

<p>An effective investigation of the underlying ecological processes that shape genetic diversity and connectivity typically requires comparisons among phylogeographic studies of multiple species. Phylogeographic studies of New Zealand’s coastal marine benthos have historically relied on post hoc speculation rather than directed research questions to investigate ecological processes. There has also been a lack of studies on direct developing marine molluscs. Direct developers are expected to have a low potential for dispersal and thus show a pattern of genetic isolation by distance across their distributions. Recent research indicates that this assumption may frequently be violated by instances of long distance dispersal/translocation. The oyster borer (Haustrum scobina) is an endemic direct-developing marine mollusc found in high abundances at rocky intertidal environments across the entirety of New Zealand. This distribution and life history makes H. scobina an ideal target to study genetic connectivity in a species expected to show low realised dispersal and high population genetic structuring. This thesis research used 379 new DNA sequences from the mitochondrial gene cytochrome c oxidase subunit 1 (COI) to investigate the phylogeography of H. scobina across the southern North Island. In addition 16 new COI sequences were inadvertently sequenced from the morphologically similar congener Haustrum albomarginatum. Results from both species support the recently proposed division of H. scobina and H. albomarginatum as separate species. H. scobina populations show significant geographic structure and a lack of haplotype diversity across the south-eastern North Island concordant with results of another previous study of a direct developer. This finding suggests that ecological processes may be producing similar population genetic structures for direct developers generally. Contrast between high and low haplotype diversities in northern and southern H. scobina populations respectively, indicates that southern H. scobina populations may have originated via recolonisation from northern populations following a range contraction during the Last Glacial Maximum. Evidence of multiple long distance dispersal/translocation events was found indicating that long distance dispersal via rafting and/or inadvertent human-mediated translocations may have occurred frequently. Results are then discussed with a view to inform further research in to New Zealand direct developers.</p>

scholarly journals Phylogeography of the oyster borer (Haustrum scobina)

2021 ◽  
Author(s):  
◽  
Sebastian Logan
Keyword(s):  
New Zealand ◽  
Dna Sequences ◽  
Population Genetic ◽  
Isolation By Distance ◽  
Haplotype Diversity ◽  
Genetic Connectivity ◽  
Long Distance Dispersal ◽  
Genetic Structuring ◽  
Long Distance ◽  
Ecological Processes

<p>An effective investigation of the underlying ecological processes that shape genetic diversity and connectivity typically requires comparisons among phylogeographic studies of multiple species. Phylogeographic studies of New Zealand’s coastal marine benthos have historically relied on post hoc speculation rather than directed research questions to investigate ecological processes. There has also been a lack of studies on direct developing marine molluscs. Direct developers are expected to have a low potential for dispersal and thus show a pattern of genetic isolation by distance across their distributions. Recent research indicates that this assumption may frequently be violated by instances of long distance dispersal/translocation. The oyster borer (Haustrum scobina) is an endemic direct-developing marine mollusc found in high abundances at rocky intertidal environments across the entirety of New Zealand. This distribution and life history makes H. scobina an ideal target to study genetic connectivity in a species expected to show low realised dispersal and high population genetic structuring. This thesis research used 379 new DNA sequences from the mitochondrial gene cytochrome c oxidase subunit 1 (COI) to investigate the phylogeography of H. scobina across the southern North Island. In addition 16 new COI sequences were inadvertently sequenced from the morphologically similar congener Haustrum albomarginatum. Results from both species support the recently proposed division of H. scobina and H. albomarginatum as separate species. H. scobina populations show significant geographic structure and a lack of haplotype diversity across the south-eastern North Island concordant with results of another previous study of a direct developer. This finding suggests that ecological processes may be producing similar population genetic structures for direct developers generally. Contrast between high and low haplotype diversities in northern and southern H. scobina populations respectively, indicates that southern H. scobina populations may have originated via recolonisation from northern populations following a range contraction during the Last Glacial Maximum. Evidence of multiple long distance dispersal/translocation events was found indicating that long distance dispersal via rafting and/or inadvertent human-mediated translocations may have occurred frequently. Results are then discussed with a view to inform further research in to New Zealand direct developers.</p>

scholarly journals Cytochrome Oxidase C Subunit I (COI) for Identification and Genetic Variation of Loaches (Nemacheilus fasciatus)

2020 ◽  
Vol 7 (3) ◽  
pp. 142-153
Author(s):  
Amalia Ayuk Riyadini ◽  
Maheno Sri Widodo ◽  
Mohamad Fadjar
Keyword(s):  
Cytochrome Oxidase ◽  
Haplotype Diversity ◽  
Coi Gene ◽  
Research Needs ◽  
Morphological Similarity ◽  
Cytochrome Oxidase Subunit ◽  
River Waters ◽  
Outgroup Species ◽  
C Subunit ◽  
Larger Sample

Nemacheilus fasciatus is an Indonesian freshwater fish species that can be found in river waters on Java. This fish has a morphological similarity between species. This study aims to identify species of samples found and know their genetic kinship. This study used the Cytochrome Oxidase subunit I (COI) gene as a molecular marker, and then the results were analyzed using MEGA X software. The genetic structure and phylogeny of N. fasciatus sequences were combined with outgroup species from GenBank and analyzed using Maximum Likehood (ML), Pairwise Genetic Distance and Bootstrapping Phylogeny Model of Kimura 2 Parameters. The results showed that the primary pairs of LCO1490 and HCO2198 used to amplify the sample N. fasciatus with COI as a marker. The nucleotide frequencies of these loaches are A=26.5%, T=23.8%, C=19.9% and G=29.9%. The estimated Transition/Transversion bias (R) is 0.60. The number of haplotype diversity (Hd) was 0.972, and nucleotide (Pi) diversity was 0.05115. The kinship of N. fasciatus compared to the outgroup is closer to N. pallidus than N. chrysolaimos. Research needs to be conducted with a larger sample size for the genetic diversity of N. fasciatus in Indonesia.

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