Genetic calibration of species diversity among North America's freshwater fishes

DNA barcode reference library of the fish larvae and eggs of the South China Sea: taxonomic effectiveness and geographic structure

Fish early-stages constitute useful indicators of the states of marine ecosystems, as well as important fishery resources. Given the spectacular phenotypic changes during ontogeny, and the paucity of diagnostic morphological characters at the species level, the identification of fish early-stages is a challenging task. DNA barcoding, the use of the mitochondrial gene of the cytochrome c oxidase subunit I (COI) as an internal species tag, opened new perspectives for the identifications of both larval fish and fish eggs. However, the accuracy of the identifications assisted by DNA barcoding are dependent of the completeness of the DNA barcode reference libraries used to assigned unknown sequences to known species. Here, we built a DNA barcode reference library for 113 species of larval fish and 85 species of fish eggs involving the production of 741 newly generated DNA barcodes from South China Sea (63 localities). Together with 514 DNA barcodes mined from Genbank for 116 species from the South China Sea regions, a reference library including 1255 DNA barcodes for 308 species (248 locations) was assembled. The present study emphasizes the importance of integrating DNA barcoding to large scale inventories of early stages, as DNA-based species delimitation analyses delimited 305 molecular operational taxonomic units (MOTUs) and multiple cases of discordance with morphological identifications were detected. Cryptic diversity is detected with 14 species displaying two MOTUs and a total of 23 species were lumped into 11 MOTUs due to low interspecific divergence and/or mixed lineages.

DNA barcoding and cryptic diversity in fishes from the Ili River Valley in China, Xinjiang

The Ili River Valley, located in the northwest of China, serves as a vital repository for fish genetic resources. Its extensive water network and diverse climate have given rise to a unique fish composition and endemic species. In this study, we collected the cytochrome c oxidase subunit I (COI) sequences from 660 fish specimens in the Ili River Valley. The effectiveness of DNA barcoding in identifying fish species in the area was assessed by examining genetic distances, constructing phylogenetic trees, and performing ABGD (Automatic Barcode Gap Discovery) analyses, among other methods. In total, 20 species were identified, including one unidentified species (Silurus sp.). Except for Silurus asotus and Hypophthalmichthys molitrix (only one sample), the maximum intraspecific genetic distance among the remaining species was smaller than the minimum interspecific distance, which proves that the species exhibit obvious barcode gaps. In the Neighbor-Joining trees, 20 species formed separate monophyletic branches. According to ABGD analysis, 660 sequences were categorized into 19 Operational Taxonomic Units, with Silurus sp. and S. asotus grouped into a single OTU. The Silurus in this study exhibits shared haplotypes and significant genetic divergence, suggesting the potential presence of cryptic species. Furthermore, the nucleotide diversity across all species fell below the threshold level, indicating that the local fish population is gradually declining. In conclusion, this study has demonstrated the effectiveness of DNA barcoding in identifying fish species in the Ili River Valley, providing valuable data to support the conservation of local fish resources.

Comparison and phylogenetic analysis of the mitochondrial genomes of Synodontis eupterus and Synodontis polli

We aimed to distinguish Synodontis eupterus and Synodontis polli. We performed sequencing and bioinformatic analysis of their mitochondrial genomes and constructed a phylogenetic tree of Mochokidae fish using maximum likelihood and Bayesian methods based on protein-coding gene (PCG) sequences of 14 Mochokidae species. The total length of the S. eupterus mitochondrial genome was 16,579 bp, including 13 (PCGs), 22 tRNA genes, two rRNA genes, and one D-loop, with an AT-biased nucleotide composition (56.0%). The total length of the S. polli mitochondrial genome was 16,544 bp, including 13 PCGs, 22 tRNA genes, two rRNA genes, and one D-loop, with an AT-biased nucleotide composition (55.0%). In both species, except for COI, PCGs use ATG as the starting codon, the vast majority use TAG or TAA as the ending codon, and a few use incomplete codons (T - or TA -) as the ending codon. Phylogenetic analysis showed that S. eupterus and Synodontis clarias converged into one branch, S. polli and Synodontis petricola converged into one branch, Mochokiella paynei, Mochokus brevis, and nine species of the genus Synodontis converged into one branch, and M. paynei clustered with the genus Synodontis. This study lays a foundation for rebuilding a clearer Mochokidae fish classification system.

DNA barcoding for the assessment of marine and coastal fish diversity from the Coast of Mozambique

The ichthyological provinces of Mozambique are understudied hotspots of global fish diversity. In this study, we applied DNA barcoding to identify the composition of the fish fauna from the coast of Mozambique. A total of 143 species belonging to 104 genera, 59 families, and 30 orders were identified. The overall K2P distance of the COI sequences within species ranged from 0.00% to 1.51%, while interspecific distances ranged from 3.64% to 24.49%. Moreover, the study revealed 15 threatened species according to the IUCN Red List of Threatened Species, with elasmobranchs being the most represented group. Additionally, the study also uncovered four new species that were not previously recorded in this geographic area, including Boleophthalmus dussumieri, Maculabatis gerrardi, Hippocampus kelloggi, and Lethrinus miniatus. This study represents the first instance of utilizing molecular references to explore the fish fauna along the Mozambican coast. Our results indicate that DNA barcoding is a dependable technique for the identification and delineation of fish species in the waters of Mozambique. The DNA barcoding library established in this research will be an invaluable asset for advancing the understanding of fish diversity and guiding future conservation initiatives.

Delimiting Species with Single-Locus DNA Sequences

DNA sequences are increasingly used for large-scale biodiversity inventories. Because these genetic data avoid the time-consuming initial sorting of specimens based on their phenotypic attributes, they have been recently incorporated into taxonomic workflows for overlooked and diverse taxa. Major statistical developments have accompanied this new practice, and several models have been proposed to delimit species with single-locus DNA sequences. However, proposed approaches to date make different assumptions regarding taxon lineage history, leading to strong discordance whenever comparisons are made among methods. Distance-based methods, such as Automatic Barcode Gap Discovery (ABGD) and Assemble Species by Automatic Partitioning (ASAP), rely on the detection of a barcode gap (i.e., the lack of overlap in the distributions of intraspecific and interspecific genetic distances) and the associated threshold in genetic distances. Network-based methods, as exemplified by the REfined Single Linkage (RESL) algorithm for the generation of Barcode Index Numbers (BINs), use connectivity statistics to hierarchically cluster-related haplotypes into molecular operational taxonomic units (MOTUs) which serve as species proxies. Tree-based methods, including Poisson Tree Processes (PTP) and the General Mixed Yule Coalescent (GMYC), fit statistical models to phylogenetic trees by maximum likelihood or Bayesian frameworks.Multiple webservers and stand-alone versions of these methods are now available, complicating decision-making regarding the most appropriate approach to use for a given taxon of interest. For instance, tree-based methods require an initial phylogenetic reconstruction, and multiple options are now available for this purpose such as RAxML and BEAST. Across all examined species delimitation methods, judicious parameter setting is paramount, as different model parameterizations can lead to differing conclusions. The objective of this chapter is to guide users step-by-step through all the procedures involved for each of these methods, while aggregating all necessary information required to conduct these analyses. The "Materials" section details how to prepare and format input files, including options to align sequences and conduct tree reconstruction with Maximum Likelihood and Bayesian inference. The Methods section presents the procedure and options available to conduct species delimitation analyses, including distance-, network-, and tree-based models. Finally, limits and future developments are discussed in the Notes section. Most importantly, species delimitation methods discussed herein are categorized based on five indicators: reliability, availability, scalability, understandability, and usability, all of which are fundamental properties needed for any approach to gain unanimous adoption within the DNA barcoding community moving forward.

DNA barcoding the ichthyofauna of the Beibu Gulf: Implications for fisheries management in a seafood market hub

The Beibu Gulf in China is situated in the tropics, in the western Pacific Ocean. It is an emblematic region combining proximity to a marine biodiversity hotspot and a major seafood hub. Intensification of marine fishing and ocean warming led to a drastic decline in fish populations in the Beibu Gulf during the last decades. This situation urges the development of molecular resources of the Beibu Gulf fish fauna in order to enable automated molecular identifications at the species level for next-generation monitoring. With this objective, we present the results of a large-scale campaign to DNA barcode fishes of the Beibu Gulf. We successfully generated 789 new DNA barcodes corresponding to 263 species which, together with 291 sequences mined from Genbank and BOLD, resulted in a reference library of 1080 sequences from 285 species. Based on the use of four DNA-based species delimitation methods (BIN, ASAP, mPTP, mGMYC), a total of 285 Molecular Operational Taxonomical Units (MOTUs). A single case of cryptic diversity was detected in Scomberomorus guttatus and a single species pair was not captured by delimitation methods. Intraspecific K2P genetic distances averaged 0.36% among sequences within species, whereas K2P genetic distances among species within genera averaged 6.96%. The most speciose families in open water trawling differ from those at fish market, and discrepancies with historical data are discussed in the light of recently documented stock collapses.

Creating, curating and evaluating a mitogenomic reference database to improve regional species identification using environmental DNA

Species detection using eDNA is revolutionizing global capacity to monitor biodiversity. However, the lack of regional, vouchered, genomic sequence information-especially sequence information that includes intraspecific variation-creates a bottleneck for management agencies wanting to harness the complete power of eDNA to monitor taxa and implement eDNA analyses. eDNA studies depend upon regional databases of mitogenomic sequence information to evaluate the effectiveness of such data to detect and identify taxa. We created the Oregon Biodiversity Genome Project to create a database of complete, nearly error-free mitogenomic sequences for all of Oregon's fishes. We have successfully assembled the complete mitogenomes of 313 specimens of freshwater, anadromous and estuarine fishes representing 24 families, 55 genera and 129 species and lineages. Comparative analyses of these sequences illustrate that many regions of the mitogenome are taxonomically informative, that the short (~150 bp) mitochondrial 'barcode' regions typically used for eDNA assays do not consistently diagnose for species and that complete single or multiple genes of the mitogenome are preferable for identifying Oregon's fishes. This project provides a blueprint for other researchers to follow as they build regional databases, illustrates the taxonomic value and limits of complete mitogenomic sequences and offers clues as to how current eDNA assays and environmental genomics methods of the future can best leverage this information.

Marine and freshwater fishes of Alabama: a revised checklist and discussion of taxonomic issues

Checklists are fundamental and important tools for organizing information about biodiversity that provide a basis for conservation and additional scientific research. While Alabama is recognized as an aquatic biodiversity hotspot with the highest native freshwater fish diversity in the contiguous United States, we currently lack an up-to-date list of the states fishes. In particular, much has changed over the past ~20 years regarding our knowledge of fishes from Alabama and the Mobile River Basin, rendering past comprehensive treatments by Mettee et al. (1996) and Boschung and Mayden (2004) out of date. Here, we provide a revised checklist of marine and freshwater fishes known from the coastal and inland waters of Alabama that includes 463 species (335 primarily freshwater fishes, and 128 marine or diadromous fishes) in 35 orders, 78 families, and 176 genera. Extant, extirpated, and extinct species are included, as are putative candidate species. The checklist is based on prior work, searches of the literature and online sources, as well as parsing a large compilation of >140,000 fish records for Alabama and the Mobile River Basin from 37 data providers in the global Fishnet2 database (www.fishnet2.net) and >4000 marine survey records from the SEAMAP database (https://www.gsmfc.org/seamap.php). After editing and quality control checks, the final combined database contained 144,215 collection records, ~95% of which were georeferenced. We discuss the species descriptions, nomenclatural changes, and updates to marine species that account for changes to the state list, and we close with a discussion of ~13 candidate species forms that remain undescribed, which represent outstanding taxonomic issues in need of further research attention.

A revision of the gudgeon genus Hypseleotris (Gobiiformes: Gobioidei: Eleotridae) of northwest Australia, describing three new species and synonymizing the genus Kimberleyeleotris

Species within the northwest Australian clade of Hypseleotris (six species) and the genus Kimberleyeleotris (two species) are reviewed following the recording of new populations in the region and a molecular study of the group that identified three undescribed candidate species. Based on the analysis of extensive morphological and nuclear and mitochondrial molecular datasets, Kimberleyeleotris is here formally synonymised with Hypseleotris. Furthermore, three species from the Kimberley region, Western Australia, are described to science: Hypseleotris maranda sp. nov., Hypseleotris wunduwala sp. nov., and Hypseleotris garawudjirri sp. nov. The presence of, or number of scales across the head and body, the pattern of sensory papillae on the head, fin ray counts, dorsal and anal fin colouration (particularly in breeding males), and body depth, can be used to distinguish the members of the northwest Australia lineage. Furthermore, the newly described species were genetically separated from all northwest Australian congeners by K2P distances ranging from 7.8-11.3% based on the CO1 gene, and 7.7-16.3 % based on the entire mitochondrial genome. Two of the new species, H. maranda sp. nov. and H. wunduwala sp. nov., have extremely narrow ranges being found in single sub-catchments of the Roe and King Edward Rivers respectively. On the other hand, H. garawudjirri sp. nov. is moderately widespread, being found across the Charnley, Calder, and Sale rivers. While the conservation risk to H. maranda sp. nov. and H. wunduwala sp. nov. is inherently high due to their small range, there are currently no obvious local threatening processes to either of these species given their remote locations that are little impacted by human activities.

Erosion of heterogeneous rock drives diversification of Appalachian fishes

The high levels of biodiversity supported by mountains suggest a possible link between geologic processes and biological evolution. Freshwater biodiversity is high not only in tectonically active settings but also in tectonically quiescent montane regions such as the Appalachian Mountains. We show that erosion through different rock types drove allopatric divergence between lineages of the Greenfin Darter (Nothonotus chlorobranchius), a fish species endemic to rivers draining metamorphic rocks in the Tennessee River basin in the United States. In the past, metamorphic rock preferred by N. chlorobranchius was more widespread, but as erosion exposed other rock types, lineages of this species were progressively isolated in tributaries farther upstream, where metamorphic rock remained. Our results suggest a geologic mechanism for initiating allopatric diversification in mountains long after tectonic activity ceases.

Phylogeography, hybridization, and species discovery in the Etheostoma nigrum complex (Percidae: Etheostoma: Boleosoma)

The history of riverine fish diversification is largely a product of geographic isolation. Physical barriers that reduce or eliminate gene flow between populations facilitate divergence via genetic drift and natural selection, eventually leading to speciation. For freshwater organisms, diversification is often the product of drainage basin rearrangements. In young clades where the history of isolation is the most recent, evolutionary relationships can resemble a tangled web. One especially recalcitrant group of freshwater fishes is the Johnny Darter (Etheostoma nigrum) species complex, where traditional taxonomy and molecular phylogenetics indicate a history of gene flow and conflicting inferences of species diversity. Here we assemble a genomic dataset using double digest restriction site associated DNA (ddRAD) sequencing and use phylogenomic and population genetic approaches to investigate the evolutionary history of the complex of species that includes E. nigrum, E. olmstedi, E. perlongum, and E. susanae. We reveal and validate several evolutionary lineages that we delimit as species, highlighting the need for additional work to formally describe the diversity of the Etheostoma nigrum complex. Our analyses also identify gene flow among recently diverged lineages, including one instance involving E. susanae, a localized and endangered species. Phylogeographic structure within the Etheostoma nigrum species complex coincides with major geologic events, such as parallel divergence in river basins during Pliocene inundation of the Atlantic coastal plain and multiple northward post-glacial colonization routes tracking river basin rearrangements. Our study serves as a nuanced example of how low dispersal rates coupled with geographic isolation among disconnected river systems in eastern North America has produced one of the world's freshwater biodiversity hotspots.

Hidden species diversity in an iconic living fossil vertebrate

Ancient, species-poor lineages persistently occur across the Tree of life. These lineages are likely to contain unrecognized species diversity masked by the low rates of morphological evolution that characterize living fossils. Halecomorphi is a lineage of ray-finned fishes that diverged from its closest relatives before 200 Ma and is represented by only one living species in eastern North America, the bowfin, Amia calva Linnaeus. Here, we use double digest restriction-site-associated DNA sequencing and morphology to illuminate recent speciation in bowfins. Our results support the delimitation of a second living species of Amia, with the timing of diversification dating to the Plio-Pleistocene. This delimitation expands the species diversity of an ancient lineage that is integral to studies of vertebrate genomics and development, yet is facing growing conservation threats driven by the caviar fishery.

DNA barcoding and species delimitation of the genus Oxynoemacheilus (Teleostei: Nemacheilidae) in Anatolia

The DNA barcoding approach was used for the determination of evolutionary relationships and species delimitation of the genus Oxynoemacheilus (Teleostei: Nemacheilidae). The COI barcode region (615 bp amplicon) was used to barcode 444 individuals from 64 morphologically identified species in the genus Oxynoemacheilus and 189 haplotypes were identified. The average of the interspecific p distance (9.59%) was about 21-fold higher than the average intraspecific distance (0.44%). A general genetic threshold of 1.46% sequence divergence was defined for species delimitation. The multiple species delimitation methods (BCM, GMYC, bPTP and TCS) revealed a total of 62 molecular operational taxonomic units for 64 morphospecies with a new loach species from the BuyukMelen River. Neighbour-joining, maximum likelihood and Bayesian inference analyses indicated that all haplotypes were clustered into 62 clades, which corresponded to Oxynoemacheilus species, with strong bootstrap support (≥95%). Furthermore, all samples grouped in concurrence with the taxonomic status of the species except for species groups (O. germencicus-O. cinicus-O. mesudae and O. leontinae-O. namiri) that were showed intraspecific overlap in genetic diversity for COI-based barcodes. In conclusion, our analyses indicate that COI-based barcodes provide reliable species discrimination. Therefore, we currently recommend COI barcodes as the suitable barcode for genus Oxynoemacheilus.

DNA barcoding of a lesser-known catfish, Clupisoma bastari (Actinopterygii: Ailiidae) from Deccan Peninsula, India

DNA barcoding substantiates species identification, and simultaneously indicates the misnomer taxa. Based on the morphological descriptions, we identified a lesser-known catfish, Clupisoma bastari, from Godavari River basin, and contributed novel DNA barcode data to the GenBank. The Kimura 2 parameter genetic divergence between species, and the neighbour-joining phylogeny clearly depicted a distinct clade of C. bastari in the studied dataset. Clupisoma bastari maintained sufficient K2P genetic divergence (8.3% to 11.2%) with other congeners, and branched as a sister-species of C. garua. The present study highlights possible existence of a few misnomer taxa in the GenBank. We encourage further extensive sampling of different congeners of Clupisoma from a wide range of habitats to explore the species diversity and phylogenetic relationship. 

Large scale DNA barcoding of the subfamily Culterinae (Cypriniformes: Xenocyprididae) in East Asia unveils geographic scale effect, taxonomic warnings and cryptic diversity

Geographical scale might be expected to impact significantly the efficiency of DNA barcoding as spatially comprehensive sampling provides opportunities to uncover intricate relationships among closely related species and to detect cryptic diversity for widespread taxa. Here, we present a DNA barcoding study on a Xencyprididae subfamily (Culterinae) involving the production of 998 newly generated DNA barcodes from East Asian drainages (80 localities). Together with 513 barcodes mined from BOLD and GenBank, a reference library consisting of 1511 DNA barcodes (116 localities) for 42 species was assembled, accounting for 66% of known Culterinae species. Intraspecific genetic distances are positively correlated to geographical scale, while a negative correlation is detected between interspecific genetic distances and geographical scale. The present study demonstrates that geographical scale influences the efficiency of DNA barcoding by narrowing the width of the barcoding gap. DNA‐based species delimitation analyses delimited 44 molecular operational taxonomic units (MOTUs). Rampant cryptic diversity is detected within eight species with multiple MOTUs, whereas 25 species present mismatch between morphological and molecular delimitations. A total of 18 species are lumped into nine MOTUs due to low interspecific divergence and/or mixed lineages. Several MOTU divergences are hypothesized to relate to known biogeographical barriers and geological events during the Pliocene and Pleistocene. This study provides new insights into the taxonomy and phylogeography of the subfamily Culterinae.

A practical approach to revise the Oxynoemacheilus bergianus species group (Teleostei: Nemacheilidae)

The Oxynoemacheilus bergianus species group is revised based on tree topology (ML, NJ, MP), distance (K2P and ASAP) and Poisson tree process analyses of DNA barcode data tested against morphometric and morphological characters including colour patterns. The O. bergianus species group is distinguished from other Oxynoemacheilus groups based on morphological characters: its constituent species have a slender caudal peduncle, a suborbital flap in the male, a mottled or blotched colour pattern, and lack bold, black spots on the caudal-fin base. It is also supported as a monophyletic unit in our molecular analysis.                 The O. bergianus group includes 10 molecular clades following congruently well-supported NJ, MP and ML based entities. Species described as O. bergianus, O. banarescui, O. erdali, O. fatsaensis, O. samanticus, and O. simavicus from Turkey, O. lenkoranensis from Azerbaijan, and O. longipinnis and O. parvinae from Iran belong to this species group. The group includes also four unnamed molecular clades. We were unable to detect external differences between any of the molecular clades in colour pattern or any morphometric or morphological characters examined. In the 10 molecular clades in the O. bergianus species group, the intraclade K2P distance ranges from 0.0–1.8% while the distances between molecular clades ranges from 0.6–5.9%. To resolve the species diversity of this group, we also analysed the intraspecific and interspecific variability in the K2P distance of DNA barcode data from 53 other Oxynoemacheilus species. Here, the intraspecific variability ranges from 0.0–2.4% while the interspecific K2P distance ranges from 1.2–20.8%. In the O. bergianus species group, only four groups are detected by the mPTP species delimitation approach distinguished by a K2P distance of 2.9% or more. We treat these four groups as valid species, corresponding to O. banarescui, O. bergianus, O. fatsaensis, and O. simavicus. Oxynoemacheilus samanticus from the Kızılırmak and Seyhan drainages, O. lenkoranensis from the Caspian basin, O. erdali from the Euphrates, and O. longipinnis and O. parvinae from the Tigris drainage are treated as synonyms of O. bergianus. Fishes from an unnamed molecular clade from the upper Tigris, and from a second unnamed clade from the upper Euphrates, are both identified as O. bergianus. Oxynoemacheilus bergianus might be a junior synonym of O. bergi from the Kura. The distribution range of O. simavicus, described from the Simav drainage in the Marmara basin, is expanded to the east and two molecularly differentiated population groups occur in the Sakarya drainage, the Büyük Melen River and potentially in other adjacent coastal streams. Oxynoemacheilus fatsaensis, described from the coastal stream Elekçi in northern Anatolia, is also widespread in the Yeşilırmak drainage. Morphological characters proposed to distinguish O. fatsaensis from the other species of the O. bergianus group could not be confirmed by our data on fishes from the Yeşilırmak. This study also discusses the theoretical background, our reasons for conducting this revision in the way we did, and what the alternatives would be.  

DNA barcoding identification of Greek freshwater fishes

Biodiversity is a key factor for the functioning and efficiency of an ecosystem. Greece, though covering a relatively small surface area, hosts a great deal of species diversity. This is especially true for freshwater fishes. In recent years, the traditional methods of species identification have been supplemented by the use of molecular markers. The present study therefore aims to extensively produce DNA barcodes for Greek freshwater fish species and investigate thoroughly if the presently accepted species classification is in agreement with molecular data. A 624-bases long fragment of the COI gene was sequenced, from 406 freshwater fish specimens belonging to 24 genera and originating from 18 lake and river sites. These sequences were used along with 596 sequences from the same genera, recovered from BOLD, for the construction of phylogenetic trees and the estimation of genetic distances between individuals. In total, 1002 sequences belonging to 72 species were analyzed. The method was found to be effective for 55 of 72 studied species. 17 closely related species with low interspecific genetic distances were observed, for which further study is proposed. It should also be noted that, in four cases, cryptic diversity was observed, where groups originally identified as one species exhibited genetic distance great enough to be separated into discrete species. Region specific haplotypes were also detected within populations of 14 species, giving the possibility to identify even the geographic origin of a species. Our findings are discussed in the light of the rich history of the Balkan peninsula and provide a significant steppingstone for the further study of Greek and European freshwater fish biodiversity.

DNA barcoding uncovers cryptic diversity in minute herbivorous mites (Acari, Eriophyoidea)

Eriophyoid mites (Acari: Eriophyoidea) are among the smallest of terrestrial arthropods and the most species-rich group of herbivorous mites with a high host specificity. However, knowledge of their species diversity has been impeded by the difficulty of their morphological differentiation. This study assembles a DNA barcode reference library that includes 1,850 mitochondrial COI sequences which provides coverage for 45% of the 930 species of eriophyoid mites known from China, and for 37 North American species. Sequence analysis showed a clear barcode gap in nearly all species, reflecting the fact that intraspecific divergences averaged 0.97% versus a mean of 18.51% for interspecific divergences (minimum nearest-neighbor distances) in taxa belonging to three families. Based on these results, we used DNA barcoding to explore the species diversity of eriophyoid mites as well as their host interactions. The 1,850 sequences were assigned to 531 Barcode Index Numbers (BINs). Analyses examining the correspondence between these BINs and species identifications based on morphology revealed that members of 45 species were assigned to two or more BINs, resulting in 1.16 times more BINs than morphospecies. Richness projections suggest that over 2,345 BINs occurred at the sampled locations. Host plant analysis showed that 89% of these mites (BINs) attack only one or two congeneric host species, but the others have several hosts. Furthermore, host-mite network analyses demonstrate that eriophyoid mites are high host-specific, and modularity is high in plant-mite networks. By creating a highly effective identification system for eriophyoid mites in BOLD, DNA barcoding will advance our understanding of the diversity of eriophyoid mites and their host interactions.

Pragmatic Applications and Universality of DNA Barcoding for Substantial Organisms at Species Level: A Review to Explore a Way Forward

DNA barcodes are regarded as hereditary succession codes that serve as a recognition marker to address several queries relating to the identification, classification, community ecology, and evolution of certain functional traits in organisms. The mitochondrial cytochrome c oxidase 1 (CO1) gene as a DNA barcode is highly efficient for discriminating vertebrate and invertebrate animal species. Similarly, different specific markers are used for other organisms, including ribulose bisphosphate carboxylase (rbcL), maturase kinase (matK), transfer RNA-H and photosystem II D1-ApbsArabidopsis thaliana (trnH-psbA), and internal transcribed spacer (ITS) for plant species; 16S ribosomal RNA (16S rRNA), elongation factor Tu gene (Tuf gene), and chaperonin for bacterial strains; and nuclear ITS for fungal strains. Nevertheless, the taxon coverage of reference sequences is far from complete for genus or species-level identification. Applying the next-generation sequencing approach to the parallel acquisition of DNA barcode sequences could greatly expand the potential for library preparation or accurate identification in biodiversity research. Overall, this review articulates on the DNA barcoding technology as applied to different organisms, its universality, applicability, and innovative approach to handling DNA-based species identification.

A genomic perspective on an old question: Salmo trouts or Salmo trutta (Teleostei: Salmonidae)?

There are particular challenges in defining the taxonomic status of recently radiated groups due to the low level of phylogenetic signal. Members of the Salmo trutta species-complex, which mostly evolved during and following the Pleistocene, show high morphological and ecological diversity that, along with their very wide geographic distribution, have led to morphological description of 47 extant nominal species. However, many of these species have not been supported by previous phylogenetic studies, which could be partly due to lack of significant genetic differences among them, the limited resolution offered by molecular methods previously used, as well as the often local scale of these studies. The development of next-generation sequencing (NGS) and related analytical tools have enhanced our ability to address such challenging questions. In this study, Genotyping-by-Sequencing (GBS) of 15,169 filtered SNPs and mitochondrial DNA (mtDNA) D-loop sequences were combined to assess the phylogenetic relationships among 166 brown trouts representing 21 described species and three undescribed groups collected from 84 localities throughout their natural distribution in Europe, west Asia, and North Africa. The data were analysed using different clustering algorithms (admixture analysis and discriminant analysis of principal components-DAPC), a Bayes Factor Delimitation (BFD) test, species tree reconstruction, gene flow tests (three- and four-population tests), and Rogue taxa identification tests. Genomic contributions of the Atlantic lineage brown trout were found in all major sea basins excluding the North African and Aral Sea basins, suggesting introgressive hybridization of native brown trouts driven by stocking using strains of the Atlantic lineage. After removing the phylogenetic noise caused by the Atlantic brown trout, admixture clusters and DAPC clustering based on GBS data, respectively, resolved 11 and 13 clusters among the previously described brown trout species, which were also supported by BFD test results. Our results suggest that natural hybridization between different brown trout lineages has probably played an important role in the origin of several of the putative species, including S. marmoratus, S. carpio, S. farioides, S. pellegrini, S. caspius (in the Kura River drainage) and Salmo sp. in the Danube River basin. Overall, our results support a multi-species taxonomy for brown trouts. They also resolve some species in the Adriatic-Mediterranean and Black Sea drainages as members of very closely related genomic clusters that may need taxonomic revision. However, any final conclusions pertaining to the taxonomy of the brown trout complex should be based on an integrative approach combining genomic, morphological, and ecological data. To avoid challenges in taxonomy and conservation of species complexes like brown trouts, it is suggested to describe species based on genomic clusters of populations instead of describing species based only on morphologically differentiated single type populations.

Exploring the vertebrate fauna of the Bird's Head Peninsula (Indonesia, West Papua) through DNA barcodes

Biodiversity knowledge is widely heterogeneous across the Earth's biomes. Some areas, due to their remoteness and difficult access, present large taxonomic knowledge gaps. Mostly located in the tropics, these areas have frequently experienced a fast development of anthropogenic activities during the last decades and are therefore of high conservation concerns. The biodiversity hotspots of Southeast Asia exemplify the stakes faced by tropical countries. While the hotspots of Sundaland (Java, Sumatra, Borneo) and Wallacea (Sulawesi, Moluccas) have long attracted the attention of biologists and conservationists alike, extensive parts of the Sahul area, in particular the island of New Guinea, have been much less explored biologically. Here, we describe the results of a DNA-based inventory of aquatic and terrestrial vertebrate communities, which was the objective of a multidisciplinary expedition to the Bird's Head Peninsula (West Papua, Indonesia) conducted between 17 October and 20 November 2014. This expedition resulted in the assembly of 1005 vertebrate DNA barcodes. Based on the use of multiple species-delimitation methods (GMYC, PTP, RESL, ABGD), 264 molecular operational taxonomic units (MOTUs) were delineated, among which 75 were unidentified and an additional 48 were considered cryptic. This study suggests that the diversity of vertebrates of the Bird's Head is severely underestimated and considerations on the evolutionary origin and taxonomic knowledge of these biotas are discussed.

The use of an integrative approach to improve accuracy of species identification and detection of new species in studies of stream fish diversity

In this study, we made an inventory of the stream and headwater ichthyofauna of the left bank of the Itaipu Dam Reservoir, located in the lower part of the Upper Paraná River basin, using an integrative approach of molecular and morphological data. The area is located in the western portion of the Paraná state in Brazil, in an area of about 8,000 km² highly impacted by deforestation and intensive agriculture. For taxonomic identification of species, we used an identification key combined with the DNA barcoding approach. We found 48 species belonging to six orders, 13 families, and 37 genera. The Siluriformes and Characiformes were the most representative orders (75%) and the Characidae was the most representative family (20.8%). Nine species prevailed in this region, making up to 86% of all specimens collected. The integrative approach proved to be useful by allowing the unambiguous identification of all species, including those cases in which morphological characters were not conclusive for species identification, cases of cryptic species, and species with high morphological plasticity. In addition, the integrative approach highlighted six to 13 new putative species depending on the approach considered. Our study provides a relevant contribution to the knowledge of fish diversity in a poorly studied area of the Paraná River basin. We showed that the use of an integrative approach in inventory studies improves species identification and the discovery of new, cryptic, and overlooked species, being a powerful and necessary tool to quantify biodiversity.

New records of the occurrence of Megaleporinus macrocephalus () (Characiformes, Anostomidae) from the basins of the Itapecuru and Mearim rivers in Maranhão, Northeastern Brazil

The "piaussu", Megaleporinus macrocephalus is an anostomatid fish species native to the basin of the Paraguay River, in the Pantanal biome of western Brazil. However, this species has now been recorded in a number of other drainages, including those of the upper Paraná, Uruguay, Jacuí, Doce, Mucuri, and Paraíba do Sulrivers. This study presents two new records of the occurrence of M. macrocephalus, in the basins of the Itapecuru and Mearim rivers in the state of Maranhão, in the Brazilian Northeast. The piaussu is a large-bodied fish of commercial interest that is widely raised on fish farms, and its occurrence in the Itapecuru and Mearim rivers is likely the result of individuals escaping from fish tanks when they overflow during the rainy season. Morphological analyses and sequences of the Cytochrome Oxidase Subunit I (COI) gene confirmed the taxonomic identification of the specimens as M. macrocephalus. The COI sequences were 99.66% similar to those of M. macrocephalus deposited in the BOLDSystems database. These records extend the known distribution of M. macrocephalus to the basins of the Itapecuru and Mearim rivers in the Brazilian Northeast, highlighting a new case of introduction of exotic fish species into Brazilian river basins.

Comparison of Larval Fish Detections Using Morphology-Based Taxonomy versus High-Throughput Sequencing for Invasive Species Early Detection

When first introduced, invasive species typically evade detection; DNA barcoding coupled with high-throughput sequencing (HTS) may be more sensitive and accurate than morphology-based taxonomy, and thereby improve invasive (or rare) species detection. We quantified the relative error of species detection between morphology-based and HTS-based taxonomic identification of ichthyoplankton collections from the Port of Duluth, Minnesota, an aquatic non-native species introduction 'hot-spot' in the Laurentian Great Lakes. We found HTS-based taxonomy identified 28 species and morphology-based taxonomy 30 species, of which 27 were common to both. Among samples, 76% of family-level taxonomic assignments agreed; however, only 42% of species assignments agreed. Most errors were attributed to morphology-based taxonomy, whereas HTS-based taxonomy error was low. For this study system, for most non-native fishes, the detection probability by randomized survey for larvae was similar to that by a survey that is optimized for non-native species early detection of juveniles and adults. We conclude that classifying taxonomic errors by comparing HTS results against morphology-based taxonomy is an important step toward incorporating HTS-based taxonomy into biodiversity surveys.

On the Challenge to Correctly Identify Rasboras (Teleostei: Cyprinidae: Danioninae) Inhabiting the Mesangat Wetlands, East Kalimantan, Indonesia

Within the subfamily Danioninae, rasborine cyprinids are known as a ‘catch-all’ group, diagnosed by only a few characteristics. Most species closely resemble each other in morphology. Species identification is therefore often challenging. In this study, we attempted to determine the number of rasborine species occurring in samples from the Mesangat wetlands in East Kalimantan, Indonesia, by using different approaches. Morphological identification resulted in the distinction of five species (Trigonopoma sp., Rasbora cf. hubbsi Brittan, 1954, R. rutteni Weber and de Beaufort, 1916, R. trilineata Steindachner, 1870, and R. vaillantii, Popta 1905). However, genetic species delimitation methods (Poisson tree processes (PTP) and multi-rate PTP (mPTP)) based on DNA barcodes and principal component analysis (PCA) based on homologous geometric morphometric landmarks, revealed a single cluster for Trigonopoma sp. and R. trilineata, respectively, whereas the remaining traditionally identified species were distinguished neither by DNA barcodes nor by the morphometry approach. A k-mean clustering based on the homologous landmarks divided the sample into 13 clusters and was thus found to be inappropriate for landmark data from species extremely resembling each other in morphology. Due to inconsistent results between the applied methods we refer to the traditional identifications and distinguish five rasborine species for the Mesangat wetlands.

Morphology-based taxonomic re-assessment of the Arctic lamprey, Lethenteron camtschaticum (Tilesius, 1811) and taxonomic position of other members of the genus

The lamprey genus Lethenteron Creaser & Hubbs, 1922 is widespread across Eurasia and North America, but the number and distribution of its constituent species is not firmly established. After a morphological examination of extant type material of the currently recognized species and their synonyms, Lethenteronmitsukurii (Hatta, 1901) is resurrected with Le.matsubarai Vladykov & Kott, 1978 as its junior synonym. Amongst nonparasitic species Le.reissneri (Dybowski, 1869) and Le.mitsukurii are confirmed as present in Japan and the former is also present on Sakhalin. An in-depth study of large samples of nonparasitic lamprey adults from Japan and Sakhalin Island is needed to determine whether the lower trunk myomere (< 66) individuals from these areas represent one or more undescribed species, or Le.mitsukurii, or Le.reissneri, or a mixture of these three alternatives. The material from the Anadyr Estuary identified by Berg (1931, 1948) as Lampetrajaponicakessleri has been re-identified as Le.camtschaticum and there is no evidence that Le.kessleri occurs there. Lethenteronreissneri is reported from the Angara River system, Yenisei River drainage, Russia. Lethenteronalaskense Vladykov & Kott, 1978 is provisionally considered to be a junior synonym of Le.kessleri (Anikin, 1905). Petromyzonernstii Dybowski, 1872, Ammocoetesaureus Bean, 1881, Petromyzondentex Anikin, 1905, Lampetramitsukuriimajor Hatta, 1911, and Lampetrajaponicaseptentrionalis Berg, 1931 are junior synonyms of Petromyzonmarinuscamtschaticus Tilesius, 1811. A key is provided to adults of the six species recognized as belonging in the genus Lethenteron.

The Effects of Ecological Traits on the Rate of Molecular Evolution in Ray-Finned Fishes: A Multivariable Approach

Myriad environmental and biological traits have been investigated for their roles in influencing the rate of molecular evolution across various taxonomic groups. However, most studies have focused on a single trait, while controlling for additional factors in an informal way, generally by excluding taxa. This study utilized a dataset of cytochrome c oxidase subunit I (COI) barcode sequences from over 7000 ray-finned fish species to test the effects of 27 traits on molecular evolutionary rates. Environmental traits such as temperature were considered, as were traits associated with effective population size including body size and age at maturity. It was hypothesized that these traits would demonstrate significant correlations with substitution rate in a multivariable analysis due to their associations with mutation and fixation rates, respectively. A bioinformatics pipeline was developed to assemble and analyze sequence data retrieved from the Barcode of Life Data System (BOLD) and trait data obtained from FishBase. For use in phylogenetic regression analyses, a maximum likelihood tree was constructed from the COI sequence data using a multi-gene backbone constraint tree covering 71% of the species. A variable selection method that included both single- and multivariable analyses was used to identify traits that contribute to rate heterogeneity estimated from different codon positions. Our analyses revealed that molecular rates associated most significantly with latitude, body size, and habitat type. Overall, this study presents a novel and systematic approach for integrative data assembly and variable selection methodology in a phylogenetic framework.

Description of a new species of cryptic snubnose darter (Percidae: Etheostomatinae) endemic to north-central Mississippi

Many subclades within the large North American freshwater fish genus Etheostoma (Percidae) show brilliant male nuptial coloration during the spring spawning season. Traditionally, perceived differences in color were often used to diagnose closely related species. More recently, perceived differences in male nuptial color have prompted further investigation of potential biodiversity using genetic tools. However, cryptic diversity among Etheostoma darters renders male nuptial color as unreliable for detecting and describing diversity, which is foundational for research and conservation efforts of this group of stream fishes. Etheostoma raneyi (Yazoo Darter) is an imperiled, range-limited fish endemic to north-central Mississippi. Existing genetic evidence indicates cryptic diversity between disjunctly distributed E. raneyi from the Little Tallahatchie and Yocona river watersheds despite no obvious differences in male color between the two drainages. Analysis of morphological truss and geometric measurements and meristic and male color characters yielded quantitative differences in E. raneyi from the two drainages consistent with genetic evidence. Morphological divergence is best explained by differences in stream gradients between the two drainages. Etheostoma faulkneri, the Yoknapatawpha Darter, is described as a species under the unified species concept. The discovery of cryptic diversity within E. raneyi would likely not have occurred without genetic tools. Cryptic diversity among Etheostoma darters and other stream fishes is common, but an overreliance on traditional methods of species delimitation (e.g., identification of a readily observable physical character to diagnose a species) impedes a full accounting of the diversity in freshwater fishes in the southeastern United States.

DNA barcoding for identification of fish species from freshwater in Enugu and Anambra States of Nigeria

Within Enugu and Anambra States, Nigeria, identification of fishes has been based on morphological traits and do not account for existing biodiversity. For DNA barcoding, assessment of biodiversity, conservation and fishery management, 44 fish sampled from Enugu and Anambra States were isolated, amplified and sequenced with mitochondrial cytochrome oxidase subunit I (COI). Twenty groups clustering at 100% bootstrap value including monophyletic ones were identified. The phylogenetic diversity (PD) ranged from 0.0397 (Synodontis obesus) to 0.2147 (Parachanna obscura). The highest percentage of genetic distance based on Kimura 2-parameter was 37.00 ± 0.0400. Intergeneric distances ranged from 15.8000 to 37.0000%. Congeneric distances were 6.9000 ± 0.0140–28.1000 ± 0.0380, with Synodontis as the existing synonymous genus. Confamilial distances in percentage were 16.0000 ± 0.0140 and 25.7000 ± 0.0300. Forty-two haplotypes and haplotype diversity of 0.9990 ± 0.0003 were detected. Nucleotide diversity was 0.7372, while Fu and Li’s D* test statistic was 2.1743 (P < 0.02). Tajima’s D was 0.2424 (P > 0.10) and nucleotide frequencies were C (17.70%), T (29.40%), A (24.82%), G (18.04%) and A + T (54.22%). Transitional mutations were more than transversions. Twenty species (99–100%) were identified with the e-value, maximum coverage and bit-score of 1e−43, 99–100 and 185–1194, respectively. Seventeen genera and 12 families were found and Clariidae (n = 14) was the most dominant among other families. The fish species resolution, diversity assessment and phylogenetic relationships were successfully obtained with the COI marker. Clariidae had the highest number of genera and families. Phylogenetic diversity analysis identified Parachanna obscura as the most evolutionarily divergent one. This study will contribute to fishery management, and conservation of freshwater fishes in Enugu and Anambra States, Nigeria.

Revalidation of the Argentinian pouched lamprey Geotria macrostoma (Burmeister, 1868) with molecular and morphological evidence

BACKGROUND

The Argentinian pouched lamprey, classified as Petromyzon macrostomus Burmeister, 1868 was first described in 1867 in De La Plata River, in Buenos Aires, Argentina, and subsequently recorded in several rivers from Patagonia. Since its original description, the validity of P. macrostomus was questioned by several ichthyologists and 36 years after its original discovery it was considered a junior synonym of Geotria australis Gray, 1851. For a long time, the taxonomic status of G. australis has been uncertain, largely due to the misinterpretations of the morphological alterations that occur during sexual maturation, including the arrangement of teeth, size and position of fins and cloaca, and the development of an exceptionally large gular pouch in males. In this study, the taxonomic status of Geotria from across the "species" range was evaluated using both molecular analysis and examination of morphological characteristics.

METHODOLOGY/PRINCIPAL FINDINGS

Phylogenetic and species delimitation analyses based on mitochondrial DNA sequences of Cytochrome b (Cyt b) and Cytochrome C Oxidase Subunit 1 (COI) genes, along with morphological analysis of diagnostic characters reported in the original descriptions of the species were used to assess genetic and morphological variation within Geotria and to determine the specific status of the Argentinian lamprey. These analyses revealed that Geotria from Argentina constitutes a well differentiated lineage from Chilean and Australasian populations. The position of the cloaca and the distance between the second dorsal and caudal fins in sub-adult individuals, and at previous life stages, can be used to distinguish between the two species. In addition, the genetic distance between G. macrostoma and G. australis for the COI and Cyt b mitochondrial genes is higher than both intra- and inter-specific distances reported for other Petromyzontiformes.

CONCLUSIONS/SIGNIFICANCE

Our results indicate that the Argentinian pouched lamprey, found along a broad latitudinal gradient on the south-west Atlantic coast of South America, should be named as Geotria macrostoma (Burmeister, 1868) and not as G. australis Gray 1851, returning to its earliest valid designation in Argentina. Geotria macrostoma can now be considered as the single lamprey species inhabiting Argentinian Patagonia, with distinct local adaptations and evolutionary potential. It is essential that this distinctiveness is recognized in order to guide future conservation and management actions against imminent threats posed by human actions in the major basins of Patagonia.

Past, present and future contributions of evolutionary biology to wildlife forensics, management and conservation

Successfully implementing fundamental concepts into concrete applications is challenging in any given field. It requires communication, collaboration and shared will between researchers and practitioners. We argue that evolutionary biology, through research work linked to conservation, management and forensics, had a significant impact on wildlife agencies and department practices, where new frameworks and applications have been implemented over the last decades. The Quebec government's Wildlife Department (MFFP: Ministère des Forêts, de la Faune et des Parcs) has been proactive in reducing the “research–implementation” gap, thanks to prolific collaborations with many academic researchers. Among these associations, our department's outstanding partnership with Dr. Louis Bernatchez yielded significant contributions to harvest management, stocking programmes, definition of conservation units, recovery of threatened species, management of invasive species and forensic applications. We discuss key evolutionary biology concepts and resulting concrete examples of their successful implementation that derives directly or indirectly from this successful partnership. While old and new threats to wildlife are bringing new challenges, we expect recent developments in eDNA and genomics to provide innovative solutions as long as the research–implementation bridge remains open.

Cryptic diversity among Yazoo Darters (Percidae: Etheostoma raneyi) in disjunct watersheds of northern Mississippi

The Yazoo Darter, Etheostoma raneyi (Percidae), is an imperiled freshwater fish species endemic to tributaries of the Yocona and Little Tallahatchie rivers of the upper Yazoo River basin, in northern Mississippi, USA. The two populations are allopatric, isolated by unsuitable lowland habitat between the two river drainages. Relevant literature suggests that populations in the Yocona River represent an undescribed species, but a lack of data prevents a thorough evaluation of possible diversity throughout the range of the species. Our goals were to estimate phylogenetic relationships of the Yazoo Darter across its distribution and identify cryptic diversity for conservation management purposes. Maximum likelihood (ML) phylogenetic analyses of the mitochondrial cytochrome b (cytb) gene returned two reciprocally monophyletic clades representing the two river drainages with high support. Bayesian analysis of cytb was consistent with the ML analysis but with low support for the Yocona River clade. Analyses of the nuclear S7 gene yielded unresolved relationships among individuals in the Little Tallahatchie River drainage with mostly low support, but returned a monophyletic clade for individuals from the Yocona River drainage with high support. No haplotypes were shared between the drainages for either gene. Additional cryptic diversity within the two drainages was not indicated. Estimated divergence between Yazoo Darters in the two drainages occurred during the Pleistocene (<1 million years ago) and was likely linked to repeated spatial shifts in suitable habitat and changes in watershed configurations during glacial cycles. Individuals from the Yocona River drainage had lower genetic diversity consistent with the literature. Our results indicate that Yazoo Darters in the Yocona River drainage are genetically distinct and that there is support for recognizing Yazoo Darter populations in the Yocona River drainage as a new species under the unified species concept.

Comparative genomics approach to evolutionary process connectivity

The influence of species life history traits and historical demography on contemporary connectivity is still poorly understood. However, these factors partly determine the evolutionary responses of species to anthropogenic landscape alterations. Genetic connectivity and its evolutionary outcomes depend on a variety of spatially dependent evolutionary processes, such as population structure, local adaptation, genetic admixture, and speciation. Over the last years, population genomic studies have been interrogating these processes with increasing resolution, revealing a large diversity of species responses to spatially structured landscapes. In parallel, multispecies meta-analyses usually based on low-genome coverage data have provided fundamental insights into the ecological determinants of genetic connectivity, such as the influence of key life history traits on population structure. However, comparative studies still lack a thorough integration of macro- and micro-evolutionary scales to fully realize their potential. Here, I present how a comparative genomics framework may provide a deeper understanding of evolutionary process connectivity. This framework relies on coupling the inference of long-term demographic and selective history with an assessment of the contemporary consequences of genetic connectivity. Standardizing this approach across several species occupying the same landscape should help understand how spatial environmental heterogeneity has shaped the diversity of historical and contemporary connectivity patterns in different taxa with contrasted life history traits. I will argue that a reasonable amount of genome sequence data can be sufficient to resolve and connect complex macro- and micro-evolutionary histories. Ultimately, implementing this framework in varied taxonomic groups is expected to improve scientific guidelines for conservation and management policies.

Assessing species diversity of Coral Triangle artisanal fisheries: A DNA barcode reference library for the shore fishes retailed at Ambon harbor (Indonesia)

The Coral Triangle (CT), a region spanning across Indonesia and Philippines, is home to about 4,350 marine fish species and is among the world's most emblematic regions in terms of conservation. Threatened by overfishing and oceans warming, the CT fisheries have faced drastic declines over the last decades. Usually monitored through a biomass-based approach, fisheries trends have rarely been characterized at the species level due to the high number of taxa involved and the difficulty to accurately and routinely identify individuals to the species level. Biomass, however, is a poor proxy of species richness, and automated methods of species identification are required to move beyond biomass-based approaches. Recent meta-analyses have demonstrated that species richness peaks at intermediary levels of biomass. Consequently, preserving biomass is not equal to preserving biodiversity. We present the results of a survey to estimate the shore fish diversity retailed at the harbor of Ambon Island, an island located at the center of the CT that display exceptionally high biomass despite high levels of threat, while building a DNA barcode reference library of CT shore fishes targeted by artisanal fisheries. We sampled 1,187 specimens and successfully barcoded 696 of the 760 selected specimens that represent 202 species. Our results show that DNA barcodes were effective in capturing species boundaries for 96% of the species examined, which opens new perspectives for the routine monitoring of the CT fisheries.

Space invaders: Searching for invasive Smallmouth Bass (Micropterus dolomieu) in a renowned Atlantic Salmon (Salmo salar) river

Humans have the ability to permanently alter aquatic ecosystems and the introduction of species is often the most serious alteration. Non-native Smallmouth Bass (Micropterus dolomieu) were identified in Miramichi Lake c. 2008, which is a headwater tributary to the Southwest Miramichi River, a renowned Atlantic Salmon (Salmo salar) river whose salmon population is dwindling. A containment programme managed by the Department of Fisheries and Oceans, Canada (DFO) was implemented in 2009 to confine Smallmouth Bass (SMB) to the lake. We utilized environmental DNA (eDNA) as a detection tool to establish the potential escape of SMB into the Southwest Miramichi River. We sampled at 26 unique sites within Miramichi Lake, the outlet of Miramichi Lake (Lake Brook), which flows into the main stem Southwest Miramichi River, and the main stem Southwest Miramichi River between August and October 2017. We observed n = 6 positive detections located in the lake, Lake Brook, and the main stem Southwest Miramichi downstream of the lake. No detections were observed upstream of the confluence of Lake Brook and the main stem Southwest Miramichi. The spatial pattern of positive eDNA detections downstream of the lake suggests the presence of individual fish versus lake-sourced DNA in the outlet stream discharging to the main river. Smallmouth Bass were later confirmed by visual observation during a snorkeling campaign, and angling. Our results, both eDNA and visual confirmation, definitively show Smallmouth Bass now occupy the main stem of the Southwest Miramichi.

Disentangling the taxonomy of the subfamily Rasborinae (Cypriniformes, Danionidae) in Sundaland using DNA barcodes

Sundaland constitutes one of the largest and most threatened biodiversity hotspots; however, our understanding of its biodiversity is afflicted by knowledge gaps in taxonomy and distribution patterns. The subfamily Rasborinae is the most diversified group of freshwater fishes in Sundaland. Uncertainties in their taxonomy and systematics have constrained its use as a model in evolutionary studies. Here, we established a DNA barcode reference library of the Rasborinae in Sundaland to examine species boundaries and range distributions through DNA-based species delimitation methods. A checklist of the Rasborinae of Sundaland was compiled based on online catalogs and used to estimate the taxonomic coverage of the present study. We generated a total of 991 DNA barcodes from 189 sampling sites in Sundaland. Together with 106 previously published sequences, we subsequently assembled a reference library of 1097 sequences that covers 65 taxa, including 61 of the 79 known Rasborinae species of Sundaland. Our library indicates that Rasborinae species are defined by distinct molecular lineages that are captured by species delimitation methods. A large overlap between intraspecific and interspecific genetic distance is observed that can be explained by the large amounts of cryptic diversity as evidenced by the 166 Operational Taxonomic Units detected. Implications for the evolutionary dynamics of species diversification are discussed.

HACSim: an R package to estimate intraspecific sample sizes for genetic diversity assessment using haplotype accumulation curves

Assessing levels of standing genetic variation within species requires a robust sampling for the purpose of accurate specimen identification using molecular techniques such as DNA barcoding; however, statistical estimators for what constitutes a robust sample are currently lacking. Moreover, such estimates are needed because most species are currently represented by only one or a few sequences in existing databases, which can safely be assumed to be undersampled. Unfortunately, sample sizes of 5-10 specimens per species typically seen in DNA barcoding studies are often insufficient to adequately capture within-species genetic diversity. Here, we introduce a novel iterative extrapolation simulation algorithm of haplotype accumulation curves, called HACSim (Haplotype Accumulation Curve Simulator) that can be employed to calculate likely sample sizes needed to observe the full range of DNA barcode haplotype variation that exists for a species. Using uniform haplotype and non-uniform haplotype frequency distributions, the notion of sampling sufficiency (the sample size at which sampling accuracy is maximized and above which no new sampling information is likely to be gained) can be gleaned. HACSim can be employed in two primary ways to estimate specimen sample sizes: (1) to simulate haplotype sampling in hypothetical species, and (2) to simulate haplotype sampling in real species mined from public reference sequence databases like the Barcode of Life Data Systems (BOLD) or GenBank for any genomic marker of interest. While our algorithm is globally convergent, runtime is heavily dependent on initial sample sizes and skewness of the corresponding haplotype frequency distribution.

Population genetics and sympatric divergence of the freshwater gudgeon, Gobiobotia filifer, in the Yangtze River inferred from mitochondrial DNA

The ecosystem and Pleistocene glaciations play important roles in population demography. The freshwater gudgeon, Gobiobotia filifer, is an endemic benthic fish in the Yangtze River and is a good model for ecological and evolutionary studies. This study aimed to decode the population structure of G. filifer in the Yangtze River and reveal whether divergence occurred before or after population radiation. A total of 292 specimens from eight locations in the upper and middle reaches of the Yangtze River were collected from 2014 to 2016 and analyzed via mitochondrial DNA Cyt b gene sequencing. A moderately high level of genetic diversity was found without structures among the population. However, phylogenetic and network topology showed two distinct haplotype groups, and each group contained a similar proportion of individuals from all sampled sites. This suggested the existence of two genetically divergent source populations in G. filifer. We deduced that a secondary contact of distinct glacial refugia was the main factor creating sympatric populations of G. filifer, and climate improvement promoted population expansion and colonization.

A molecular assessment of species diversity in Tympanopleura and Ageneiosus catfishes (Auchenipteridae: Siluriformes)

In order to test the congruence of genetic data to the morphologically defined Neotropical catfish genera Tympanopleura and Ageneiosus and explore species diversity, we generated 17 DNA barcodes from five of six species of Tympanopleura and 12 of 13 species of Ageneiosus. To discriminate limits between species, an automatic barcode gap discovery (ABGD), a generalised mixed yule-coalescent model (GYMC) and fixed distance thresholds Kimura two-parameter (K2P; 3%) were used to discriminate putative species limits from the DNA barcodes. The ABGD, GMYC and K2P methods agreed by each generating 13 clusters: six in Tympanopleura (five nominal plus one undescribed species) and seven in Ageneiosus. These clusters corresponded broadly to the described species, except in the case of the Ageneiosus ucayalensis group (A. akamai, A. dentatus, A. intrusus, A. ucayalensis, A. uranophthalmus and A. vittatus). Haplotype sharing and low divergences may have prevented molecular methods from distinguishing these species. We hypothesise that this is the result of a recent radiation of a sympatric species group distributed throughout the Amazon Basin. One putative new species of Tympanopleura was also supported by the molecular data. These results taken together highlight the utility of molecular methods such as DNA barcoding in understanding patterns of diversification across large geographic areas and in recognising overlooked diversity.