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

Pereira, Luiz Henrique Garcia; Castro, Jerson Rogelio Chanchay; Vargas, Pilar Mireya Huatatoca; Gómez, José Alejandro Morales; Oliveira, Cláudio

doi:10.1007/s10709-021-00118-6

Cited by 15 publications

(12 citation statements)

References 63 publications

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“…According to what was observed in 1088 fish species [ 80 ], sequences with a divergence of greater than 2% or 3% likely belong to different species (with a probability greater than 95%). This COI divergence threshold was generally confirmed with an analysis implementing several methods for species delimitations in fishes and allowed for the identification of cryptic species [ 81 , 82 , 83 ] even in Leuciscidae [ 84 ]; furthermore, 2–3% divergence was observed between many Leucos and Rutilus taxa whose status as good species is not debated. Although our nuclear dataset is limited, a substantial divergence (almost 4%) and a slight difference in length were observed between Cyfun P sequences exclusive to VAR sites and mostly present in specimens belonging to mitochondrial lineage C, and those widespread across S. rubilio populations.…”

Section: Discussionmentioning

confidence: 62%

Phylogeography of Sarmarutilus rubilio (Cypriniformes: Leuciscidae): Complex Genetic Structure, Clues to a New Cryptic Species and Further Insights into Roaches Phylogeny

Petrosino

Tancioni

Turani

et al. 2022

Genes

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Italy hosts a large number of endemic freshwater fish species due to complex geological events which promoted genetic differentiation and allopatric speciation. Among them, the South European roach Sarmarutilus rubilio inhabits various freshwater environments in three different ichthyogeographic districts. We investigated the genetic diversity of S. rubilio using two different mitochondrial markers (COI and CR), aiming to define its relationship with other similar taxa from the Balkan area and, from a phylogeographic perspective, test the effects of past hydrogeological dynamics of Italian river basins on its genetic structure and demographic history. Our analysis highlighted a marked genetic divergence between S. rubilio and all other roach species and, among Italian samples, revealed the existence of three deeply divergent geographic haplogroups, named A, B and C. Haplogroup C likely corresponds to a new putative cryptic species and is located at the northern border of the South European roach range; haplogroup B is restricted to Southern Italy; and haplogroup A is widespread across the entire range and in some sites it is in co-occurrence with C or B. Their origin is probably related to the tectonic uplifting of the Apuan Alps in the north and of the Colli Albani Volcano in the south during the Pleistocene, which promoted isolation and vicariance followed by secondary contacts.

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Section: Discussionmentioning

confidence: 62%

Phylogeography of Sarmarutilus rubilio (Cypriniformes: Leuciscidae): Complex Genetic Structure, Clues to a New Cryptic Species and Further Insights into Roaches Phylogeny

Petrosino

Tancioni

Turani

et al. 2022

Genes

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“…The current research on fish species identification is mainly aimed at the static images of fish in marine and aquatic fields (Pepe et al, 2007;Bingpeng et al, 2018;Chai et al, 2021;Pereira et al, 2021). Although some achievements have been made, however, the actual situation is that the fish swimming through fishway is a dynamic process, and the body of fish is often in a torsional state of deformation, making it difficult to directly carry out research on the identification of passing fish targets in real fishways engineering scenarios using existing algorithms.…”

Section: Research Backgroundmentioning

confidence: 99%

Dynamic identification and automatic counting of the number of passing fish species based on the improved DeepSORT algorithm

Liu

Jiang

et al. 2023

Front. Environ. Sci.

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In this paper, based on the improved DeepSORT algorithm, four target species of passing fish (Schizothorax o’connori, Schizothorax waltoni, Oxygymnocypris stewartii and Schizopygopsis younghusbandi) from a fishway project in the middle reaches of the Y River were used to achieve dynamic identification and automatic counting of passing fish species using fishways monitoring video. This method used the YOLOv5 model as the target detection model. In view of the large deformation by fish body twisting, the network structure of the re-identification (ReID) model was deepened to strengthen the feature extraction ability of the model. It was proposed to identify and track fish that cross the line by setting a virtual baseline to achieve the dynamic identification of fish species passing and the automatic counting of upward and downward quantities. The results showed that 1) among the five models, YOLOv5n, YOLOv5s, YOLOv5m, YOLOv5l, and YOLOv5x, the highest value of mean average precision (mAP) was 92.8% achieved by the YOLOv5x model. Specifically, recognition accuracies of 96.95%, 94.95%, 88.79%, and 91.93% were recorded for Schizothorax o’connori, S. waltoni, S. younghusbandi and O. stewartii, respectively. 2) The error rate of the improved ReID model was 20.3%, which was 20% lower than that before the improvement, making it easier for the model to obtain target features. 3) The average accuracy of the improved DeepSORT algorithm for counting four target fishes was 75.5%, among which the accuracy of Schizothorax o’connori, S. waltoni, S. younghusbandi and O. stewartii were 83.6%, 71.1%, 68.1%, and 79.3%, respectively. Meanwhile, the running speed was 44.6 fps, which met the real-time monitoring. This method is the first to implement intelligent identification of the target passing fish in fishways projects, which can accumulate long series monitoring data for fishways operation and management and provide a technical solution and reference for the work related to the realization of intelligent and informative passing fish monitoring.

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“…Morphology-based identifications make use of different sets of quantitative and qualitative phenotypic characters, which include allometry, phylogenetics, morphometrics, and meristics (Hebert et al, 2003; Ward et al, 2009). For certain taxonomic groups, convergence in morphologically diagnostic characters and cryptic species pose a challenge for morphological-based identification (Pires & Marinoni, 2010; Marancik et al, 2020; Pereira et al, 2021). In addition, the ‘taxonomic impediment’: the small number of trained taxonomists and funding compared to the need for these specialists, complicates these issues further creating an intrinsic problem with incomplete/outdated references (Pires & Marinoni, 2010; Sheth & Thaker, 2017; Riccardi et al, 2020; Engel et al, 2021).…”

Section: Introductionmentioning

confidence: 99%

“…Integrative taxonomic approaches that combine complementary datasets such as DNA and morphology, have proven to be efficient in addressing gaps left by each individual method (Breedy et al, 2012; Riedel et al, 2013; von Beeren et al, 2016; Duong et al, 2020; Zamani et al, 2022). The term ‘integrative taxonomy’ can be used to describe two processes, species delimitation/discovery and specimen identification (Pires & Marinoni, 2010; Pereira et al, 2021); herein we use the term integrative taxonomy to refer to specimen identification. The use of multiple data sources to support a specimen identity and subsequently the species presence in an area provides strong evidence that can be used for implementation of conservation plans, a key component to secure financial support for conservation (Sheth & Thaker, 2017).…”

Section: Introductionmentioning

confidence: 99%

Comparing Approaches to Specimen Identification using Neotropical Freshwater Fishes in the Barra del Colorado Wildlife Refuge, Costa Rica

Perez,

Fontenelle,

Kolmann

et al. 2023

Preprint

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As global biodiversity declines continue, conservation efforts are increasingly important in megadiverse areas such as the Neotropics where biodiversity is especially imperiled. The accurate identification of specimens is critical to successful conservation plans. However, in groups such as freshwater fishes, different identification methodologies have documented challenges. Using a biodiversity survey of fishes from the Barra del Colorado Wildlife Refuge in northeastern Costa Rica, we compared: (1) morphological identifications in the field, (2) morphological identifications in the lab by experts, (3) DNA barcode-based identifications, and (4) identifications based on an integrative approach. Our results suggest that both barcode-based identifications and field morphological identifications provided fewer correct species identifications than lab identifications performed by experts using morphology. We attribute shortfalls of DNA barcoding in this case to the misidentification of reference material, the use of outdated taxonomy for references sequences, and the non-uniform representation of groups in public databases across taxa. We suggest the use of an integrative approach to identify freshwater fishes in Costa Rica and other megadiverse areas of the Neotropics where similar issues with public barcode reference libraries exist. We also recommend the creation of regional curated barcode reference libraries to aid in the identification of traditionally difficult to identify species/specimens. We also provide the most up to date species list for the ichthyofauna of the Barra del Colorado Wildlife Refuge identifying 51 species from 42 genera, 21 families, and 17 orders. Generating accurate species lists for protected areas and areas of importance will provide conservation practitioners with effective tools for tracking diversity changes over time.

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

Cited by 15 publications

References 63 publications

Phylogeography of Sarmarutilus rubilio (Cypriniformes: Leuciscidae): Complex Genetic Structure, Clues to a New Cryptic Species and Further Insights into Roaches Phylogeny

Phylogeography of Sarmarutilus rubilio (Cypriniformes: Leuciscidae): Complex Genetic Structure, Clues to a New Cryptic Species and Further Insights into Roaches Phylogeny

Dynamic identification and automatic counting of the number of passing fish species based on the improved DeepSORT algorithm

Comparing Approaches to Specimen Identification using Neotropical Freshwater Fishes in the Barra del Colorado Wildlife Refuge, Costa Rica

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