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Figure S5. Heat maps (left) and PCA (right) of the lowest inter-and intra-basins divergences of each haplotype of the Maroni basin. Columns and rows of heatmaps are ordered from West to East (left to right and top to bottom). Two examples among the 31 species investigated (Supplemental Material 3).
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The Maroni is one of the most speciose basins of the Guianas and hosts a megadiverse freshwater fish community. Although taxonomical references based on morphological identification exist for both the Surinamese and Guianese parts of the basin, there are still taxonomical uncertainties concerning the status of several species. We used COI sequences...
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... C. timbuiense, C. zebra and Characidium sp. 1) plus species of Characidium from other ecoregions and other genera of Crenuchidae (i.e., Ammocryptocharax elegans Weitzman & Weitzman, Leptocharacidium sp., Melanocharacidium blennioides Eigenmann, Melanocharacidium dispilomma Buckup, Microcharacidium eleotrioides G ery, and Poecilocharax weitzmani G ery; see Supplemental Appendix S1) were obtained from GenBank (https://www.ncbi.nlm.nih.gov) or Barcode of Life Data Systems (BOLD) (https://www.boldsystems.org/index.php/), where they have been deposited by several authors (i.e., Agudelo-Zamora, Tavera et al., 2020;Bagley et al., 2019;Carvalho et al., 2011;Malanski et al., 2019;Oliveira-Silva et al., 2023;Pansonato-Alves et al., 2014;Papa et al., 2021;Sales et al., 2018;Scacchetti et al., 2014Scacchetti et al., , 2015Serrano et al., 2018). These sequences were also used for phylogenetic reconstruction. ...
Characidium represents the most widely distributed and species-rich fish genus within the family Crenuchidae in the Neotropical region, with numerous species described over the last decade. Despite this taxonomic progress, the understanding of species boundaries and population variation within the genus remains limited. In response, an integrative study was undertaken, utilizing both morphological and molecular data from neotropical freshwater ecoregions with rivers that drain the Brazilian northeastern. The primary objective of this investigation was to elucidate taxonomic delimitations and, where relevant, propose new species hypotheses. Our results propose the existence of 15 operational taxonomic units (OTUs) as species hypotheses. Among these, 10 were identified as valid species, four represented morphotypes that hold the potential of constituting new species, and one OTU was determined as a new species, corroborated by all proposed delimitation methods. Our results demonstrated discrepancies between morphological and molecular data, highlighting the challenges in defining taxonomic boundaries within Characidium. Moreover, our findings provided insights into the intricate diversification history of Characidium species, applied to the species that occur in northeastern Brazilian drainages. We proposed that historical events, such as river connections and barriers, have played a significant role in shaping the current distribution patterns of the genus.
... A total of 119 COI sequences of mtDNA were used (Supplementary material S1). Seven new COI sequences (Table 1) were generated and incorporated in the analyses, in addition to an additional 111 sequences available in Genbank and BOLD (Bagley et al., 2019;Bernt et al., 2019;Carvalho et al., 2011;Díaz et al., 2016;Frantine-Silva et al., 2015;Garcia-Davila et al., 2021;Herrera-Collazos et al., 2020;Janzen et al., 2022;Maldonado-Ocampo et al., 2014;Papa et al., 2021;Pereira et al., 2011;Pereira et al., 2011Pereira et al., , 2013Picq et al., 2014;Rincón-Sandoval et al., 2018;Saitoh et al., 2003;Tagliacollo et al., 2016). One sequence of Sternopygus macrurus (GenBank accession KF533349; Maldonado-Ocampo et al., 2014) was included as an out-group. ...
A new species of Eigenmannia is described from the Rio Branco basin, Roraima, Brazil, based on morphological and molecular datasets. It is distinguished from all congeners by the following combination of characters: lateral line stripe extending from first perforated lateral line scale to distal portion of caudal filament, presence of superior midlateral stripe with origin posterior to end of body cavity anal‐fin hyaline, caudal filament corresponding to 15.2%–43.1% LEA, subterminal mouth, ii,14–16 pectoral‐fin rays, 166–219 anal‐fin rays, 10–13 scale rows above lateral line at vertical through posterior tip of pectoral fin, 100–128 scales on lateral line, 22–28 premaxillary teeth, 19–23 dentary teeth, 7–10 endopterygoid teeth, depth of posterodorsal expansion on infraorbitals 1 + 2 half as long as infraorbitals 1 + 2 length, basibranchial 1 unossified, 13 precaudal vertebrae, and length of coronomeckelian bone corresponding to 20% of Meckel's cartilage length. The new species has significant genetic divergence from species with accessible DNA sequences in public repositories, ranging from 10.8% to 17.7%. An osteological description of the new species, a review of Eigenmannia cytochrome c oxidase subunit I (COI) sequences available in public repositories based on voucher examination, and a hypothesis of phylogenetic relationships for the new species based on COI are provided. The critical importance of including voucher examination as one of the steps in the pipeline for using DNA sequences present in public repositories in taxonomic and phylogenetic studies is discussed.
... Maroni, from an additional ten localities in lower and upper Maroni basin. In the same study, Papa et al. (2021) studied the coI barcode sequences of C. karipuna from eastern French Guiana. ...
... Marowijne River Suriname and French Guiana (Fig. 5, yellow dots). The species was also previously recorded from the Maroni River (¼Marowijne) in French Guiana by Le Bail et al. (2000) and Papa et al. (2021; see Figure 5, squares). Both watersheds that harbor the new species drain the Guiana Shield northward. ...
... Curculionichthys karipuna was originally described from the Cassiporé River in the Brazilian State of Amapá, with additional, non-type specimens reported from the Jari River basin, lower Amazon drainage. More recently, Papa et al. (2021) recorded the species in several localities of the Oyapock and Approuague Rivers in French Guiana, expanding the species distribution northward and establishing the distribution limit with C. monolechis. ...
... The database analyzed in the present study included 83 COI sequences of Pimelodus specimens collected during previous studies in a number of different South American basins (Supplementary Table S2). These areas include the Maroni River [26], the basin of the Magdalena-Cauca and Orinoco Rivers [23], the Amazon River [27,28], the São Francisco River [29,30], the Paraíba do Sul River [31], the Paraguay River [32], the upper and lower Paraná basins [33][34][35][36], and the plains of the Argentinian Pampa [37]. In all these cases, the taxonomic identification of the species followed the original denomination presented in the respective study. ...
Pimelodus is the most speciose genus of the family Pimelodidae, and is amply distributed in the Neotropical region. The species-level taxonomy and phylogenetic relationships within this genus are still poorly resolved, however. These taxonomic problems and the general lack of data have generated major uncertainties with regard to the identification of specimens from different localities. In the present study, we applied a single-locus species delimitation approach to identify the MOTUs found within the genus Pimelodus and provide sound evidence for the evaluation of the species richness of this genus in the different river basins of the Neotropical region. The study was based on the analysis of sequences of the mitochondrial COI gene of 13 nominal species, which resulted in the identification of 24 consensus MOTUs. Only six nominal species were recovered as well-defined molecular entities by both the traditional barcoding analysis and the molecular delimitation methods, while the other seven presented cryptic diversity or persistent taxonomic uncertainties. The lineages identified from the Parnaíba ecoregions, Amazonas Estuary and Coastal Drainages may represent a much greater diversity of Pimelodus species than that recognized currently, although a more detailed study of this diversity will be necessary to provide a more definitive classification of the genus.
... Although the genetic data provided by our database have inherent limitations due to the nature of the used marker (COI), we believe our collection of DNA data can help contributing to studies aimed at unraveling biodiversity patterns and enabling spatial genetic assessments. Leveraging methods like the geographical projection of genetic patterns through genetic divergence landscapes, our database facilitates the identification of diversity and evolutionary hotspots, potential barriers to gene flow and spatial genetic patterns across different lineages (54). The utility extends to dealing with multiple species, where the calculation of an average 'multispecies landscape' aids in detecting shared spatial components with similar evolutionary effects. ...
Insect decline has become a growing concern in recent years, with studies showing alarming declines in populations of several taxa. Our knowledge about genetic spatial patterns and evolutionary history of insects still exhibits significant gaps hindering our ability to effectively conserve and manage insect populations and species. Genetic data may provide valuable insights into the diversity and the evolutionary relationships of insects’ species and populations. Public repositories, such as GenBank and BOLD, containing vast archives of genetic data with associated metadata, offer an irreplaceable resource for researchers contributing to our understanding of species diversity, population structure and evolutionary relationships. However, there are some issues in using these data, as they are often scattered and may lack accuracy due to inconsistent sampling protocols and incomplete information. In this paper we describe a curated georeferenced database of genetic data collected in GenBank and BOLD, for insects listed in the International Union for Conservation of Nature (IUCN) Italian Red Lists (dragonflies, bees, saproxylic beetles and butterflies). After querying these repositories, we performed quality control and data standardization steps. We created a dataset containing approximately 33 000 mitochondrial sequences and associated metadata about taxonomy, collection localities, geographic coordinates and IUCN Red List status for 1466 species across the four insect lists. We describe the current state of geographical metadata in queried repositories for species listed under different conservation status in the Italian Red Lists to quantify data gaps posing barriers to prioritization of conservation actions. Our curated dataset is available for data repurposing and analysis, enabling researchers to conduct comparative studies. We emphasize the importance of filling knowledge gaps in insect diversity and distribution and highlight the potential of this dataset for promoting other research fields like phylogeography, macrogenetics and conservation strategies. Our database can be downloaded through the Zenodo repository in SQL format.
Database URL: https://zenodo.org/records/8375181
... nickeriensis were obtained from Genbank (Tab. 4) from Papa et al. (2021), including fishes from the Maroni River (close to the type locality of the species, see Discussion below). It was found that between L. nimairaco (n = 2) and L. cf. ...
... We analyzed four samples identified as L. cataphracta from Genbank (Tab. 4), all from the Maroni River (Papa et al., 2021). The new species was 6.0% divergent from L. cataphracta, the type species of the genus. ...
A new species of Loricaria is described from the upper Amazon River basin, Colombia. The new species is distinguished from its congeners primarily by having the dorsal portion of head with uniform black or dark brown coloration extending to three or four plates posterior to dorsal fin base, or with two longitudinal bands from tip of the snout to origin of dorsal fin; abdominal plates tightly joined and completely covering the median abdominal space and pectoral girdle; and pectoral and dorsal fins totally black or dark brown, without bands, spots, or blotches. The new species is further distinguished by plate counts, and body measurements. An analysis of genetic distances using the cytochrome oxidase c subunit 1 marker of the mitochondrial genome showed a clear differentiation between the new species and Loricaria cataphracta (5.8–7.6%), L. nickeriensis (5.7–6.1%), and L. simillima (2.7–7.0%). Species delimitation analyses were carried out, which further supported the new species as a divergent lineage within the genus. Fish species diversity of the upper Amazon River basin and taxonomic issues related to L. simillima are included as part of the discussion.
... Thus, this visualization created from hierarchical clustering can be used to assess this study. Many studies with DNA Barcoding continue to use hierarchical clustering techniques due to its ubiquity and relative simplicity [50][51][52][53][54][55][56]. In this study, hierarchical clustering with DNA Barcodes will be used to achieve two objectives. ...
The DNA barcoding approach has been used extensively in taxonomy and phylogenetics. The differences in certain DNA sequences are able to differentiate and help classify organisms into taxa. It has been used in cases of taxonomic disputes where morphology by itself is insufficient. This research aimed to utilize hierarchical clustering, an unsupervised machine learning method, to determine and resolve disputes in plant family taxonomy. We take a case study of Leguminosae that historically some classify into three families (Fabaceae, Caesalpiniaceae, and Mimosaceae) but others classify into one family (Leguminosae). This study is divided into several phases, which are: (i) data collection, (ii) data preprocessing, (iii) finding the best distance method, and (iv) determining disputed family. The data used are collected from several sources, including National Center for Biotechnology Information (NCBI), journals, and websites. The data for validation of the methods were collected from NCBI. This was used to determine the best distance method for differentiating families or genera. The data for the case study in the Leguminosae group was collected from journals and a website. From the experiment that we have conducted, we found that the Pearson method is the best distance method to do clustering ITS sequence of plants, both in accuracy and computational cost. We use the Pearson method to determine the disputed family between Leguminosae. We found that the case study of Leguminosae should be grouped into one family based on our research.
... Coastal rivers in the Guiana Shield are smaller than in other Neotropical regions, yet contain similar habitats and exceptional ichthyodiversity. The Maroni is one of its most speciose basins, with 264 strictly freshwater fish species, of which 16.9% are considered endemic (Le Bail et al. 2012; see also Papa et al. 2021 suggesting 25 additional cryptic species using molecular data). This unique biodiversity heritage provides cultural and commercial resources for an expanding community of native people (Longin et al. 2021a;b). ...
... In the Maroni though, diversification and past colonization routes of most fish taxa were documented as resulting from the formation of a Pleistocene refuge and relatively ancient stream-capture events between headwaters of the Maroni and neighboring watersheds (e.g., between the Litani and the river Jari in the Tucumaque mountains, Fisch-Muller et al. 2018) and less likely from exchanges of fish with other coastal rivers through estuaries (Lemopoulos and Covain 2019). In addition, current patterns of landscape genetic variation are considered to result mainly from environmental heterogeneity (Borstein et al. 2022) and species life history traits (Papa et al. 2021), although specific reconstructions of past demography and evolutionary trajectories are missing. Thus, upstream-directed colonization from the river outlet to the headwaters seems less likely to have occurred in our study zone, unless it relies on contemporary non-equilibrium processes such as extinction-recolonization of upstream reaches due to local environment constraints. ...
... This diverging trend suggests that the dendritic structure of the river network is not the only feature that influences spatial patterns of genetic diversity along the upstream gradient. At a larger geographical scale, Papa et al. (2021) identified significant global genetic divergence between western (i.e., Suriname) and eastern (i.e., our study zone) regions of the Maroni River using multispecies genetic landscapes based on the mitochondrial gene COI. This may result from current expansion of population ranges from the Maroni toward adjacent watersheds. ...
Spatial patterns of genetic variation compared across species provide information about the predictability of genetic diversity in natural populations, and areas requiring conservation measures. Due to their remarkable fish diversity, rivers in Neotropical regions are ideal systems to confront theory with observations and would benefit greatly from such approaches given their increasing vulnerability to anthropogenic pressures. We used SNP data from 18 fish species with contrasting life-history traits, co-sampled across 12 sites in the Maroni– a major river system from the Guiana Shield –, to compare patterns of intraspecific genetic variation and identify their underlying drivers. Analyses of covariance revealed a decrease in genetic diversity as distance from the river outlet increased for 5 of the 18 species, illustrating a pattern commonly observed in riverscapes for species with low-to-medium dispersal abilities. However, the mean within-site genetic diversity was lowest in the two easternmost tributaries of the Upper Maroni and around an urbanized location downstream, indicating the need to address the potential influence of local pressures in these areas, such as gold mining or fishing. Finally, the relative influence of isolation by stream distance, isolation by discontinuous river flow, and isolation by spatial heterogeneity in effective size on pairwise genetic differentiation varied across species. Species with similar dispersal and reproductive guilds did not necessarily display shared patterns of population structure. Increasing the knowledge of specific life history traits and ecological requirements of fish species in these remote areas should help further understand factors that influence their current patterns of genetic variation.
... Voucher specimens for the molecular study are deposited and preserved in 95% ethanol in the collection of LBP (Table 1). Nine sequences were generated herein, and 25 sequences were obtained from Mattox et al. (2020Mattox et al. ( , 2021 plus one sequence of the outgroup taxon Jupiaba keithi (Géry, Planquette and Le Bail, 1996) deposited in the GenBank database by Papa et al. (2021). DNA extraction followed Ivanova et al. (2006). ...
Two new miniature tetra species of the Neotropical characid genus Priocharax Weitzman and Vari, 1987 are described, raising the known species diversity to seven. Both species occur in the Rio Juruá system, Cruzeiro do Sul municipality, Acre State, Brazil. Priocharax toledopizae sp. nov. occurs in streams flowing to the lower Rio Moa, a tributary of Rio Juruá, and is distinguished from congeners by a combination of presence of claustrum and infraorbitals 1 and 2, absence of infraorbital 3, and presence of five branched pelvic-fin rays. Priocharax marupiara sp. nov. is known from Igarapé Canela Fina, tributary of Rio Juruá, and is diagnosed by a combination of fewer maxillary teeth (21-27 vs. 27-58 in remaining species), fewer branched anal-fin rays (18-23 vs. 22-27 in two species) and colour pattern. Both species differ from each other in the general body shape: Priocharax toledopizae is more robust with deep body and Priocharax marupiara more elongate. DNA barcode data support the specific distinctness of the two new species and that of the other five species in the genus. We describe a remarkable sexual dimorphism of the pelvic girdle of Priocharax toledopizae in which the pelvic musculature is enlarged forming a pedicel for the fin in mature males. Most localities where these species were found suffer from significant degradation mainly due to litter accumulation and suppression of the riparian forest, raising concerns about their conservation status.
... Thus, the barcoding method is not aimed at replacing taxonomy but rather at providing a useful additional tool in case of unclear identification (in particular for disputed fish species) to assess biodiversity. As a result, various analysis methods combined with traditional morphological identification are used to define species in DNA barcoding studies to improve the accuracy of taxonomic identification, enhance the discovery of cryptic species and enrich the genetic diversity of species [20][21][22][23][24][25]. ...
... Reassessment was conducted for some samples that were difficult to identify and those that were not successfully compared in the database. The assessment criteria were based on the distribution location of the species, the species morphology, and the position of the sequences on the phylogenetic tree [23]. The R package ape 5.0 [36] was used to calculate Kimura two-parameter (K2P) [37] pairwise genetic distances. ...
Guizhou is an important ecological barrier in the upper reaches of the Yangtze River and the Pearl River basins with abundant fish species. However, fish from these regions are threatened by anthropogenic activities, including overfishing and habitat destruction. Here, we assessed the fish diversity including more than half of the species from the region using DNA barcoding (partial sequence of cytochrome c oxidase subunit I (COI) gene). We obtained 800 mitochondrial COI barcode sequences from 82 genera, 18 families and 8 orders of fishes. The average Kimura two-parameter (K2P) distances within species and genera were 0.35% and 5.44%, respectively. The average interspecific distance was 15.54 times higher than the mean intraspecific distance. Moreover, DNA barcodes revealed 175 operational taxonomic units (OTUs) based on consensus demarcation schemes. Barcoding gaps were detected in 94.81% of morphospecies. Three fish species (Schistura fasciolata, Vanmanenia pingchowensis, and Misgurnus dabryanus) have considerable intraspecific variability, and each was divided into multiple molecular operational taxonomic units (MOTUs) using molecular definition methods (Automatic Barcode Gap Discovery, Refined Single Linkage, General Mixed Yule Coalescent, and Poisson Tree Processes), possibly indicating the occurrence of cryptic species. Altogether, our study reveals the complex diversity of fish species in Guizhou Province, serving as a reference for the conservation and monitoring of fish species in this region.
