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10 pages, 1353 KiB

Open AccessArticle

Revealing the Differences in Ulnaria acus and Fragilaria radians Distribution in Lake Baikal via Analysis of Existing Metabarcoding Data

by Alexey Morozov, Yuri Galachyants, Artem Marchenkov, Yulia Zakharova and Darya Petrova

Diversity 2023, 15(2), 280; https://doi.org/10.3390/d15020280 - 15 Feb 2023

Cited by 1 | Viewed by 1832

Abstract

Two diatom species, Ulnaria acus and Fragilaria radians, are morphologically very similar and often coexist, which makes it difficult to compare their abundances. However, they are easily separated by molecular data; thus, in this work, we attempted to estimate the differences in [...] Read more.

Two diatom species, Ulnaria acus and Fragilaria radians, are morphologically very similar and often coexist, which makes it difficult to compare their abundances. However, they are easily separated by molecular data; thus, in this work, we attempted to estimate the differences in their spatial and temporal distribution from existing metabarcoding datasets. Reanalyzing published sequences with an ASV-based pipeline and ad hoc classification routine allowed us to estimate the relative abundances of the two species, increasing the precision compared to usual OTU-based analyses. Existing data permit qualitative comparisons between two species that cannot be differentiated by other methods, detecting the distinct seasonal peaks and spatial distributions of F. radians and U. acus. Full article

(This article belongs to the Special Issue Aquatic Organisms Research with DNA Barcodes)

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17 pages, 31381 KiB

Open AccessArticle

Diversity and Life-Cycle Analysis of Pacific Ocean Zooplankton by Videomicroscopy and DNA Barcoding: Gastropods

by Peter J. Bryant and Timothy Arehart

Diversity 2022, 14(11), 912; https://doi.org/10.3390/d14110912 - 27 Oct 2022

Viewed by 2000

Abstract

The life cycles and biodiversity of Pacific coast gastropods were analyzed by videomicroscopy and DNA barcoding of individuals collected from tide pools and in plankton nets from a variety of shore stations. In many species (Families Calyptraeidae, Cerithiopsidae, Strombidae, Vermetidae, Columbellidae, Nassariidae, Olivellidae, [...] Read more.

The life cycles and biodiversity of Pacific coast gastropods were analyzed by videomicroscopy and DNA barcoding of individuals collected from tide pools and in plankton nets from a variety of shore stations. In many species (Families Calyptraeidae, Cerithiopsidae, Strombidae, Vermetidae, Columbellidae, Nassariidae, Olivellidae, Hermaeidae, Onchidorididae, Gastropteridae, Haminoeidae), the free-swimming veligers were recovered from plankton collections; in Roperia poulsoni (family Muricidae) veligers were usually recovered from egg sacs where they had been retained although some escapees were found in plankton collections; in Pteropurpura festiva (family Muricidae) free-living veligers were also found; and in Atlanta californiensis (family Atlantidae) both veligers and adults were obtained from plankton collections making this a holoplanktonic species. The results confirm that DNA barcoding based on COI gene sequencing is a useful strategy to match life-cycle stages within species as well as to identify species and to document the level of biodiversity within the gastropods. Full article

(This article belongs to the Special Issue Aquatic Organisms Research with DNA Barcodes)

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11 pages, 1555 KiB

Open AccessArticle

A Demonstration of DNA Barcoding-Based Identification of Blade-Form Ulva (Ulvophyceae, Chlorophyta) Species from Three Site in the San Juan Islands, Washington, USA

by Gabrielle M. Kuba, Brenda Carpio-Aguilar, Jason Eklund and D. Wilson Freshwater

Diversity 2022, 14(11), 899; https://doi.org/10.3390/d14110899 - 24 Oct 2022

Cited by 1 | Viewed by 2439

Abstract

Marine macroalgae are foundation species that play a critical ecological role in coastal communities as primary producers. The macroalgal genus Ulva is vital in intertidal communities, serving as a food source and shelter for organisms, but these species also form environment-damaging nuisance blooms. [...] Read more.

Marine macroalgae are foundation species that play a critical ecological role in coastal communities as primary producers. The macroalgal genus Ulva is vital in intertidal communities, serving as a food source and shelter for organisms, but these species also form environment-damaging nuisance blooms. This project aimed to demonstrate the utility of DNA barcoding for determining the diversity of Ulva species in the San Juan Islands (Washington, DC, USA). Blade-form Ulva (Ulvophyceae) specimens were collected from the lower, mid, and upper intertidal zones at three sites experiencing different levels of wave exposure. Sequences of plastid-encoded tufA were generated for each specimen and cluster analyses revealed the presence of four species at the collection sites. Two species were positively identified as Ulva expansa and Ulva fenestrata based on their sharing identical tufA sequences with those of the holotype specimens. Sequences of plastid-encoded rbcL and the nuclear-encoded ribosomal ITS regions of representative specimens were used to identify the other two species as Ulva prolifera and Ulva californica based on their similarity to epitype and topotype specimen sequences, respectively. Additional types of specimen sequencing efforts are needed to increase the number of Ulva species that can be accurately identified and realize their true biodiversity. Full article

(This article belongs to the Special Issue Aquatic Organisms Research with DNA Barcodes)

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27 pages, 3636 KiB

Open AccessArticle

The Mitogenome Structure of Righteye Flounders (Pleuronectidae): Molecular Phylogeny and Systematics of the Family in East Asia

by Alexander D. Redin and Yuri Ph. Kartavtsev

Diversity 2022, 14(10), 805; https://doi.org/10.3390/d14100805 - 27 Sep 2022

Cited by 3 | Viewed by 1993

Abstract

This paper reports the first complete sequence of the mitochondrial genome (mitogenome) of the yellow-striped flounder Pseudopleuronectes herzensteini (Pleuronectoidei: Pleuronectidae). Mitogenome evolution, and molecular phylogenetic reconstruction based on four to six techniques, including coalescent analysis, were performed for flatfish. The genome size of [...] Read more.

This paper reports the first complete sequence of the mitochondrial genome (mitogenome) of the yellow-striped flounder Pseudopleuronectes herzensteini (Pleuronectoidei: Pleuronectidae). Mitogenome evolution, and molecular phylogenetic reconstruction based on four to six techniques, including coalescent analysis, were performed for flatfish. The genome size of the specimen sampled was 16,845 bp, including 13 protein-coding genes, 22 tRNA genes, 12S, and 16S rRNA genes, and the control region, CR. The composition and arrangement of the genes are similar to those in other teleost fish, including the second mitogenome reported in this paper. The frequency of A, C, G, and T nucleotides in the P. herzensteini mitogenome is 27%, 29.2%, 17.6%, and 26.2%, respectively. The ratio of complementary nucleotides in the mitogenome of this and other species of the family was A+T:G+C (53.2: 46.8%) and do not deviate significantly from the expected equilibrium proportion. The submission to the global database (GenBank) of two new mitogenomes along with 106 analyzed GenBank sequences will contribute to phylogenetic studies of flounders at the family and suborder levels. Based on 26 and 108 nucleotide sequences of protein-coding genes (PCGs), we investigated the molecular phylogeny of flounders and performed analysis for two sets of sequences, including those of members of the family Pleuronectidae and the suborder Pleuronectoidei and estimated their importance in establishing the taxonomy at these two levels. Data obtained by up to six techniques of multigene phylogenetic reconstructions support monophyly within the family Pleuronectidae with high statistical confidence; however, conclusions regarding the phylogenetics at the suborder level require further investigation. Our results also revealed paraphyletic and weakly supported branches that are especially numerous at the suborder level; thus, there is a clear need for taxonomic revisions at the suborder, and possibly family levels. Genetic distance analysis reveals the suitability for DNA barcoding of species specimens at single genes as well as at whole mitogenome data. Full article

(This article belongs to the Special Issue Aquatic Organisms Research with DNA Barcodes)

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16 pages, 2768 KiB

Open AccessArticle

DNA Barcoding and Distribution of Gastropods and Malacostracans in the Lower Danube Region

by Selma Menabit, Tatiana Begun, Adrian Teacă, Mihaela Mureşan, Paris Lavin and Cristina Purcarea

Diversity 2022, 14(7), 533; https://doi.org/10.3390/d14070533 - 30 Jun 2022

Cited by 1 | Viewed by 2512

Abstract

This survey reports the spatial distribution of gastropods belonging to Caenogastropoda, Architaenioglossa, Littorinimorpha, Cycloneritida and Hygrophila orders, and malacostracans from Amphipoda and Mysida orders in the lower sector of the Danube River, Romania, using DNA barcoding based on the cytochrome C oxidase I [...] Read more.

This survey reports the spatial distribution of gastropods belonging to Caenogastropoda, Architaenioglossa, Littorinimorpha, Cycloneritida and Hygrophila orders, and malacostracans from Amphipoda and Mysida orders in the lower sector of the Danube River, Romania, using DNA barcoding based on the cytochrome C oxidase I (COI) gene sequence. Sampling was performed for eight locations of Danube Delta branches and Bechet area during three consecutive years (2019–2021). Molecular identification of sixteen gastropods and twelve crustacean individuals was confirmed to the species level, providing the first molecular identification of gastropods from the Lower Danube sector. Phylogenetic analysis showed that species of gastropods and crustaceans clustered in monophyletic groups. Among gastropods, Microcolpia daudebartii acicularis, Viviparus viviparus, Bithynia tentaculata, Physa fontinalis, Ampullaceana lagotis and Planorbarius corneus were identified in Chilia and Sulina branches; and the Bechet area was populated by Holandriana holandrii, Theodoxus transversalis and Gyraulus parvus. The amphipods and mysids were present along the three main Danube branches. The calculated density of these species revealed an abundant community of crustacean Chelicorophium robustum on Sulina branch, and Dikerogammarus haemobaphes and D. villosus in extended areas of the Danube Delta. The presence of these invertebrates along Danube River was reported in relation to the sediment type and water depth. Full article

(This article belongs to the Special Issue Aquatic Organisms Research with DNA Barcodes)

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25 pages, 11648 KiB

Open AccessArticle

Checklist of Arrenurids (Acari: Hydrachnidia: Arrenuridae) of Mexico, with New Records from the Yucatan Peninsula, and the Description of Five New Species of the Subgenera Megaluracarus and Dadayella

by Lucia Montes-Ortiz, Manuel Elías-Gutiérrez and Marcia María Ramírez-Sánchez

Diversity 2022, 14(4), 276; https://doi.org/10.3390/d14040276 - 7 Apr 2022

Cited by 5 | Viewed by 2902

Abstract

A checklist of arrenurids of Mexico is presented, including three new records from the Yucatan Peninsula. We provide updated descriptions of Arrenurus mexicanus, A. (Megaluracarus) colitus, and A. (Megaluracarus) marshalli. Additionally, four new species of the [...] Read more.

A checklist of arrenurids of Mexico is presented, including three new records from the Yucatan Peninsula. We provide updated descriptions of Arrenurus mexicanus, A. (Megaluracarus) colitus, and A. (Megaluracarus) marshalli. Additionally, four new species of the subgenus Megaluracarus and one of Dadayella are described by using integrative taxonomy: Arrenurus (Megaluracarus) eduardoi n. sp., characterized by a large, thorn-shaped hump in the middle dorsal shield; Arrenurus (Megaluracaurus) federicoi n. sp., with large pores in the body, including the idiosoma; Arrenurus (Megaluracarus) ecosur n. sp., with a peculiar pattern of setation in the legs; Arrenurus (Megaluracarus) beatrizae n. sp., with a short cauda with two pairs of lateral notches, and Arrenurrus (Dadayella) cristinae n. sp., characterized by a male cauda with two falcate setae. Non-destructive methods allowed the taking of scanning electron microscope images and DNA sequencing of the designed type material. All new species have a divergence using the DNA mitochondrial gene COI from 21.1% to 28.6% within them. With these records and descriptions, the number of Arrenurus registered for Mexico increases to 42, most of them from a single locality. Full article

(This article belongs to the Special Issue Aquatic Organisms Research with DNA Barcodes)

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20 pages, 9173 KiB

Open AccessEditor’s ChoiceArticle

Improved Chironomid Barcode Database Enhances Identification of Water Mite Dietary Content

by Adrian A. Vasquez, Brittany L. Bonnici, Safia Haniya Yusuf, Janiel I. Cruz, Patrick L. Hudson and Jeffrey L. Ram

Diversity 2022, 14(2), 65; https://doi.org/10.3390/d14020065 - 19 Jan 2022

Cited by 7 | Viewed by 3352

Abstract

Chironomids are one of the most biodiverse and abundant members of freshwater ecosystems. They are a food source for many organisms, including fish and water mites. The accurate identification of chironomids is essential for many applications in ecological research, including determining which chironomid [...] Read more.

Chironomids are one of the most biodiverse and abundant members of freshwater ecosystems. They are a food source for many organisms, including fish and water mites. The accurate identification of chironomids is essential for many applications in ecological research, including determining which chironomid species are present in the diets of diverse predators. Larval and adult chironomids from diverse habitats, including lakes, rivers, inland gardens, coastal vegetation, and nearshore habitats of the Great Lakes, were collected from 2012 to 2019. After morphological identification of chironomids, DNA was extracted and cytochrome oxidase I (COI) barcodes were PCR amplified and sequenced. Here we describe an analysis of biodiverse adult and larval chironomids in the Great Lakes region of North America based on new collections to improve chironomid identification by curating a chironomid DNA barcode database, thereby expanding the diversity and taxonomic specificity of DNA reference libraries for the Chironomidae family. In addition to reporting many novel chironomid DNA barcodes, we demonstrate here the use of this chironomid COI barcode database to improve the identification of DNA barcodes of prey in the liquefied diets of water mites. The species identifications of the COI barcodes of chironomids ingested by Lebertia davidcooki and L. quinquemaculosa are more diverse for L. davidcooki and include Parachironomus abortivus, Cryptochironomus ponderosus. Parachironomus tenuicaudatus, Glyptotendipes senilis, Dicrotendipes modestus, Chironomus riparius, Chironomus entis/plumosus, Chironomus maturus, Chironomus crassicaudatus, Endochironomus subtendens, Cricotopus sylvestris, Cricotopus festivellus, Orthocladius obumbratus, Tanypus punctipennis, Rheotanytarsus exiguus gr., and Paratanytarsus nr. bituberculatus. Full article

(This article belongs to the Special Issue Aquatic Organisms Research with DNA Barcodes)

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21 pages, 5939 KiB

Open AccessArticle

Uncovering Hidden Diversity: Three New Species of the Keratella Genus (Rotifera, Monogononta, Brachionidae) of High Altitude Water Systems from Central Mexico

by Alma E. García-Morales, Omar Domínguez-Domínguez and Manuel Elías-Gutiérrez

Diversity 2021, 13(12), 676; https://doi.org/10.3390/d13120676 - 17 Dec 2021

Cited by 5 | Viewed by 3748

Abstract

The correct identification of species is an essential step before any study on biodiversity, ecology or genetics. Keratella is a genus with a predominantly temperate distribution and with several species being endemics or restricted geographically. Its diversity may be underestimated considering the confusing [...] Read more.

The correct identification of species is an essential step before any study on biodiversity, ecology or genetics. Keratella is a genus with a predominantly temperate distribution and with several species being endemics or restricted geographically. Its diversity may be underestimated considering the confusing taxonomy of species complexes such as K. cochlearis. In this study, we examined genetic diversity and morphology among some Keratella populations from Mexico in order to determine if these populations represent different species. We analyzed a dataset of previously published and newly generated sequences of the mitochondrial COI gene and the nuclear ITS1 marker. We conducted phylogenetic analyses and applied three methods of species delimitation (ABGD, PTP and GMYC) to identify evolutionary significant units (ESUs) equivalent to species. Morphological analyses were conducted through scanning electron microscope (SEM) and morphometry under a compound microscope. In the present study, three new species Keratella cuitzeiensis sp. nov., Keratella huapanguensis sp. nov., and Keratella albertae sp. nov., are formally described. These species were collected in high-altitude water bodies located in the Central Plateau of Mexico. Combining DNA results through COI and ITS1 molecular markers and morphology it was possible to confirm the identity of the new species. Full article

(This article belongs to the Special Issue Aquatic Organisms Research with DNA Barcodes)

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25 pages, 6191 KiB

Open AccessArticle

Integrative Taxonomy of Two Peruvian Strains of Brachionus plicatilis Complex with Potential in Aquaculture

by Pedro Pablo Alonso Sánchez-Dávila, Giovanna Sotil, Araceli Adabache-Ortiz, Deivis Cueva and Marcelo Silva-Briano

Diversity 2021, 13(12), 671; https://doi.org/10.3390/d13120671 - 15 Dec 2021

Cited by 2 | Viewed by 3394

Abstract

Two Peruvian strains of the genus Brachionus were isolated from impacted coastal wetlands. With an integrative taxonomic view, we described their taxonomic status, morphological characters, productive parameters, and phylogenetic position. In the case of both strains, the relationship between biometrics and productive parameters [...] Read more.

Two Peruvian strains of the genus Brachionus were isolated from impacted coastal wetlands. With an integrative taxonomic view, we described their taxonomic status, morphological characters, productive parameters, and phylogenetic position. In the case of both strains, the relationship between biometrics and productive parameters obtained with Principal Components Analysis indicated that the lorica length was associated with longevity, progeny, egg production, and reproductive age, while the lorica width and aperture were associated with the maximum number of eggs carried. Maximum Likelihood and Bayesian Inference analysis carried out with mtDNA COI gene and rDNA ITS1 region showed that both strains were clustered in two clades with distinct phylogenetic positioning from what is currently known for Brachionus plicatilis s.l. One of the strains, Z010-VL, is proposed to be a subspecies of L4 (B. paranguensis), and the other strain, Z018-SD, is proposed as a sub species of SM2 (B. koreanus). In addition, 33 and 31 aquaculture production lineages are proposed, delimited by COI and concatenated COI+ITS1 sequences, respectively. Finally, this study provides new tools that enhance the traceability of the origin of each sub-species throughout the world. Full article

(This article belongs to the Special Issue Aquatic Organisms Research with DNA Barcodes)

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15 pages, 2276 KiB

Open AccessArticle

Validity of Pampus liuorum Liu & Li, 2013, Revealed by the DNA Barcoding of Pampus Fishes (Perciformes, Stromateidae)

by Jiehong Wei, Renxie Wu, Yongshuang Xiao, Haoran Zhang, Laith A. Jawad, Yajun Wang, Jing Liu and Mustafa A. Al-Mukhtar

Diversity 2021, 13(12), 618; https://doi.org/10.3390/d13120618 - 25 Nov 2021

Cited by 9 | Viewed by 2755

Abstract

The genus Pampus contains seven valid species, which are commercially important fishery species in the Indo-Pacific area. Due to their highly similar external morphologies, Pampus liuorum has been proposed as a synonym of Pampus cinereus. In this study, partial sequences of [...] Read more.

The genus Pampus contains seven valid species, which are commercially important fishery species in the Indo-Pacific area. Due to their highly similar external morphologies, Pampus liuorum has been proposed as a synonym of Pampus cinereus. In this study, partial sequences of COI (582 bp) and Cytb (1077 bp) were presented as potential DNA barcodes of six valid Pampus species and the controversial species P. liuorum. A species delimitation of the seven Pampus species was performed to verify their validities. Explicit COI barcoding gaps were found in all assessed species, except for P. liuorum and P. cinereus, which resulted from their smaller interspecific K2P distance (0.0034–0.0069). A Cytb barcoding gap (0.0200) of the two species was revealed, with a K2P distance ranging from 0.0237 to 0.0277. The longer Cytb fragment is thus a more suitable DNA barcode for the genus Pampus. In the genetic tree, using concatenated Cytb and COI sequences, the seven species reciprocally formed well-supported clades. Species delimitations with ABGD, GMYC, and bPTP models identified seven operational taxonomic units, which were congruent with the seven morphological species. Therefore, all of the seven analyzed species, including P. liuorum, should be kept as valid species. Full article

(This article belongs to the Special Issue Aquatic Organisms Research with DNA Barcodes)

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17 pages, 9781 KiB

Open AccessFeature PaperArticle

Identifying Early Stages of Freshwater Fish with DNA Barcodes in Several Sinkholes and Lagoons from the East of Yucatan Peninsula, Mexico

by Adrián Emmanuel Uh-Navarrete, Carmen Amelia Villegas-Sánchez, José Angel Cohuo-Colli, Ángel Omar Ortíz-Moreno and Martha Valdez-Moreno

Diversity 2021, 13(11), 513; https://doi.org/10.3390/d13110513 - 22 Oct 2021

Cited by 2 | Viewed by 2877

Abstract

Our work shows the efficacy of DNA barcoding for recognizing the early stages of freshwater fish. We collected 3195 larvae and juveniles. Of them, we identified 43 different morphotypes. After DNA barcodes of 350 specimens, we ascertained 7 orders, 12 families, 19 genera, [...] Read more.

Our work shows the efficacy of DNA barcoding for recognizing the early stages of freshwater fish. We collected 3195 larvae and juveniles. Of them, we identified 43 different morphotypes. After DNA barcodes of 350 specimens, we ascertained 7 orders, 12 families, 19 genera, 20 species, and 20 Barcode Index Numbers, corresponding to putative species. For the first time, we reported the presence of the brackish species, Gobiosoma yucatanum in Lake Bacalar. Specimens of the genus Atherinella sp. and Anchoa sp. are possibly new species. Using both methods, morphology, and DNA barcodes, we identified 95% of the total larvae collected (2953 to species, and 78 to genus), and all of them were native. From them, the order Gobiiformes represented 87%. The most abundant species were Lophogobius cyprinoides and Dormitator maculatus, followed by Gobiosoma yucatanum and Ctenobius fasciatus. The Muyil and Chuyanché lagoons have the highest number of species. We present for the first time a short description of Cyprinodon artifrons and Floridichthys polyommus. This information conforms an indispensable baseline for ecological monitoring, to evaluate impacts, and developing management and conservation plans of biodiversity, principally in areas under human pressure such as Sian Ka’an, and Lake Bacalar, where tourism is high and growing in disorder. Full article

(This article belongs to the Special Issue Aquatic Organisms Research with DNA Barcodes)

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15 pages, 3878 KiB

Open AccessArticle

DNA Barcoding of Penaeidae (Decapoda; Crustacea): Non-Distance-Based Species Delimitation of the Most Economically Important Shrimp Family

by Jorge L. Ramirez, Luisa Simbine, Carla G. Marques, Eliana Zelada-Mázmela, Lorenzo E. Reyes-Flores, Adolfo S. López, Jaqueline Gusmão, Carolina Tavares, Pedro M. Galetti, Jr. and Patricia D. Freitas

Diversity 2021, 13(10), 460; https://doi.org/10.3390/d13100460 - 23 Sep 2021

Cited by 6 | Viewed by 4515

Abstract

The Penaeidae family includes some of the most economic and ecological important marine shrimp, comprising hundreds of species. Despite this importance and diversity, the taxonomic classification for penaeid shrimp has constantly been revised, and issues related to the species identification are common. In [...] Read more.

The Penaeidae family includes some of the most economic and ecological important marine shrimp, comprising hundreds of species. Despite this importance and diversity, the taxonomic classification for penaeid shrimp has constantly been revised, and issues related to the species identification are common. In this study, we implemented DNA barcoding analyses in addition to single-gene species delimitation analyses in order to identify molecular operational taxonomy units (MOTUs) and to generate robust molecular information for penaeid shrimp based on the cytochrome oxidase subunit I (COI) mitochondrial gene. Our final data set includes COI sequences from 112 taxa distributed in 23 genera of penaeids. We employed the general mixed Yule coalescent (GMYC) model, the Poisson tree processes (PTP), and the Bayesian PTP model (bPTP) for MOTUs delimitation. Intraspecific and interspecific genetic distances were also calculated. Our findings evidenced a high level of hidden diversity, showing 143 MOTUs, with 27 nominal species not agreeing with the genetic delimitation obtained here. These data represent potential new species or highly structured populations, showing the importance of including a non-distance-based species delimitation approach in biodiversity studies. The results raised by this study shed light on the Penaeidae biodiversity, addressing important issues about taxonomy and mislabeling in databases and contributing to a better comprehension of the group, which can certainly help management policies for shrimp fishery activity in addition to conservation programs. Full article

(This article belongs to the Special Issue Aquatic Organisms Research with DNA Barcodes)

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11 pages, 1311 KiB

Open AccessArticle

Application of COI Primers 30F/885R in Rotifers to Regional Species Diversity in (Sub)Tropical China

by Ya-Nan Zhang, Shao-Lin Xu, Qi Huang, Ping Liu and Bo-Ping Han

Diversity 2021, 13(8), 390; https://doi.org/10.3390/d13080390 - 19 Aug 2021

Cited by 1 | Viewed by 2459

Abstract

Rotifers are the most diverse group in freshwater zooplankton and play an important role in food webs and ecosystems. DNA barcoding has become a useful approach to investigate species diversity at local and regional scales, but its application is still limited by efficient [...] Read more.

Rotifers are the most diverse group in freshwater zooplankton and play an important role in food webs and ecosystems. DNA barcoding has become a useful approach to investigate species diversity at local and regional scales, but its application is still limited by efficient primers for the group. To test a pair of primers 30F/885R recently designed for rotifers, we applied them to investigating regional species diversity in the freshwater of South China. We sequenced the cytochrome c oxidase subunit I (COI) gene of rotifers collected from the investigated 23 reservoirs in a large river basin and obtained 145 COI sequences from 33 species in 14 genera. The mean PCR success rate for all tested species was 50%. The 145 sequenced mtCOI in this study covered 33 of 64 identified morphological taxa, including most of the common species in the basin. The intraspecific genetic distance was calculated with a K2P model for 24 rotifer species occurring in the quantitative samples, in which 15 rotifers, such as Keratella cochlearis and Brachionus calyciflorus, had a genetic distance higher than 5%. The high intraspecific genetic differentiation indicates that cryptic species are probably common in (sub)tropical China. Full article

(This article belongs to the Special Issue Aquatic Organisms Research with DNA Barcodes)

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20 pages, 2187 KiB

Open AccessArticle

Molecular Characterization of the Common Snook, Centropomus undecimalis (Bloch, 1792) in the Usumacinta Basin

by Jazmín Terán-Martínez, Rocío Rodiles-Hernández, Marco A. A. Garduño-Sánchez and Claudia Patricia Ornelas-García

Diversity 2021, 13(8), 347; https://doi.org/10.3390/d13080347 - 29 Jul 2021

Cited by 3 | Viewed by 2872

Abstract

The common snook is one of the most abundant and economically important species in the Usumacinta basin in the Gulf of Mexico, which has led to overfishing, threatening their populations. The main goal of the present study was to assess the genetic diversity [...] Read more.

The common snook is one of the most abundant and economically important species in the Usumacinta basin in the Gulf of Mexico, which has led to overfishing, threatening their populations. The main goal of the present study was to assess the genetic diversity and structure of the common snook along the Usumacinta River in order to understand the population dynamics and conservation status of the species. We characterized two mitochondrial markers (mtCox1 and mtCytb) and 11 microsatellites in the Usumacinta basin, which was divided into three zones: rainforest, floodplain and river delta. The mitochondrial data showed very low diversity, showing some haplotypic diversity differences between the rainforest and delta zones. In contrast, we consistently recovered two genetic clusters in the Usumacinta River basin with the nuclear data in both the DAPC and STRUCTURE analyses. These results were consistent with the AMOVA analyses, which showed significant differences among the genetic clusters previously recovered by DAPC and STRUCTURE. In terms of diversity distribution, the floodplain zone corresponded to the most diverse zone according to the mitochondrial and nuclear data, suggesting that this is a transition zone in the basin. Our results support the relevance of the molecular characterization and monitoring of the fishery resources at the Usumacinta River to better understand their connectivity, which could help in their conservation and management. Full article

(This article belongs to the Special Issue Aquatic Organisms Research with DNA Barcodes)

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22 pages, 4080 KiB

Open AccessArticle

DNA Barcodes Applied to a Rapid Baseline Construction in Biodiversity Monitoring for the Conservation of Aquatic Ecosystems in the Sian Ka’an Reserve (Mexico) and Adjacent Areas

by Martha Valdez-Moreno, Manuel Mendoza-Carranza, Eduardo Rendón-Hernández, Erika Alarcón-Chavira and Manuel Elías-Gutiérrez

Diversity 2021, 13(7), 292; https://doi.org/10.3390/d13070292 - 28 Jun 2021

Cited by 5 | Viewed by 3697

Abstract

This study is focused on the aquatic environments of the Sian Ka’an reserve, a World Heritage Site. We applied recently developed protocols for the rapid assessment of most animal taxa inhabiting any freshwater system using light traps and DNA barcodes, represented by the [...] Read more.

This study is focused on the aquatic environments of the Sian Ka’an reserve, a World Heritage Site. We applied recently developed protocols for the rapid assessment of most animal taxa inhabiting any freshwater system using light traps and DNA barcodes, represented by the mitochondrial gene Cytochrome Oxidase I (COI). We DNA barcoded 1037 specimens comprising mites, crustaceans, insects, and fish larvae from 13 aquatic environments close or inside the reserve, with a success rate of 99.8%. In total, 167 barcode index numbers (BINs) were detected. From them, we identified 43 species. All others remain as a BIN. Besides, we applied the non-invasive method of environmental DNA (eDNA) to analyze the adult fish communities and identified the sequences obtained with the Barcode of Life Database (BOLD). All round, we found 25 fish species and other terrestrial vertebrates from this region. No alien species was found. After comparing the BINs from all systems, we found that each water body was unique with respect to the communities observed. The reference library presented here represents the first step for future programs to detect any change in these ecosystems, including invasive species, and to improve the knowledge of freshwater zooplankton, enhancing the task of compiling the species barcodes not yet stored in databases (such as BOLD or GenBank). Full article

(This article belongs to the Special Issue Aquatic Organisms Research with DNA Barcodes)

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12 pages, 1220 KiB

Open AccessFeature PaperArticle

Revisiting the Diversity of Barbonymus (Cypriniformes, Cyprinidae) in Sundaland Using DNA-Based Species Delimitation Methods

by Hadi Dahruddin, Arni Sholihah, Tedjo Sukmono, Sopian Sauri, Ujang Nurhaman, Daisy Wowor, Dirk Steinke and Nicolas Hubert

Diversity 2021, 13(7), 283; https://doi.org/10.3390/d13070283 - 23 Jun 2021

Cited by 7 | Viewed by 3050

Abstract

Biodiversity hotspots often suffer from a lack of taxonomic knowledge, particularly those in tropical regions. However, accurate taxonomic knowledge is needed to support sustainable management of biodiversity, especially when it is harvested for human sustenance. Sundaland, the biodiversity hotspot encompassing the islands of [...] Read more.

Biodiversity hotspots often suffer from a lack of taxonomic knowledge, particularly those in tropical regions. However, accurate taxonomic knowledge is needed to support sustainable management of biodiversity, especially when it is harvested for human sustenance. Sundaland, the biodiversity hotspot encompassing the islands of Java, Sumatra, Borneo, and Peninsular Malaysia, is one of those. With more than 900 species, its freshwater ichthyofauna includes a large number of medium- to large-size species, which are targeted by inland fisheries. Stock assessment requires accurate taxonomy; however, several species groups targeted by inland fisheries are still poorly known. One of those cases is the cyprinid genus Barbonymus. For this study, we assembled a consolidated DNA barcode reference library for Barbonymus spp. of Sundaland, consisting of mined sequences from BOLD, as well as newly generated sequences for hitherto under-sampled islands such as Borneo. A total of 173 sequences were analyzed using several DNA-based species delimitation methods. We unambiguously detected a total of 6 Molecular Operational Taxonomic Units (MOTUs) and were able to resolve several conflicting assignments to the species level. Furthermore, we clarified the identity of MOTUs occurring in Java. Full article

(This article belongs to the Special Issue Aquatic Organisms Research with DNA Barcodes)

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11 pages, 10825 KiB

Open AccessArticle

Mitochondrial Genetic Diversity among Farmed Stocks of Oreochromis spp. (Perciformes, Cichlidae) in Madagascar

by Nicolas Hubert, Elodie Pepey, Jean-Michel Mortillaro, Dirk Steinke, Diana Edithe Andria-Mananjara and Hugues de Verdal

Diversity 2021, 13(7), 281; https://doi.org/10.3390/d13070281 - 22 Jun 2021

Cited by 2 | Viewed by 2585

Abstract

The fast development of aquaculture over the past decades has made it the main source of fish protein and led to its integration into the global food system. Mostly originating from inland production systems, aquaculture has emerged as strategy to decrease malnutrition in [...] Read more.

The fast development of aquaculture over the past decades has made it the main source of fish protein and led to its integration into the global food system. Mostly originating from inland production systems, aquaculture has emerged as strategy to decrease malnutrition in low-income countries. The Nile tilapia (Oreochromis niloticus) was introduced to Madagascar in the 1950s, and is now produced nationally at various scales. Aquaculture mostly relies on fry harvested from wild populations and grow-out in ponds for decades. It has recently been diversified by the introduction of several fast-growing strains. Little is known how local genetic diversity compares to recently introduced strains, although high and comparable levels of genetic diversity have previously been observed for both wild populations and local stocks. Our study compares DNA barcode genetic diversity among eight farms and several strains belonging to three species sampled. DNA-based lineage delimitation methods were applied and resulted in the detection of six well differentiated and highly divergent lineages. A comparison of DNA barcode records to sequences on the Barcode of Life Data System (BOLD) helped to trace the origin of several of them. Both haplotype and nucleotide diversity indices highlight high levels of mitochondrial genetic diversity, with several local strains displaying higher diversity than recently introduced strains. This allows for multiple options to maintain high levels of genetic diversity in broodstock and provides more options for selective breeding programs. Full article

(This article belongs to the Special Issue Aquatic Organisms Research with DNA Barcodes)

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11 pages, 3052 KiB

Open AccessFeature PaperArticle

Phenetic and Genetic Variability of Continental and Island Populations of the Freshwater Copepod Mastigodiaptomus ha Cervantes, 2020 (Copepoda): A Case of Dispersal?

by Adrián Cervantes-Martínez, Martha Angélica Gutiérrez-Aguirre, Eduardo Suárez-Morales and Sarahi Jaime

Diversity 2021, 13(6), 279; https://doi.org/10.3390/d13060279 - 21 Jun 2021

Cited by 1 | Viewed by 2715

Abstract

The diversity of freshwater zooplankton is still little known in Mexico, particularly in reference to insular zooplankton communities. Diaptomid copepods (Crustacea: Copepoda: Calanoida) are a widespread group worldwide, and Mexico harbours high diaptomid diversity. Based on a recent sampling of freshwater zooplankton on [...] Read more.

The diversity of freshwater zooplankton is still little known in Mexico, particularly in reference to insular zooplankton communities. Diaptomid copepods (Crustacea: Copepoda: Calanoida) are a widespread group worldwide, and Mexico harbours high diaptomid diversity. Based on a recent sampling of freshwater zooplankton on a Caribbean Island of Mexico, we present the first record of a diaptomid copepod from an island freshwater ecosystem. It shows the well-known tendency of Neotropical diaptomids to have restricted distributional patterns and high levels of endemism. The species recorded, Mastigodiaptomus ha (Cervantes-Martínez, 2020) appears to have a restricted distribution in the Yucatan Peninsula (YP), and the island as well. In order to explore potential differences between the island and continental populations of this species, its phenetic and genetic diversity was analysed by performing morphological comparisons and also by exploring differences of the habitat conditions and genetic sequences (CO1 gene). Our analysis revealed a low (average = 0.33%) genetic divergence between both populations; likewise, both the morphology and habitat conditions closely resemble each other in these two populations. The low genetic divergence between the continental and island populations of M. ha suggests an early common origin of the species in the geological history of the YP. Full article

(This article belongs to the Special Issue Aquatic Organisms Research with DNA Barcodes)

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16 pages, 14684 KiB

Open AccessArticle

Record of Caromiobenella (Copepoda, Monstrilloida) in Brazil and Discovery of the Male of C. brasiliensis: Morphological and Molecular Evidence

by Judson da Cruz Lopes da Rosa, Cristina de Oliveira Dias, Eduardo Suárez-Morales, Laura Isabel Weber and Luciano Gomes Fischer

Diversity 2021, 13(6), 241; https://doi.org/10.3390/d13060241 - 31 May 2021

Cited by 7 | Viewed by 2681

Abstract

Monstrilloid copepods are protelean parasites with a complex life cycle that includes an endoparasitic juvenile phase and free-living early naupliar and adult phases. The monstrilloid copepod genus Caromiobenella Jeon, Lee and Soh, 2018 is known to contain nine species, each one with a [...] Read more.

Monstrilloid copepods are protelean parasites with a complex life cycle that includes an endoparasitic juvenile phase and free-living early naupliar and adult phases. The monstrilloid copepod genus Caromiobenella Jeon, Lee and Soh, 2018 is known to contain nine species, each one with a limited distribution; except for two species, members of this widespread genus are known exclusively from males. Hitherto, members of Caromiobenella have not been recorded from tropical waters of the South Western Atlantic (SWA). The nominal species Monstrilla brasiliensis Dias and Suárez-Morales, 2000 was originally described from female specimens collected in coastal waters of Espírito Santo and Rio de Janeiro (Brazil), but the male remained unknown. The failure to reliably link both sexes of monstrilloid species is one of the main problems in the current taxonomy of the group, thus leading to a separate treatment for each sex. New zooplankton collections in coastal waters and intertidal rocky pools of the SWA yielded several male and female monstrilloid copepods tentatively identified as Monstrilla brasiliensis. Our results of both morphologic and molecular (mtCOI) analyses allowed us to confirm that these males and females were conspecific. We also found evidence suggesting that Caromiobenella is not a monophyletic taxon. Our male specimens are morphologically assignable to Caromiobenella, therefore, females of the nominal species Monstrilla brasiliensis, are matched here with the aforementioned males and, thus, the species should be known as C. brasiliensis comb. nov. (Dias and Suárez-Morales, 2000). This finding represents the third documented discovery of a female of Caromiobenella, the first record of the genus in the Southwestern Atlantic, and the first documented record of monstrilloids from coastal tidepools. With the addition of C. brasiliensis, Caromiobenella now includes 10 valid species worldwide. This work represents the second successful use of molecular methods to link both sexes of a monstrilloid copepod. The male of C. brasiliensis is herein described, and a key to the known species of Caromiobenella and data on the habitat and local abundance of C. brasiliensis are also provided. Full article

(This article belongs to the Special Issue Aquatic Organisms Research with DNA Barcodes)

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9 pages, 2202 KiB

Open AccessArticle

Integrative Taxonomy Reveals That the Marine Brachyuran Crab Pyromaia tuberculata (Lockington, 1877) Reached Eastern Atlantic

by Jorge Lobo-Arteaga, Miriam Tuaty-Guerra and Maria José Gaudêncio

Diversity 2021, 13(6), 225; https://doi.org/10.3390/d13060225 - 23 May 2021

Viewed by 2291

Abstract

Pyromaia tuberculata is native to the north-eastern Pacific Ocean and currently established in distant regions in the Pacific Ocean and southwest Atlantic. Outside its native range, this species has become established in organically polluted enclosed waters, such as bays. The Tagus estuary, with [...] Read more.

Pyromaia tuberculata is native to the north-eastern Pacific Ocean and currently established in distant regions in the Pacific Ocean and southwest Atlantic. Outside its native range, this species has become established in organically polluted enclosed waters, such as bays. The Tagus estuary, with a broad shallow bay, is one of the largest estuaries in the west coast of Europe, located in western mainland Portugal, bordering the city of Lisbon. In this study, sediment samples were collected in the estuary between 2016 and 2017. Several adult specimens of P. tuberculata, including one ovigerous female, were morphologically and genetically identified, resulting in accurate identification of the species. The constant presence of adults over a 16-month sampling period suggests that the species has become established in the Tagus estuary. Moreover, their short life cycle, which allows for the production of at least two generations per year, with females reaching maturity within six months after settlement, favours population establishment. Despite being referred to as invasive, there are no records of adverse effects of P. tuberculata to the environment and socio-economy in regions outside its native range. However, due to its expanding ability, its inclusion in European monitoring programmes would indeed be desirable. Full article

(This article belongs to the Special Issue Aquatic Organisms Research with DNA Barcodes)

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15 pages, 1445 KiB

Open AccessFeature PaperArticle

Assessing Temporal Patterns and Species Composition of Glass Eel (Anguilla spp.) Cohorts in Sumatra and Java Using DNA Barcodes

by Arif Wibowo, Nicolas Hubert, Hadi Dahruddin, Dirk Steinke, Rezki Antoni Suhaimi, Samuel, Dwi Atminarso, Dian Pamularsih Anggraeni, Ike Trismawanti, Lee J. Baumgartner and Nathan Ning

Diversity 2021, 13(5), 193; https://doi.org/10.3390/d13050193 - 29 Apr 2021

Cited by 6 | Viewed by 3827

Abstract

Anguillid eels are widely acknowledged for their ecological and socio-economic value in many countries. Yet, knowledge regarding their biodiversity, distribution and abundance remains superficial—particularly in tropical countries such as Indonesia, where demand for anguillid eels is steadily increasing along with the threat imposed [...] Read more.

Anguillid eels are widely acknowledged for their ecological and socio-economic value in many countries. Yet, knowledge regarding their biodiversity, distribution and abundance remains superficial—particularly in tropical countries such as Indonesia, where demand for anguillid eels is steadily increasing along with the threat imposed by river infrastructure developments. We investigated the diversity of anguillid eels on the western Indonesian islands of Sumatra and Java using automated molecular classification and genetic species delimitation methods to explore temporal patterns of glass eel cohorts entering inland waters. A total of 278 glass eels were collected from monthly samplings along the west coast of Sumatra and the south coast of Java between March 2017 and February 2018. An automated, DNA-based glass eel identification was performed using a DNA barcode reference library consisting of 64 newly generated DNA barcodes and 117 DNA barcodes retrieved from BOLD for all nine Anguilla species known to occur in Indonesia. Species delimitation methods converged in delineating eight Molecular Operational Taxonomic Units (MOTUs), with A. nebolusa and A. bengalensis being undistinguishable by DNA barcodes. A total of four MOTUs were detected within the glass eel samples, corresponding to Anguilla bicolor, A. interioris, A. marmorata, and A. nebulosa/A. bengalensis. Monthly captures indicated that glass eel recruitment peaks in June, during the onset of the dry season, and that A. bicolor is the most prevalent species. Comparing indices of mitochondrial genetic diversity between yellow/silver eels, originating from several sites across the species range distribution, and glass eels, collected in West Sumatra and Java, indicated a marked difference. Glass eels displayed a much lower diversity than yellow/silver eels. Implications for the management of glass eel fisheries and species conservation are discussed. Full article

(This article belongs to the Special Issue Aquatic Organisms Research with DNA Barcodes)

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16 pages, 3318 KiB

Open AccessArticle

Species Delimitation of Southeast Pacific Angel Sharks (Squatina spp.) Reveals Hidden Diversity through DNA Barcoding

by Rosa M. Cañedo-Apolaya, Clara Ortiz-Alvarez, Eliana Alfaro-Cordova, Joanna Alfaro-Shigueto, Ximena Velez-Zuazo, Jeffrey C. Mangel, Raquel Siccha-Ramirez, Carmen Yamashiro and Jorge L. Ramirez

Diversity 2021, 13(5), 177; https://doi.org/10.3390/d13050177 - 21 Apr 2021

Cited by 6 | Viewed by 5074

Abstract

Angel sharks are distributed worldwide in tropical to subtropical waters. Across the Eastern Pacific Ocean (EPO), two valid species are reported: The Pacific angelshark Squatina californica and the Chilean angelshark Squatina armata; however, there is still uncertainty about their geographic distribution, mainly [...] Read more.

Angel sharks are distributed worldwide in tropical to subtropical waters. Across the Eastern Pacific Ocean (EPO), two valid species are reported: The Pacific angelshark Squatina californica and the Chilean angelshark Squatina armata; however, there is still uncertainty about their geographic distribution, mainly along the northern Peru coast where the species have been reported to be sympatric. The aim of this study is to describe the genetic differences between the genus Squatina from the EPO, including samples from northern Peru, and using DNA barcoding and three species delimitation models: Poisson tree processes (PTP) model, Bayesian implementation of the PTP (bPTP) model and the general mixed Yule coalescent (GMYC) model. The three approaches summarized 19 nominal Squatina species in 23 consensus Molecular Taxonomic Units (MOTU). Only 16 of them were in accordance with taxonomic identifications. From the EPO, four Squatina MOTUs were identified, one from North America (S. californica USA/Mexico) and three sampled in northern Peru, S. californica Peru, S. armata and Squatina sp. (a potential new species). This study contributes to the management and conservation policies of angel sharks in Peru, suggesting the presence of an undescribed species inhabiting the northern Peruvian coast. The use of molecular approaches, such as DNA barcoding, has the potential to quickly flag undescribed species in poorly studied regions, including the Southeast Pacific, within groups of ecologically and economically important groups like angel sharks. Full article

(This article belongs to the Special Issue Aquatic Organisms Research with DNA Barcodes)

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13 pages, 1944 KiB

Open AccessArticle

The Introduction of the Asian Red Algae Melanothamnus japonicus (Harvey) Díaz-Tapia & Maggs in Peru as a Means to Adopt Management Strategies to Reduce Invasive Non-Indigenous Species

by Julissa J. Sánchez-Velásquez, Lorenzo E. Reyes-Flores, Carmen Yzásiga-Barrera and Eliana Zelada-Mázmela

Diversity 2021, 13(5), 176; https://doi.org/10.3390/d13050176 - 21 Apr 2021

Cited by 4 | Viewed by 3961

Abstract

Early detection of non-indigenous species is crucial to reduce, mitigate, and manage their impacts on the ecosystems into which they were introduced. However, assessment frameworks for identifying introduced species on the Pacific Coast of South America are scarce and even non-existent for certain [...] Read more.

Early detection of non-indigenous species is crucial to reduce, mitigate, and manage their impacts on the ecosystems into which they were introduced. However, assessment frameworks for identifying introduced species on the Pacific Coast of South America are scarce and even non-existent for certain countries. In order to identify species’ boundaries and to determine the presence of non-native species, through morphological examinations and the analysis of the plastid ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit (rbcL-5P) gene, we investigated the phylogenetic relationships among species of the class Florideophyceae from the coast of Ancash, Peru. The rbcL-5P dataset revealed 10 Florideophyceae species distributed in the following four orders: Gigartinales, Ceramiales, Halymeniales, and Corallinales, among which the Asian species, Melanothamnus japonicus (Harvey) Díaz-Tapia & Maggs was identified. M. japonicus showed a pairwise divergence of 0% with sequences of M. japonicus from South Korea, the USA, and Italy, the latter two being countries where M. japonicus has been reported as introduced species. Our data indicate a recent introduction event of M. japonicus in Peru, and consequently, the extension of its distribution into South America. These findings could help to adopt management strategies for reducing the spread and impact of M. japonicus on the Pacific Coast of South America. Full article

(This article belongs to the Special Issue Aquatic Organisms Research with DNA Barcodes)

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13 pages, 541 KiB

Open AccessReview

Aquatic Organisms Research with DNA Barcodes

by Manuel Elías-Gutiérrez, Nicolas Hubert, Rupert A. Collins and Camilo Andrade-Sossa

Diversity 2021, 13(7), 306; https://doi.org/10.3390/d13070306 - 6 Jul 2021

Cited by 11 | Viewed by 4874

Abstract

Since their inception, DNA barcodes have become a powerful tool for understanding the biodiversity and biology of aquatic species, with multiple applications in diverse fields such as food security, fisheries, environmental DNA, conservation, and exotic species detection. Nevertheless, most aquatic ecosystems, from marine [...] Read more.

Since their inception, DNA barcodes have become a powerful tool for understanding the biodiversity and biology of aquatic species, with multiple applications in diverse fields such as food security, fisheries, environmental DNA, conservation, and exotic species detection. Nevertheless, most aquatic ecosystems, from marine to freshwater, are understudied, with many species disappearing due to environmental stress, mostly caused by human activities. Here we highlight the progress that has been made in studying aquatic organisms with DNA barcodes, and encourage its further development in assisting sustainable use of aquatic resources and conservation. Full article

(This article belongs to the Special Issue Aquatic Organisms Research with DNA Barcodes)

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