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. 2026 Sep 18;21(9):e0347004. doi: 10.1371/journal.pone.0347004

Cryptic diversity in Astyanax (Characiformes: Acestrorhamphidae) from the Magdalena basin, Colombia: Insights from molecular and morphometric evidence

Edna Judith Márquez 1,*, Kevin León García-Castro 1, Daniela Ramírez Álvarez 1, Carlos DoNascimiento 2
Editor: Caio Santos Nogueira3
PMCID: PMC13588355  PMID: 42758695

Abstract

Astyanax Baird & Girard, 1854 is a widely distributed and species-rich genus of Acestrorhamphidae, whose abundant populations in Neotropical basins play a crucial ecological role at the trophic level. Taxonomic uncertainties persist within the genus, as seen in Astyanax sp. (formerly designated as A. fasciatus) from the Magdalena basin in Colombia. Concerns about its genetic status are heightened due to ecological threats posed by hydroelectric dams, from habitat loss to river connectivity. We isolated and characterized 17 microsatellite loci to assess the population genetics of this species in a broad sample from the middle and lower sections of the Cauca River, now interrupted by the Ituango dam. Furthermore, a multidisciplinary approach integrating phylogenetic analyses of mitochondrial (COI) and nuclear (rag2) markers with geometric morphometric analyses was employed to evaluate potential cryptic diversity within Astyanax sp. Microsatellites revealed two genetic groups in the studied area, strongly supported as distinct lineages by phylogenetic analyses. Unexpectedly, one of these lineages of Astyanax sp. was recovered in an unresolved clade with samples of A. microlepis and allopatric samples of A. viejita from the Maracaibo Lake basin. Each genetic group showed high genetic diversity, but also evidence of recent bottleneck events and significant-high values of inbreeding. Morphometric analyses provided evidence of significant phenotypic differentiation among A. microlepis, Astyanax sp. 1 (Asp1), and Astyanax sp. 2 (Asp2). Morphological patterns ranged from the robust profile of A. microlepis to the streamlined shape of Astyanax sp. 2 (Asp2), with Astyanax sp. 1 (Asp1) displaying intermediate traits and localized differences in head length and fin placement. Statistical support from permutation tests and a high overall classification accuracy (95.65%) underscore the existence of distinct morphospecies, suggesting that phenotypic differentiation is well-established, despite the complex evolutionary history of the group. This study suggests the presence of cryptic diversity within Astyanax sp. and provides valuable genetic information for the conservation and management of their populations in the Magdalena basin.

Introduction

Astyanax Baird & Girard, 1854 is a genus of tetra fishes with broad distribution across the American continent, extending from Texas to the Río de la Plata estuary in Argentina, and is especially abundant in the Amazon and Orinoco basins. The genus currently includes 122 valid species, comprising approximately 2.8% of the taxonomic diversity of the entire order Characiformes [1], and recently was reallocated into the family Acestrorhamphidae from its traditional placement in Characidae [2]. Due to non-exclusive diagnostic characters, phenotypic plasticity, and limited resolution by COI-based molecular analyses, Astyanax remains a non-monophyletic group [2–5], complicating species-level taxonomic identification within the genus.

In Colombia, 22 Astyanax species are reported, nine of them in the Magdalena basin [6], including Astyanax sp., formerly designated as Astyanax fasciatus (Cuvier, 1819) [7]. Astyanax fasciatus was reallocated in Psalidodon Eigenmann, 1911 [5] and its geographic distribution restricted to the São Francisco basin in southeastern Brazil [5], leaving at least five allopatric species from remote cis-Andean or even trans-Andean basins that are still listed as synonyms of P. fasciatus [8], in a taxonomic limbo.

Species of Astyanax from the Magdalena basin have been reported as omnivorous, with seasonal life strategies, early maturation, body size ranging from 60 to 183 mm of standard length (SL), and short-range migrations [9]. They are also considered the most abundant species both in numerical abundance and biomass in the Magdalena basin, even in reservoir systems, and play a fundamental role in the food chain [9]. Local fishermen recognize that Astyanax species are among the first populations to leave floodplains and signal upstream migrations for other species during periods of water descent [9,10]. Some of these species, such as A. magdalenae Eigenmann & Henn, 1916 and Astyanax sp., have also been reported for ornamental and/or consumption purposes in the last two decades [9].

Despite Astyanax’s high species diversity, taxonomic uncertainty, and multiple threats, few studies have examined its microevolutionary genetics scale. These studies have focused mainly on populations from Mexico and Brazil [11–14]). In Colombia, only one study has assessed population genetics of A. caucanus (Steindachner, 1879), using species-specific microsatellite loci [15]. That study reported high gene flow along a 340 km stretch of the Cauca River, even among sectors recently isolated by the Ituango dam, as well as high genetic diversity (as in other congeners) and large effective population sizes [15]. However, it also found evidence of recent bottleneck events and significant inbreeding [15].

Astyanax is characterized by high phenotypic plasticity and a remarkable capacity to adapt to diverse habitats [16,17]. This plasticity has motivated numerous studies using geometric morphometrics, a tool for quantifying body shape variation among genera, species, populations, and sexes [18]. Such data are crucial for refining species boundaries and assessing the influence of both genetic and environmental factors [19–23], especially in groups like Characidae, where morphological conservatism often masks underlying genetic differences.

Several studies have combined genetics and morphometrics to explore their interplay in Astyanax and related genera [23–27]. For instance, ecologically distinct morphs of Astyanax have been identified in the San Juan River basin (Central America), with marked morphological differentiation (one morph with elongated body and predatory features and the other morph with deep body and generalist traits), despite limited genetic divergence between them [22]. Morphological distinction has also been corroborated by genetic evidence in the Psalidodon scabripinnis (Jenyns, 1842) complex, where P. paranae (Eigenmann, 1914) exhibits a more fusiform body than P. rivularis (Lütken, 1875) [26]. However, a clear correspondence between morphological and genetic patterns is often absent. Studies on sympatric populations of A. caballeroi (Contreras-Balderas & Rivera-Teillery, 1985) and A. aeneus (Günther, 1860) in Mexico have revealed significant differences in body depth, head profile, and fin morphology that are not reflected by the molecular data [19].

Geometric morphometrics also enables analyses of environmental effects on body shape, such as habitat type and water flow [28–31]. Ecomorphological divergence is well-documented in Astyanax and related genera. A common pattern is the correlation between body shape and water velocity, species inhabiting lotic environments, such as Psalidodon rivularis and P. paranae, typically have fusiform bodies adapted to swimming against currents, whereas species from lentic habitats, like A. abramis (Jenyns, 1842), A. lacustris (Lütken, 1875), and A. asuncionensis Géry, 1972, exhibit deeper, laterally compressed bodies, suited for maneuverability [20]. This pattern also occurs within single species. In river populations, A. lacustris have a fusiform shape with a deep caudal peduncle, while their lagoon-dwelling counterparts are deeper-bodied with a shallower caudal peduncle [21]. Likewise, A. bimaculatus (Linnaeus, 1758) from reservoirs have deeper bodies and longer fin bases than those from rivers [20]. Some species that occupy both environments, such as P. fasciatus, display an intermediate body shape, reflecting their ecological flexibility [20,23].

In the present work, we designed and evaluated a set of microsatellite loci to assess genetic diversity and population structure of Astyanax sp. in the middle and lower sections of the Cauca River, spanning sectors upstream and downstream of the Ituango dam. Additionally, COI and rag2 sequences were compared within a broad phylogenetic framework (with emphasis on trans-Andean representatives of Astyanax and species of the resurrected Psalidodon [5], including the true nominal P. fasciatus), to determine whether groups potentially identified through microsatellites correspond to divergent lineages within the genus. Finally, geometric morphometric analyses were conducted to investigate potential drivers of diversification in Astyanax.

Materials and methods

Sampling

The Cauca River, stretching 1,350 km from Laguna del Buey in the south to its confluence with the Magdalena River, flows along the inter-Andean valley and canyon delimited by the Western and Central Cordilleras of the northern Andes mountains, with its upper section at around 900 m asl, the final 500 km features a steep, narrow canyon, dominated by rapids and waterfalls, which posed challenges for migrating fishes, even before the Ituango dam construction. This dam is the largest in Colombia, standing at 225 m high, and it is expected to contribute approximately 2,400 MW of power annually [32,33].

Between 2019 and 2021, a total of 324 muscle and fin tissue samples of Astyanax sp. were collected from eight sections in the middle and lower parts of the Cauca River (Fig 1). High-resolution photographs were captured for each specimen and standardized for landmark digitization, providing the framework for subsequent geometric morphometric analyses. These sections were chosen due to their contrasting hydrological and geographical characteristics [34]. Two sections, namely S1 and PHI, were located upstream of the Ituango dam, while the remaining sections (S2, S3, S4, S5, S6, and S7/S8) were situated downstream of the dam. The PHI section represents the current reservoir of the dam. Collections were conducted by Grupo de Ictiología from the Universidad de Antioquia (GIUA), Fundación Humedales, and Grupo de Biotecnología Animal from Universidad Nacional de Colombia, campus Medellín.

Fig 1. Geographic location of sampling sectors in the Cauca River basin, Colombia.

Fig 1

Blue lines represent upstream and dam-proximate sectors (S1, PHI, S2, S3, and S4) predominated by genetic stock Asp1, while orange lines denote downstream sectors (S5, S6, S7, and S8) predominated by genetic stock Asp2 (see Results). Map layers: Colombia boundary from the DANE Marco Geoestadístico Nacional (2024; CC BY 4.0), available at https://geoportal.dane.gov.co/servicios/descarga-y-metadatos/datos-geoestadisticos/; inset country boundaries from Natural Earth Admin 0 Countries (scale 1:10m; public domain), available at https://www.naturalearthdata.com/downloads/10m-cultural-vectors/10m-admin-0-countries/; rivers and highlighted river segments from RiverATLAS v1.0/HydroATLAS (CC BY 4.0), available at https://www.hydrosheds.org/hydroatlas; elevation from the USGS Global Multi-resolution Terrain Elevation Data 2010 (GMTED2010) mean-elevation grid at 7.5 arc-second resolution (~250 m; public domain), with hillshade derived from these data in QGIS; and physical background from Natural Earth II high-resolution raster data (scale 1:10m; public domain), available at https://www.naturalearthdata.com/downloads/10m-raster-data/10m-natural-earth-2/. Map created in QGIS without proprietary satellite imagery or proprietary basemaps.

Isolation and characterization of microsatellite loci

We designed and assessed 42 specific primer pairs (Afa01-Afa42; S1 Table) to amplify microsatellite loci containing tri-, tetra-, and pentanucleotide motifs to assess population genetics in samples of Astyanax sp. We applied Illumina’s MiSeq v2 technology and followed a previously established methodology [34] to identify and isolate microsatellite loci, using a sample (P730) of Astyanax sp. collected in the Cauca River. Prinseqlite v0.20.4 was used to refine the 250-base paired-end reads generated in the sequencing, followed by Abyss v1.3.5 assembly and PAL_FINDER v.0.02.03 analysis to locate microsatellite loci with perfect repeats [35]. Primer pairs for amplification were designed via Primer3 v.2.0, and electronic PCR validation ensured accurate primer alignment for the amplifiable loci.

PCR amplifications were conducted in a final reaction volume of 10 µl, following a three-primer methodology [36,37]. The reaction mixture contained 1X Platinum™ Multiplex PCR Master Mix, 0.25% Enhancer/GC, 0.20 pmol/µl of forward primer with a universal tail, 0.40 pmol/µl of reverse primer, and 0.20 pmol/µl of fluorescently labeled tail. The thermal profile involved an initial step at 95°C for 3 minutes, followed by 35 cycles of 90°C for 30 seconds and 56°C for 35 seconds, without final extension. Fragment separation was carried out on a SeqStudio Genetic Analyzer, using LIZ600 as an internal molecular marker. Allelic assignment was performed using GeneMarker v3.0.0, while Micro-Checker v.2.2.3 [38] was employed to identify potential genotyping errors in the data matrix.

We employed 36 random samples representing all sections of the studied river to characterize each of the amplified loci. These samples were used to calculate various genetic diversity metrics (detailed below), including polymorphic information content (PIC), using CERVUS v3.0.7 [39].

Population genetics analyses

Genetic differentiation and structure among sections were assessed using three complementary approaches: (i) Bayesian analysis of co-ancestry performed in Structure v2.3.4 [40], with optimal number of populations determined via estimators in Structure Selector [41]; (ii) analysis of molecular variance (AMOVA) and the calculation of pairwise F´ST and Jost’s DEST indices using GenAlEx v6.502 [42]; and (iii) discriminant analysis of principal components (DAPC) implemented with the Adegenet package [43] in R v3.4.0.

To assess genetic diversity and demographic events, we calculated genetic diversity metrics (Na: average number of alleles per locus, HO, HE: observed and expected heterozygosity, respectively) and the inbreeding coefficient (FIS) for each section and genetic group, using Arlequin v3.5.2.2 [44]. Additionally, allelic richness (Ar) was determined using FSTAT v.2.9 [45]. Deviations from Hardy-Weinberg equilibrium (HWE) were analyzed using the web version of GENEPOP v4.7.5 [46]. The effective population size (Ne) was estimated through NeEstimator v2.1 [47]. Furthermore, identification of genetic evidence for recent bottlenecks was assessed using the excess heterozygosity method in BOTTLENECK v1.2.02 [48] and the calculation of the M index [49]. Statistical significance in multiple comparisons was evaluated after applying the Bonferroni sequential correction.

Phylogenetic analyses

Our study involved the amplification and concatenation of the COI and rag2 genes, including samples of Astyanax sp. genotyped in this study and selected, according to genetic stocks detected by genetic structure analyses (Table 1). Additional sequences analyzed included Astyanax sp. from the Cauca and Magdalena Rivers, as well as A. microlepis collected at its type locality in the upper Cauca River. Furthermore, GenBank sequences of A. caucanus, A. viejita sensu Rossini et al., 2016 [3], from the Maracaibo Lake basin and other congeners were incorporated (Table 2). Representatives of the genera Astyanacinus, Carlana, Ctenobrycon, Jupiaba, Oligosarcus, Parastremma, and Psalidodon were included as outgroups (Table 2). Taxonomic nomenclature of species names followed [2].

Table 1. List of sequences of Astyanax, Astyanacinus, and Ctenobrycon from Colombia generated in this study for phylogenetic analyses.

Species Sample ID/Name Locality/Basin rag2 COI
Astyanax microlepis 7927 Piedra Moler – Valle del Cauca*/upper Cauca OR992015 OR981620
Astyanax microlepis 7965A Piedra Moler – Valle del Cauca*/upper Cauca OR992016 OR981621
Astyanax microlepis 7965B Piedra Moler – Valle del Cauca*/upper Cauca OR992017 OR981622
Astyanax microlepis 7965C Piedra Moler – Valle del Cauca*/ upper Cauca OR992018 OR981623
Astyanax sp UN636 Santa Fé de Antioquia- Bolombolo/middle Cauca OR992030 OR981635
Astyanax sp A2907 Ituango reservoir tail/middle Cauca OR992019 OR981624
Astyanax sp UN1556 Puente Tarazá/lower Cauca OR992020 OR981625
Astyanax sp UN1557 Puente Tarazá/lower Cauca OR992022 OR981627
Astyanax sp UN1565 Puente Tarazá/lower Cauca OR992031 OR981636
Astyanax sp UN1560 Puente Tarazá/lower Cauca OR992023 OR981628
Astyanax sp UN1564 Puente Tarazá/lower Cauca OR992029 OR981634
Astyanax sp UN1561 Puente Tarazá/lower Cauca OR992021 OR981626
Astyanax sp UN1566 Puente Tarazá/lower Cauca OR992024 OR981629
Astyanax sp C37450 Margento/lower Cauca OR992025 OR981630
Astyanax sp C11854 Tres Cruces/lower Cauca OR992026 OR981631
Astyanax sp C11862 Tres Cruces/lower Cauca OR992027 OR981632
Astyanax sp C11877 Tres Cruces/lower Cauca OR992028 OR981633
Astyanax sp IAvH-CT-24548 Barrancabermeja – Santander/middle Magdalena – OR064742
Astyanax sp IAvH-CT-24679 Cimitarra – Santander/middle Magdalena OR992033 OR064743
Astyanax sp IAvH-CT-17785 Colosó – Sucre/lower Magdalena OR992032 OR064741
Astyanacinus yarigues IAvH-23068 Carmen de Chucurí -Santander/middle Magdalena OR992034 OR981637
Ctenobrycon caucanus UN1536 Tarazá River*/middle Cauca OR992035 OR064739a

*Type locality; a [15].

Table 2. List of sequences retrieved from GeneBank for phylogenetic analysis.

Species Sample ID/Name Country rag2 COI
Astyanacinus moorii LBP5783–28195 HQ289447
Astyanax aeneus LBP8938–42019/ ECO-CH-P5526A Mexico HQ289511.1 EU751628.1
Astyanax bimaculatus -/ BPV-70579-LBP-17743 Perú AY804025.1 KY268210.1
Astyanax caballeroi LBPV-8939 HQ289512.1 MH002919.1
Astyanax jordani LBP4511–24599/ LBPV-24614 Brazil HQ289423.1 KY267487.1
Astyanax lacustris UFRGS19151-TEC4869A/ LBPV-68019 Brazil MN011703.1 KY268125.1
Astyanax mexicanus LBP8937–42016/MX003A Mexico HQ289510.1 EU751652.1
Astyanax viejita BAST232−12 Venezuela KY267682
Astyanax viejita BAST231−12 Venezuela KY268184
Astyanax viejita BAST230−12 Venezuela KY268055
Carlana eigenmanni Car-S2 Nicaragua OP654742.1 MZ820764.1
Ctenobrycon kennedyi LBP6578–31813/LBPV-6578 HQ289459.1 MH003289.1
Jupiaba polylepis MCP 32548 FJ749124.1 FJ749068.1
Oligosarcus argenteus UFRGS 19745-TEC5290B Brazil MN011640.1 MN119394.1
Oligosarcus jacuiensis UFRGS 22247-TEC7078F Brazil MN011660.1 MN119414.1
Oligosarcus pintoi UFRGS 22535-TEC7237B Brazil MN011685.1 MN119439.1
Oligosarcus robustus UFRGS 19946-TEC5414B Brazil MN011691.1 MN119445.1
Parastremma sadina T25082 Colombia OP654743.1 MZ820762.1
Psalidodon eigenmanniorum UFRGS19221-TEC4916A Brazil MN011700.1 MN119462.1
Psalidodon fasciatus UFRGS19135-TEC4853B/LBPV-68322 Brazil MN011702.1 KY267533.1
Psalidodon scabripinnis MZUFV 4456-CT2773/ LBPV-8982 Brazil MN011705.1 KY267728
Psalidodon xiru UFRGS18438-TEC3831 Brazil MN011706.1 MN119472

Phylogenetic reconstruction was conducted using the ‘A la Carte’ workflow integrated in NGPhylogeny.fr [50]. Sequences were aligned with MAFFT [51] and the resulting alignment was optimized using TrimAl [52] to remove poorly aligned regions and gaps. The best-fit evolutionary model was determined using IQ-TREE [53], which identified TIM2e+I + R2 as the optimal model for the dataset based on the Bayesian Information Criterion (BIC). Bayesian Inference was performed in MrBayes v3.2 [54] implementing as selected evolutionary model, a General Time Reversible (GTR) model with a proportion of invariant sites and Gamma-distributed rate variation (+I + G; nst = 6, rates = invgamma). The Metropolis-coupled Markov Chain Monte Carlo analysis consisted of two independent runs (nrun = 2), each utilizing four chains (one cold and three heated), for 2,000,000 generations. To ensure scientific reproducibility, the analysis was executed with fixed starting seeds (Seed = 5, Swapseed = 5). Parameters and trees were sampled every 500 generations, and a 25% burn-in fraction was applied, discarding the initial 500,000 generations. Convergence and stationary distributions were assessed using Tracer v1.7.2 [55], ensuring that all parameters reached an Effective Sample Size (ESS) greater than 200. The consensus tree was rooted using Jupiaba polylepis as the outgroup and visualized using Newick Display [56] and iTOL [57].

Geometric morphometrics

A total of 138 specimens were collected during the dry season. Each specimen was photographed in left lateral view (Fig 2), inside a diffuse light box, using a 12 MP Samsung digital camera, with focal length of 47 cm. Landmark digitization was conducted using the XYOM v. 3.0 application [58] (https://xyom.io/), marking on each image, eight type I landmarks (juxtaposition of tissues) and one type II landmark (tip of snout; [59]). The digitization process was repeated twice to ensure precision, and a Generalized Procrustes Analysis [60] was applied to align landmark coordinates (S2 Table), removing variation due to size, rotation, and position [61]. Body shape variables (partial warps and uniform components) were analyzed using linear discriminant analysis, implemented with the R packages MASS [62] for analysis, and ggplot2 [63] for visualization. Additionally, a classification approach based on cross-validation was applied using the R package caret [64] to evaluate model performance. The statistical significance of Euclidean distances to explore differences among genetic groups was assessed through 1,000 permutations using CLIC software [58]. Additionally, a multivariate regression was used to assess the effect of size on shape (allometry). When significant allometry was detected, size correction of shape was performed if the allometric slopes fitted a common model, which was evaluated using multivariate analysis of covariance (MANCOVA). A thin-plate spline graphical analysis was conducted using tpsRegr v.1.45 [65] and mean objects (residual coordinates obtained after Procrustes superimposition), generated with CLIC, to illustrate body shape deformations.

Fig 2. Landmarks selected as body shape coordinates for morphometric analysis of Astyanax species.

Fig 2

1, tip of snout; 2, dorsal-fin origin; 3, adipose-fin origin; 4-5, origin of uppermost and lowermost caudal-fin rays; 6-7, anal-fin insertion; 8, pelvic-fin origin; 9, pectoral-fin origin.

Results

STR development and polymorphism

Among the initially 42 evaluated loci, 17 were polymorphic, consistently amplified, and exhibited PIC values above 0.500 (Table 3). The number of alleles per locus ranged from 4 to 31, with an allelic range (Ra) of 105–381, and expected heterozygosity values between 0.656 and 0.965. Some of these loci exhibited a high fixation index, and 11 showed significant deviation from Hardy-Weinberg equilibrium. Due to limited sample quantity, loci Afa18, Afa36, and Afa38 were not amplified in the broader sample set. Consequently, a final suite of 14 loci was selected for subsequent population genetic analyses.

Table 3. Characteristics of 17 loci isolated from Astyanax sp.

Locus Forward sequence 5´-3´ Reverse sequence 5´-3´ Motif Na Ra HO HE F HWE PIC
Afa01 GCCTTGCCAGCCCGCTCACCCACCTCTATTGTGACC TCATTAGAGCATAAATTGTACAAAGACC ATT 17 208-307 0.428 0.927 0.367 0.000 0.921
Afa03 GCCTTGCCAGCCCGCTTTCATATAATTGTTGAATGCCTGG TGCCCTATGAAAATAGCTGCC ATCT 25 193-381 0.565 0.965 0.260 0.000 0.962
Afa08 GCCTTGCCAGCCCGCTGGAAGTGTGGACATTTGTGG TGTCCTTCTACTTGTGTGGTTGC ATCT 26 124-288 0.508 0.965 0.309 0.000 0.962
Afa23 CGGAGAGCCGAGAGGTGTCTGCTCCCAGTACCACACC GAAGACTGGAACCACAATCGC ATCT 29 177-329 0.919 0.952 0.017 0.114 0.948
Afa26 CAGGACCAGGCTACCGTGGATACACCTCCATGCCTCAGC CCCCTTGTGTTAGGATTGGC ATT 18 119-212 0.723 0.931 0.126 0.042 0.925
Afa27 CAGGACCAGGCTACCGTGCCCACATGAGAGAAAACCACC TCTGTTGTGGTGAGTGTGCG ATT 12 194-239 0.516 0.863 0.243 0.000 0.847
Afa29 CAGGACCAGGCTACCGTGCCACCTGTTGGCTGAAAACC CATGCAATGTGACCAGGACC ATCT 31 163-339 0.917 0.965 0.025 0.125 0.962
Afa34 GCCTTGCCAGCCCGCTGGGAAATGAAGCTGAAAACG CACTGAACAGTGCCACTCGC TGC 7 257-284 0.759 0.758 −0.007 0.020 0.722
Afa35 GCCTTGCCAGCCCGCTCAGGATGAGGAGACCCAGG TGTCCTTCAGCTTCACCTCG ATC 18 144-210 0.700 0.905 0.128 0.000 0.896
Afa37 GCCTTGCCAGCCCGCCAGTCGTGGCCTAACAGTCG GAGATCATCATGTTGTGCCG ATC 14 105-150 0.783 0.867 0.050 0.043 0.851
Afa39 GCCTCCCTCGCGCCAGGTCTGCTTGTTCCTCCAGC TCACACTGGTCAGCCATTCC ATC 10 122-221 0.608 0.845 0.164 0.000 0.825
Afa40 GCCTCCCTCGCGCCATGGTACACACAGCGTAATGGG GAATCATGCTAGCTCTGTAAATTGC TCC 7 130-169 0.736 0.760 0.018 0.394 0.738
Afa41 GCCTCCCTCGCGCCATTGCACTCTCAATACATCGGC AAGCGTCCCTCTACACAGGC TGC 5 262-289 0.481 0.656 0.153 0.008 0.609
Afa42 GCCTCCCTCGCGCCAAAGGGAGCATTCAGAGAAGG CATATCGTCATATTGCCCAGC TGC 12 144-186 0.716 0.797 0.054 0.047 0.770
Afa18 CGGAGAGCCGAGAGGTGGAAGGGCTGTGTTCCTGTCC AGACCATGTACCACCAATGACC ATTAC 4 298-313 0.158 0.735 0.785 0.000 0.686
Afa36 GCCTTGCCAGCCCGCCCGATCTGTCTATCCGGAGG CTGATTCTCCTCCACGGTGC TCC 5 130-142 0.650 0.703 0.075 0.161 0.653
Afa38 GCCTCCCTCGCGCCAGCATGAATCATTGCACCTAGC GGTGCCTCTGTGCATGTAGC ATC 8 151-175 0.900 0.763 −0.180 0.982 0.730

Na: average number of alleles, Ra: allelic range, HO: observed heterozygosity, HE: expected heterozygosity, HWE: p-value of the Hardy-Weinberg equilibrium test, PIC: polymorphic information content. Bold values are significant in HWE. Universal Primers. A: GCCTCCCTCGCGCCA, B: GCCTTGCCAGCCCGC, D: CGGAGAGCCGAGAGGTG [36].

Population genetics analysis

The Bayesian clustering analysis (K = 2) identified two distinct genetic stocks, hereafter referred to as Asp1 and Asp2 (Fig 3; S3 Table). Asp1 was the predominant stock in sectors S1–S4 and PHI, whereas Asp2 prevailed in the downstream sections S5, S6, and S7/S8.

Fig 3. Histogram of genetic co-ancestry for K = 2 (A) and K = 3 (B) populations.

Fig 3

Each vertical bar represents an individual, with color indicating the membership probability for each genetic stock (color). The K = 2 model was supported by ΔK method, while K = 3 was suggested by the MedMeaK, MaxMeaK, MedMedK and MaxMedK estimators. In both plots, blue and orange represent Stock 1 (Asp1) and Stock2 (Asp2), respectively.

Genetic differentiation was further supported by the AMOVA [F´ST (7, 647) = 0.073, P = 0.001], pairwise structure indices (Table 4), and the DAPC (Fig 4), which showed a clear separation between downstream sectors (S5-S8) and both upstream (S1 and PHI) and dam-proximate sectors (S2 and S3). Furthermore, differentiation was higher and consistently significant across both estimators (F´ST > 12% and DEST > 8%) when comparing the upstream and dam-proximate sectors (S1, PHI, S2, and S3) with the most downstream sites (S5, S6 and S7/S8).

Table 4. Pairwise indices of genetic structure of Astyanax sp.

S1 PHI S2 S3 S4 S5 S6 S7/S8
S1 −0.005 0.004 0.030 0.094 0.100 0.140 0.146
PHI −0.005 −0.006 0.000 0.042 0.082 0.135 0.137
S2 −0.007 0.005 0.022 0.084 0.085 0.129 0.136
S3 0.006 0.048 0.034 0.075 0.072 0.141 0.166
S4 0.053 0.114 0.096 0.088 0.054 0.060 0.112
S5 0.138 0.146 0.122 0.134 0.095 0.004 0.015
S6 0.157 0.156 0.141 0.174 0.069 0.008 −0.013
S7/S8 0.165 0.165 0.150 0.195 0.123 0.011 −0.014

F´ST below and DEST above. Significant values in bold.

Fig 4. Discriminant analysis of principal components of samples of Astyanax sp.

Fig 4

Across the eight evaluated sectors (Table 5), Astyanax sp. exhibited comparable levels of genetic diversity (Ar: 7.7–8.7; HO: 0.549–0.694; HE: 0.827–0.855). However, a generalized heterozygote deficit was observed, with significant inbreeding coefficients (FIS > 0.10) that were relatively higher in downstream areas. Consistent with these sector-wide patterns, the downstream stock (Asp2) displayed a higher inbreeding coefficient than its upstream counterpart, despite maintaining similar overall levels of genetic diversity.

Table 5. Genetic diversity and inbreeding coefficient in samples of Astyanax sp.

Sample N Na Ar HO HE FIS P-FIS HWE
S1 59 15.7 8.1 0.689 0.835 0.160 0.000 0.000
PHI 96 17.3 8.3 0.658 0.836 0.202 0.000 0.000
S2 61 16.3 8.2 0.664 0.827 0.175 0.000 0.000
S3 19 10.8 8.0 0.694 0.842 0.148 0.000 0.000
S4 9 7.6 7.7 0.637 0.843 0.222 0.000 0.000
S5 25 13.1 8.7 0.581 0.855 0.263 0.000 0.000
S6 23 12.4 8.4 0.602 0.844 0.260 0.000 0.000
S7/S8 32 13.0 8.4 0.549 0.845 0.305 0.000 0.000
Asp1 245 21.4 17.2 0.692 0.859 0.176 0.000 0.000
Asp2 79 17.3 16.8 0.587 0.869 0.274 0.000 0.000
Global 324 23.3 8.7 0.668 0.868 0.205 0.000 0.000

N: sample size, Na: average number of alleles, Ar: allelic richness, HO: observed heterozygosity, HE: expected heterozygosity, FIS: inbreeding coefficient, P-FIS: p-value of the inbreeding coefficient, HWE: p-value of the Hardy-Weinberg equilibrium test. Bold values are significant. Asp1: Stock 1; Asp2: Stock2.

Evidence of recent bottleneck events was observed across all sectors and stocks, with significant results obtained from both estimation methods in at least one of the three mutational models (Table 6). Successful estimations of effective population size (Ne) were limited; however, values exceeding 600 were recorded for sectors in the vicinity of the dam. The overall population displayed an Ne estimate surpassing 1000, with a 95% confidence interval ranging from 850 to 3150.

Table 6. Bottleneck and effective population size estimations of Astyanax sp.

Sample N M ratio IAM TPM SMM Ne IC
S1 59 0.254 0.000 0.003 0.852 668.5 248.7-inf
PHI 96 0.270 0.000 0.015 0.966 2240 536.3-inf
S2 61 0.277 0.000 0.039 0.988 1138.9 405.2-inf
S3 19 0.221 0.000 0.000 0.729 inf 100.7-inf
S4 9 0.213 0.000 0.001 0.077 inf 32.5-inf
S5 25 0.236 0.000 0.002 0.108 inf 120-inf
S6 23 0.249 0.000 0.010 0.687 inf 144.6-inf
S7/S8 32 0.267 0.000 0.000 0.195 inf 166.2-inf
Asp1 245 0.277 0.000 0.024 1.000 inf 2093.4-inf
Asp2 79 0.257 0.000 0.000 0.380 inf 2050.6-inf
Global 324 0.280 0.000 0.012 0.997 1364.0 850.8-3150.1

N: sample size, IAM, TPM, and SMM: p-values from the method used by BOTTLENECK v. 1.2.02 [43] for the three mutational models, M: index proportion between number of alleles and allelic range, indicating recent bottleneck events when less than 0.68 [44], Ne: estimated effective population size, using the linkage disequilibrium method, IC: Jackknife confidence intervals. Inf: infinite estimation. Asp1: Stock 1; Asp2: Stock2.

Phylogenetics analysis

The phylogenetic tree reveals two well-supported divergent clades encompassing the samples from the middle and lower Cauca River (Fig 5). Lineage 1 (blue clade) clustered samples corresponding to Asp1 (Fig 3), alongside sequences of Astyanax microlepis and A. viejita. Conversely, Lineage 2 (orange clade) grouped samples corresponding to Asp2 (Fig 3) with samples of Astyanax sp. from the Magdalena River. Both clades were distinct from all other reference sequences. Furthermore, previous taxonomic assignment to Psalidodon fasciatus is unequivocally dismissed, as Psalidodon samples occupy a distinct phylogenetic position.

Fig 5. Bayesian phylogenetic tree based on concatenated mitochondrial (COI) and nuclear (rag2) gene sequences, illustrating the relationships of Astyanax sp. from the Cauca River.

Fig 5

Blue and orange clades correspond to stocks Asp1 and Asp2, respectively, as identified in the genetic structure analyses (Fig 3). The purple clade represents A. microlepis collected from its type locality in the upper Cauca River. The analysis incorporates GenBank sequences of A. viejita [4] from the Lake Maracaibo basin and other congeners (Table 2). Members of the genera Astyanacinus, Carlana, Ctenobrycon, Jupiaba, Oligosarcus, Parastremma, and Psalidodon were utilized as outgroups.

Geometric morphometric analyses

Linear discriminant analysis revealed clear morphological differentiation among three analyzed groups of Astyanax, based on body shape variables (Fig 6). The first discriminant function accounted for 58.12% of the total variance, separating A. microlepis (red triangles) from the other groups. The second discriminant function accounted for 41.88% of the variance, separating Astyanax sp. 1 (Asp1; blue squares) from Astyanax sp. 2 (Asp2; orange circles).

Fig 6. Linear discriminant analysis plot showing morphological differentiation among three Astyanax groups, based on body shape variables (partial warps and uniform components).

Fig 6

The first two linear discriminants (LD1 and LD2) explain 58.12% and 41.88% of the total variation, respectively. Red triangles: Astyanax microlepis; blue squares: Astyanax sp. 1 (Asp1); orange circles: Astyanax sp. 2 (Asp2). Thin-plate spline deformation grids reflect the relative deformation from the consensus shape, highlighting intergroup variation.

Thin-plate spline deformation grids based on mean shapes revealed distinct morphological patterns among groups (Fig 7). Astyanax microlepis exhibited a more robust body profile, Asp1 displayed an intermediate and slightly deeper body shape, while Asp2 was characterized by a more streamlined morphology. Specifically, Asp1 exhibited a shorter head than Asp2, a more posterior position of the adipose fin, and a more ventral position of both anal-fin insertion and pelvic-fin origin.

Fig 7. Body shape average of genetic groups of Astyanax sp. after generalized Procrustes analysis.

Fig 7

Morphological differences among groups were supported by both allometric and non-allometric components of body shape variation, quantified using Euclidean distances and tested for significance through 1,000 permutations (Table 7).

Table 7. Euclidean distances uncorrected (ED) and size-corrected (cED), along with their statistical significance (P), for body shape differences among Astyanax groups.

Comparison ED P(ED) cED P(cED)
Astyanax microlepis vs. Astyanax sp. 1 (Asp1) 0.133 0.000 0.133 0.000
Astyanax microlepis vs. Astyanax sp. 2 (Asp2) 0.144 0.000 0.143 0.000
Asp1 vs. Asp2 0.027 0.002 0.025 0.000

The classification approach, based on cross-validation, showed high classification accuracy among the three groups. Astyanax microlepis specimens were correctly classified in 100% of cases (8/8), Asp1 in 98.85% (86/87), and Asp2 in 88.37% (38/43). The overall classification success rate was 95.65%, indicating high morphological differentiation among groups (Table 8).

Table 8. Cross-validation classification results, based on body shape variables among Astyanax groups.

A. microlepis Asp1 Asp2 %
Astyanax microlepis 8 0 0 100
Astyanax sp. 1 (Asp1) 0 86 1 98.85
Astyanax sp. 2 (Asp2) 0 5 38 88.37
Total 95.65

Discussion

Neotropical freshwater fish evolution reflects a complex interplay between contemporary demographic processes and deep-time cladogenesis. In this study, we integrated newly developed microsatellite loci to disentangle these scales in Astyanax sp. from the Cauca River. Although microsatellites are established tools for testing microevolutionary hypotheses [35,66,67], this work represents only the second instance in Colombia where species-specific markers have been successfully developed for this group, following the previous effort on Ctenobrycon caucanus (formerly Astyanax caucanus) [15]. The high-resolution of these new loci enabled the detection of fine-scale genetic discontinuities in the middle and lower sections of the basin, and provided highly informative baselines for monitoring the genetic health of Astyanax populations. This is particularly relevant in sectors impacted by the Ituango dam, where microevolutionary forces are actively shaping the genomic landscape.

Genetic diversity in terms of alleles and expected heterozygosity was similar and high between both genetic stocks, compared to other Neotropical characiforms (Na: 10.1, HE: 0.675; [68]) and cis-Andean congeners (e.g., Astyanax scabripinnis) [12]. Nonetheless, both genetic stocks showed high inbreeding levels, particularly higher in Asp2 from the lower section of the river. These levels of genetic diversity and inbreeding were comparable to those reported for Ctenobrycon caucanus (HE: 0.832–0.840; FIS: 0.307–0.351; [15]), another sympatric species in the Cauca River, and to Central American congeners such as A. aeneus and A. caballeroi [14].

Although much is still unknown about the life cycle of Acestrorhamphidae species from the Magdalena basin, similar genetic features among coinhabiting species, like Astyanax sp. and C. caucanus, such as inbreeding, genetic diversity, and bottleneck events (see [69]), may reflect a shared biogeographic history, coupled with as-yet-unknown intrinsic biological factors of their life cycle.

Despite the observed genetic evidence indicating bottleneck events in the samples analyzed, the estimated effective population size for Asp1 was high, consistent with reports for other species of the Magdalena basin [69]. This is also congruent with abundant populations [70–72], as observed in Astyanax sp. and A. microlepis, reported to be the most common species, in terms of abundance and biomass in the basin, even in dammed environments [9]. Such demographic robustness suggests that while these populations experience historical or contemporary fluctuations, they maintain large reproductive pools capable of preserving high levels of genetic variation.

The implications of these population-level findings extend beyond contemporary demographics. To determine whether the Asp1 and Asp2 genetic stocks represent incipient speciation or established evolutionary lineages, we bridged the gap between micro- and macroevolutionary scales by integrating a dual-gene phylogenetic approach (COI and rag2) with geometric morphometrics. This framework allowed us to assess the taxonomic congruence of the clusters detected by microsatellites in a broader evolutionary context, providing a robust characterization of the diversity within trans-Andean Astyanax. Collectively, these independent lines of evidence are essential for a more comprehensive understanding of the complex biodiversity of trans-Andean ichthyofauna.

Such integration is critical as taxonomic uncertainties at the species level, together with the non-monophyletic condition defining the sensu lato concept of Astyanax (still in use), have led to the conspicuous proliferation of samples identified only to the genus level in ichthyological collections [4,5]. This has also been the case for Astyanax sp. from the Magdalena basin in Colombia. This species had traditionally been identified as Astyanax fasciatus [7] until this nominal species was reallocated to the recently resurrected Psalidodon. Species currently assigned to Psalidodon are geographically restricted to South American river basins, including the Rio São Francisco (type locality of P. fasciatus) and the Paraná-Paraguay basin [2,5]. This taxonomic uncertainty of the Magdalena species raises concerns for its populations from the Cauca River, given their trophic importance into the local fish assemblages, reports of increasing human consumption, and environmental threats in the basin, by pollution of aquatic habitats and by habitat fragmentation due to the Ituango dam [9,33,73].

Phylogenetic analyses showed that the two genetic stocks identified by microsatellites also fall into two distinct lineages strongly supported using both mitochondrial and nuclear genes. Lineage 1 consisted of samples from Asp1, but surprisingly, this lineage also encompasses samples of A. microlepis (from its type locality, in the upper basin of the Cauca River), and A. viejita (from the Maracaibo Lake basin).

Astyanax microlepis has been reported throughout the Cauca River [10,74] and was recovered as sister to the clades A. bimaculatus and A. argentatus [5]. Conversely, sequences of Astyanax viejita are exclusive from the Maracaibo Lake basin in Venezuela [3], with no previous reports of its presence in Colombia [6]. Lineage 2 comprised samples from Asp2, including sequences of Astyanax sp. collected in the main channel of the middle section of the Magdalena River.

Despite genetic similarity between Astyanax microlepis and Asp1 (based at least on partial cox1 sequences), results of the linear discriminant analysis revealed clear morphological differentiation between both species. Sympatric divergence in Astyanax has been documented in the Nicaraguan lakes Managua [comprising the deep-bodied A. nasutus Meek, 1907 and A. nicaraguensis Eigenmann & Ogle, 1907, and the elongate A. bransfordii (Gill, 1877)] and Nicaragua (where A. nicaraguensis and A. bransfordii also co-occur). In both lakes, these species exhibit differences in premaxilla shape, in addition to differences in body shape. Such variations correlate strongly with trophic ecology, suggesting adaptive divergence [22,71]. Similar findings have been reported for A. aeneus and A. caballeroi in Lake Catemaco, Mexico [14,19].

This discordance between phenotypic and genotypic variation can be explained by some non-mutually exclusive hypotheses. One possible explanation is that morphotypes are undergoing incipient speciation. In this scenario, the lack of widespread genetic differentiation is an expected consequence of recent divergence, which leads to incomplete sorting of ancestral lineages [75–77]. Consistent with this interpretation, low mitochondrial divergence based on COI barcodes has been reported among closely related lineages of Astyanax, a pattern that may reflect relatively recent evolutionary radiation and the incomplete sorting of mitochondrial lineages [17]. Furthermore, a divergence-with-gene-flow model may explain how strong selection on a few “genomic islands” can still create distinct phenotypes under these conditions [77,78]. Our results are concordant with this model, which is supported by examples in related species like A. aeneus and A. caballeroi that maintain distinctiveness amid significant admixture [14].

The discordance observed between phenotypic and mitochondrial data for A. microlepis and Asp1 can be explained by a scenario of allopatric divergence followed by secondary contact. This evolutionary model has been previously invoked to explain the lack of correspondence between pronounced morphological divergence and genetic structure in sympatric Astyanax morphotypes [19]. In such cases, the maintenance of distinct phenotypes despite gene flow depends on the strength of natural and sexual selection, as well as the robustness of reproductive isolating barriers [19,79]. Under this scenario, our findings suggest a process of unidirectional introgression, where recent hybridization has eroded the molecular signals of previous isolation at the organellar level. Similar patterns of secondary contact and subsequent genetic exchange have been documented in other Neotropical contexts; for instance, the complex hydrological history of the San Juan River basin seems to reflect secondary contact between deep- and elongated-bodied Astyanax morphs [22], while significant introgression has been reported in Herichthys, following recent contact between divergent lineages [80]. Taken together, these precedents suggest that the phenotypic integrity of A. microlepis and Asp1 is likely maintained by strong divergent selection, even if their mitochondrial lineages have been homogenized. However, as mitochondrial DNA represents only a single maternal locus, further research using high-resolution genomic tools is required to confirm the extent, directionality, and nuclear impact of this gene flow.

A third possibility is that these morphotypes represent a case of stable polymorphism within a single species. Under this model, divergent morphs develop from a single gene pool, where the developmental trajectory is maintained by balancing selection or frequency-dependent mechanisms rather than a transitional phase towards speciation [80–83]. This scenario has been strongly suggested for other Astyanax populations, where marked morphological divergence occurs in the absence of genetic structure, such as in Lake Catemaco [14] and the San Juan River basin [22]. Similar examples of stable trophic polymorphism include the cichlid Herichthys minckleyi [80] and the mouth asymmetry in Perissodus microlepis [84].

Closely related to this is the hypothesis of phenotypic plasticity, where a single genotype produces alternative phenotypes in response to environmental cues. In Neotropical fishes, plasticity is frequently invoked to explain ecomorphological divergence in the absence of genetic differentiation. For instance, some authors suggested that the extreme trophic morphotypes in Mesoamerican Astyanax (formerly Bramocharax) are plastic expressions within a single lineage [17]. Similarly, the body shape in Astyanax and Psalidodon has been shown to be directly influenced by lentic-lotic gradients of their habitats [23].

However, both hypotheses (stable polymorphism and phenotypic plasticity) are difficult to reconcile with the geographical and ecological patterns observed in the species of our study. First, geographic distributions are discordant: while Asp1 is widespread throughout the Magdalena and Cauca river drainages, A. microlepis is notably absent in the Magdalena River [6,74]. If these forms were merely plastic responses or a localized polymorphism, similar phenotypic ranges would be expected in the whole Magdalena basin. Second, and most importantly, both phenotypes occur syntopically across all sampled habitats in the Cauca River (including lotic, lentic, and artificial reservoir environments; [74]; this study). The fact that A. microlepis and Asp1 maintain their distinct morphologies, despite sharing the same range of habitats suggests a significant heritable component, rather than purely environmentally induced morphs.

In summary, while the mitochondrial genome shows lack of differentiation (potentially due to recent introgression or a selective sweep), the persistence of these phenotypes in syntopy points toward a stable evolutionary divergence. Therefore, A. microlepis and Asp1 likely represent separate evolutionary lineages with divergence occurring at the nuclear level, a pattern that requires confirmation through high-resolution genomic tools to fully unravel the history of this complex group.

Conversely, the more genetically divergent pair of Asp1 and Asp2 displayed greater overall morphological similarity. Despite their general resemblance, our analysis detected fine-scale yet significant differences, particularly in head length, position of pectoral and adipose fins, and displacement of the origin of the dorsal and anal-fins. This phenomenon, where lineages diverge genetically while their morphology remains constrained, points toward non-mutually exclusive evolutionary mechanisms.

An explanation for the conserved morphology in the face of genetic drift is the action of strong stabilizing selection, coupled with niche conservatism [85]. If both lineages inhabit similar ecological contexts, as their sympatric distribution in the Cauca River basin suggests, any significant deviation from an optimal, time-tested body plan would likely be disadvantageous and selected against. Consequently, while neutral genetic markers accumulate differences over time, functional morphology of organisms remains evolutionarily conserved by selection. This process results in the formation of cryptic species, which are genetically distinct but physically almost identical, a pattern increasingly uncovered in diverse taxonomic groups, including Neotropical freshwater fishes (e.g., [86–88]).

Alternatively, the subtle yet significant differences observed in head profile and relative position of fin insertions between Asp1 and Asp2, may reflect divergent evolutionary trajectories resulting from their independent histories, rather than specific adaptations to micro-niches within their shared habitat. Common inherited genetic architecture may impose developmental limitations to respond to selective pressures similarly [89]. Therefore, the morphological similarity between these stocks suggests a conserved body plan, potentially maintained by stabilizing selection or representing a symplesiomorphic condition within the clade. Distinguishing between these scenarios (the retention of ancestral traits [90] versus parallel evolution toward a common optimum [91]) will require broader morphometric analyses. Integrating additional species from the same clade into a phylomorphospace framework would clarify whether this shared morphology is a derived convergence or reflects the ancestral pattern of the group.

In conclusion, integrated molecular and morphometric approaches provide compelling evidence for the existence of two distinct evolutionary lineages within Astyanax sp. in the Cauca River. Additionally, the grouping of A. microlepis, A. viejita, and Asp1 into a single mitochondrial lineage, despite their differing geographic distribution and morphological distinctness, introduces a novel hypothesis regarding the taxonomic status and evolutionary history of these species. This study not only challenges traditional taxonomic boundaries but also provides a crucial molecular foundation for future systematic revisions. Ultimately, recognizing these lineages is essential for the design of effective management and conservation strategies, aimed at preserving the ichthyofaunal genetic diversity in the Magdalena and Maracaibo basins.

Supporting information

S1 Table. Microsatellite loci and primer pairs developed and tested for Astyanax sp. in this study.

Universal Primers. A: GCCTCCCTCGCGCCA, B: GCCTTGCCAGCCCGC, D: CGGAGAGCCGAGAGGTG [36].

(DOCX)

pone.0347004.s001.docx (19.7KB, docx)
S2 Table. Data matrix for the geometric morphometric analysis of Astyanax species.

The table provides the unique specimen identifier (Sample ID), the assigned genetic lineage or group (Genetic stock), and the two-dimensional raw coordinates (x, y) derived from the anatomical landmarks digitized for body shape evaluation.

(XLSX)

pone.0347004.s002.xlsx (42.4KB, xlsx)
S3 Table. Multilocus genotypes of 14 microsatellite loci for Astyanax sp.

The first row contains summary metadata: number of loci, individuals, populations (genetic stocks), and sample sizes. The third row provides individual identifiers (Sample ID), sampling sections (genetic stocks), and locus-specific information (name and repeat motif).

(XLSX)

pone.0347004.s003.xlsx (59.6KB, xlsx)

Data Availability

All relevant data are within the manuscript and its Supporting Information files. All DNA sequences generated during this study have been deposited in GenBank under the accession numbers OR992015–OR992035 for rag2 and OR981620–OR064739 for COI (see Table 3 for details).

Funding Statement

This study was supported by a grant awarded within the framework of the project ‘Genetic Variability of a Fish Bank from the Middle and Lower Sections of the Cauca River’ (CT2019-000661), funded by Empresas Públicas de Medellín and Universidad Nacional de Colombia, Medellín Campus. The funders had no role in the study design, data collection and analysis, decision to publish, or preparation of the manuscript. No additional external funding was received for this study.

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Decision Letter 0

Caio Nogueira

22 Jun 2026

Dear Dr. Márquez,

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The manuscript was evaluated by two expert reviewers, both of whom recognized the relevance of the research question, the robustness of the methodological approaches employed, and the overall quality of the results presented. Both reviewers considered the study to be an important contribution to the understanding of cryptic diversity and diversification processes within Astyanax, one of the most taxonomically challenging groups among Neotropical fishes.

After carefully considering the reviewers’ comments and conducting my own evaluation of the manuscript, I believe that the study has sufficient scientific merit for publication. However, before a final decision can be made, I ask that the authors address the few comments and suggestions provided by the reviewers.

Therefore, the editorial decision for this manuscript is Minor Revision. I kindly request that the authors submit a revised version of the manuscript together with a detailed response letter explaining how each reviewer comment has been addressed.

I congratulate the authors on their work and look forward to receiving the revised version of the manuscript.

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Reviewers' comments:

Reviewer's Responses to Questions

Comments to the Author

1. Is the manuscript technically sound, and do the data support the conclusions?

Reviewer #1: Yes

Reviewer #2: Yes

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2. Has the statistical analysis been performed appropriately and rigorously? -->?>

Reviewer #1: Yes

Reviewer #2: Yes

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3. Have the authors made all data underlying the findings in their manuscript fully available??>

The PLOS Data policy

Reviewer #1: Yes

Reviewer #2: Yes

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4. Is the manuscript presented in an intelligible fashion and written in standard English??>

Reviewer #1: Yes

Reviewer #2: Yes

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Reviewer #1: The manuscript “Cryptic diversity in Astyanax (Characiformes: Acestrorhamphidae) from the Magdalena basin, Colombia: Insights from molecular and morphometric evidence” from Márquez et al. designed and evaluated a set of microsatellite loci to assess genetic diversity and population structure of Astyanax sp. in the middle and lower sections of the Cauca River. Additionally, COI and rag2 sequences were compared within a broad phylogenetic framework, to determine whether groups potentially identified through microsatellites correspond to divergent lineages within the genus, and additionally geometric morphometric analyses were conducted to investigate potential drivers of diversification in Astyanax. The MS by Márquez et al. presents the conditions and quality of literature review and adjusted the scope of this journal. Science is good and the MS is competently presented. The theoretical grounding as well as the proposed methodology are relevant and appropriate. I have made a few corrections throughout the text errors (pointed out in the attached document) that do not depreciate anywhere the results and discussion. In my opinion, the paper is worthily and should be accepted after adjustments.

In relation to the mitochondrial (COI) similarity between A. microlepis and Asp1, I suggest to the authors include in discussion this point of view/possibility. This would bring more robustness to their results.

Barcoding analyses for species identification have been widely used with effective results in several fish species; however, it does not always bring concise results, especially in morphologically cryptic species and complex groups like Astyanax and Psalidodon. Taxonomic uncertainties may result from a combination of aspects such as rapid speciation, species with a wide geographic distribution, lack of descriptions of local morphotypes, and inadequate phylogenetic analyses. Low genetic diversity using DNA barcoding (COI sequences) in Astyanax and Psalidodon (formerly referred to as Astyanax) may be the result of the recent evolutionary process of radiation. (see Ornelas-García et al. 2008 - https://doi.org/10.1186/1471-2148-8-340; Pereira et al. 2011 - https://doi.org/10.3109/19401736.2011.588213; Gavazzoni et al. 2023 - https://doi.org/10.1093/biolinnean/blac139; Gavazzoni et al. 2024 - https://doi.org/10.1089/zeb.2024.0; Silva et al 2024 - https://doi.org/10.1590/1982-0224-2024-0069)

Reviewer #2: That's an very interesting contribution, dealing with the genus Astyanax in the río Magdalena basin in Colombia. The genus Astyanax is one of the most taxonomically-challenging genera among Neotropical freshwater fishes, with a high diversity but relatively little morphological variation across Central and South America. The present MS showcases a particularly complex example, showing that phenotypic divergence in the genus may not be coupled with genetic divergence. The MS is overall very good and I have just very few suggestions to make, which follows below:

1) P. 11, l. 50: The genus does not occurs as far south as Patagonia. The southernmost record for the genus, in its present circunscripion, is the occurrence of Astyanax abramis and A. lacustris in the estuary of the Río de La Plata in Argentina. Some species formerly assigned to the genus occurs in the Pampasic area to the south, but these species were transferred to the genus Psalidodon (e.g., Psalidodon pampa).

2) P. 28, second paragraph (line 8): Change "configuration" for "shape"

3) P. 44, fig. 2: the quality of the figure is not good, it needs to be improved.

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Reviewer #1: No

Reviewer #2: No

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Attachment

Submitted filename: PONE-D-26-14913_reviewer.pdf

pone.0347004.s004.pdf (2.3MB, pdf)
PLoS One. 2026 Sep 18;21(9):e0347004. doi: 10.1371/journal.pone.0347004.r002

Author response to Decision Letter 1


4 Aug 2026

Response to the Editor and Reviewers

Manuscript ID: PONE-D-26-14913

Title: Cryptic diversity in Astyanax (Characiformes: Acestrorhamphidae) from the Magdalena basin, Colombia: Insights from molecular and morphometric evidence

Dear Dr. Nogueira,

We sincerely appreciate the careful evaluation of our manuscript and the detailed and constructive comments provided by the Academic Editor and the reviewers. We have revised the manuscript accordingly, and we believe that these changes have substantially improved its clarity and scientific quality.

Below, we provide a point-by-point response to all comments. The reviewers’ and editor’s comments are reproduced in bold, followed by our responses. All changes are indicated in the revised manuscript with track changes.

We hope that the revised manuscript is now suitable for publication in PLOS ONE.

Sincerely,

Edna J. Márquez

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Responses to the Journal Requirements

Journal Requirement 1: Please ensure that your manuscript meets PLOS ONE’s style requirements, including those for file naming.

Response: We have reviewed the manuscript and accompanying files to ensure compliance with PLOS ONE’s formatting and file-naming requirements.

Journal Requirement 2: Please review PLOS ONE’s guidelines on sharing author-generated code and ensure that the code supporting the findings is made available without restrictions.

Response: No original author-generated code was developed specifically for this study.

Journal Requirement 3: Please provide an amended Funding Statement declaring all funding or sources of support and include the statement: “There was no additional external funding received for this study.”

Response: We have amended the Funding Statement and included the complete updated wording in the cover letter, as requested. The revised Funding Statement reads:

“This study was supported by a grant framed under the project ‘Variabilidad genética de un banco de peces de los sectores medio y bajo del río Cauca’ (CT-2019-000661), funded by Empresas Públicas de Medellín and Universidad Nacional de Colombia, Sede Medellín. The funders had no role in the study design, data collection and analysis, decision to publish, or preparation of the manuscript. There was no additional external funding received for this study.”

Journal Requirement 4: Figure 1 appears to contain map or satellite imagery that may be copyrighted. Please provide permission or replace the figure with one that complies with the CC BY 4.0 license.

Response: We have replaced Figure 1 with a new map prepared in QGIS using nonproprietary and appropriately licensed or public-domain geographic data. The revised figure does not contain Google Maps, Google Earth, proprietary satellite imagery, or proprietary basemaps.

We also revised the figure legend to identify the geographic data sources as follows:

“Fig 1. Geographic location of the sampling sectors in the Cauca River basin, Colombia. Blue lines represent upstream and dam-proximate sectors (S1, PHI, S2, S3, and S4), in which genetic stock Asp1 predominated, while orange lines indicate downstream sectors (S5, S6, S7, and S8), in which genetic stock Asp2 predominated (see Results). Map layers: Colombia boundary from DANE Marco Geoestadístico Nacional (2024), available at https://geoportal.dane.gov.co/servicios/descarga-y-metadatos/datos-geoestadisticos/; inset boundaries from Natural Earth Admin 0 Countries (scale 1:10m), available at https://www.naturalearthdata.com/downloads/10m-cultural-vectors/10m-admin-0-countries/; rivers from HydroRIVERS v1.0/HydroSHEDS (15 arc-second resolution), available at https://www.hydrosheds.org/products/hydrorivers; elevation and hillshade from the HydroSHEDS void-filled DEM for South America (3 arc-second resolution), available at https://www.hydrosheds.org/hydrosheds-core-downloads; and physical background from Natural Earth II high-resolution raster data (scale 1:10m), available at https://www.naturalearthdata.com/downloads/10m-raster-data/10m-natural-earth-2/. Map created in QGIS without proprietary satellite imagery or basemaps.”

Journal Requirement 5: Please evaluate any references recommended by the reviewers and cite them only if they are relevant.

Response: We evaluated all publications recommended by the reviewers and incorporated those that were directly relevant to the interpretation and discussion of our results. The corresponding changes are described in our responses to Reviewer 1 below.

Journal Requirement 6: Please review the reference list to ensure that it is complete and correct and address any retracted publications.

Response: We carefully reviewed the reference list for completeness and accuracy. We also verified the status of the cited publications and found no retracted articles requiring removal or specific justification.

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Response to the Academic Editor

The manuscript was evaluated by two expert reviewers, both of whom recognized the relevance of the research question, the robustness of the methodological approaches employed, and the overall quality of the results presented. Before a final decision can be made, the authors should address the comments and suggestions provided by the reviewers.

Response: We thank the Academic Editor for the positive assessment of our study. We have carefully considered and addressed all comments raised by the reviewers. The manuscript has been revised accordingly, and a detailed description of each modification is provided below.

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Responses to Reviewer 1

We sincerely thank Reviewer 1 for the careful evaluation of our manuscript, the positive assessment of its scientific contribution, and the constructive suggestions.

Comment 1: In relation to the mitochondrial COI similarity between A. microlepis and Asp1, I suggest that the authors include this possibility in the Discussion. This would bring more robustness to the results. Barcoding analyses do not always provide conclusive results in morphologically cryptic species and complex groups such as Astyanax and Psalidodon. Low COI divergence may result from recent evolutionary radiation and other taxonomic and evolutionary processes.

Response: We agree with the reviewer that the mitochondrial similarity between A. microlepis and Asp1 deserves further consideration. We have expanded the Discussion to acknowledge that low COI divergence among closely related lineages may result from relatively recent evolutionary radiation and incomplete sorting of mitochondrial lineages.

The revised text reads:

“Consistent with this interpretation, low mitochondrial divergence based on COI barcodes has been reported among closely related lineages of Astyanax, a pattern that may reflect relatively recent evolutionary radiation and incomplete sorting of mitochondrial lineages [17].”

We evaluated the references suggested by the reviewer and incorporated those that were directly relevant to Astyanax and to the interpretation of our results.

Comment 2 — Line 61: "this is not the correct reference"

Response: The text has been corrected as suggested. The revised reference 8 in the list is:

“Toledo-Piza M, Baena EG, Dagosta FCP, Menezes NA, Ândrade M, Benine RC, et al. Checklist of the species of the Order Characiformes (Teleostei: Ostariophysi). Neotrop Ichthyol. 2024;22(1). doi:10.1590/1982-0224-2023-0086.”

Comment 3 — Line 71: "s in Astyanax´s, not in italic"

Response: The text has been corrected as suggested.

Comment 4: The name Psalidodon fasciatus should be used only for populations from the type locality in the São Francisco River basin.

Response: We thank the reviewer for this important clarification. We agree that the name Psalidodon fasciatus should be restricted to populations from its type locality in the São Francisco River basin.

Our original sentence was intended to describe the geographic distribution of species currently assigned to Psalidodon as a whole, rather than to suggest that P. fasciatus occurs throughout all the river basins mentioned. To remove this ambiguity, we revised the passage as follows:

“This species had traditionally been identified as Astyanax fasciatus [7] until this nominal species was reallocated to the recently resurrected genus Psalidodon. Species currently assigned to Psalidodon are geographically restricted to South American river basins, including the Rio São Francisco, the type locality of P. fasciatus, and the Paraná–Paraguay basin [2,5].”

---

Responses to Reviewer 2

We sincerely thank Reviewer 2 for the positive assessment of our manuscript and for the helpful suggestions.

Comment 1: Page 11, line 50: The genus does not occur as far south as Patagonia. The southernmost records of Astyanax, under its current circumscription, are A. abramis and A. lacustris in the Río de la Plata estuary in Argentina.

Response: We thank the reviewer for identifying this geographic inaccuracy. We have revised the sentence accordingly. It now reads:

“...extending from Texas to the Río de la Plata estuary in Argentina.”

Comment 2: Page 28, second paragraph, line 8: Change “configuration” to “shape.”

Response: We have replaced “configuration” with “shape,” as suggested.

Comment 3: Page 44, Figure 2: The quality of the figure is not good and needs to be improved.

Response: We have replaced Figure 2 with a higher-resolution version and improved the legibility of its labels and graphical elements.

Attachment

Submitted filename: Response to reviewers.docx

pone.0347004.s006.docx (20.8KB, docx)

Decision Letter 1

Caio Nogueira

1 Sep 2026

Cryptic diversity in Astyanax (Characiformes: Acestrorhamphidae) from the Magdalena basin, Colombia: Insights from molecular and morphometric evidence

PONE-D-26-14913R1

Dear Dr. Márquez,

We’re pleased to inform you that your manuscript has been judged scientifically suitable for publication and will be formally accepted for publication once it meets all outstanding technical requirements.

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Kind regards,

Caio Santos Nogueira, PhD

Academic Editor

PLOS One

Additional Editor Comments (optional):

Dear Authors,

One of the original reviewers has evaluated the revised version of the manuscript and indicated that the manuscript is now suitable for publication. Therefore, I would like to congratulate you on the work you have done and on the improvements made to the manuscript.

Reviewers' comments:

Reviewer's Responses to Questions

Comments to the Author

Reviewer #1: All comments have been addressed

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2. Is the manuscript technically sound, and do the data support the conclusions??>

Reviewer #1: Yes

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3. Has the statistical analysis been performed appropriately and rigorously? -->?>

Reviewer #1: Yes

**********

4. Have the authors made all data underlying the findings in their manuscript fully available??>

The PLOS Data policy

Reviewer #1: Yes

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5. Is the manuscript presented in an intelligible fashion and written in standard English??>

Reviewer #1: Yes

**********

Reviewer #1: All suggestions made by the reviewers have been incorporated into the text. The manuscript is now more fluid and concise. Consequently, the manuscript is ready for publication.

**********

what does this mean?). If published, this will include your full peer review and any attached files.

If you choose “no”, your identity will remain anonymous but your review may still be made public.

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Reviewer #1: No

**********

Acceptance letter

Caio Nogueira

PONE-D-26-14913R1

PLOS One

Dear Dr. Márquez,

I'm pleased to inform you that your manuscript has been deemed suitable for publication in PLOS One. Congratulations! Your manuscript is now being handed over to our production team.

At this stage, our production department will prepare your paper for publication. This includes ensuring the following:

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Academic Editor

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Associated Data

    This section collects any data citations, data availability statements, or supplementary materials included in this article.

    Supplementary Materials

    S1 Table. Microsatellite loci and primer pairs developed and tested for Astyanax sp. in this study.

    Universal Primers. A: GCCTCCCTCGCGCCA, B: GCCTTGCCAGCCCGC, D: CGGAGAGCCGAGAGGTG [36].

    (DOCX)

    pone.0347004.s001.docx (19.7KB, docx)
    S2 Table. Data matrix for the geometric morphometric analysis of Astyanax species.

    The table provides the unique specimen identifier (Sample ID), the assigned genetic lineage or group (Genetic stock), and the two-dimensional raw coordinates (x, y) derived from the anatomical landmarks digitized for body shape evaluation.

    (XLSX)

    pone.0347004.s002.xlsx (42.4KB, xlsx)
    S3 Table. Multilocus genotypes of 14 microsatellite loci for Astyanax sp.

    The first row contains summary metadata: number of loci, individuals, populations (genetic stocks), and sample sizes. The third row provides individual identifiers (Sample ID), sampling sections (genetic stocks), and locus-specific information (name and repeat motif).

    (XLSX)

    pone.0347004.s003.xlsx (59.6KB, xlsx)
    Attachment

    Submitted filename: PONE-D-26-14913_reviewer.pdf

    pone.0347004.s004.pdf (2.3MB, pdf)
    Attachment

    Submitted filename: Response to reviewers.docx

    pone.0347004.s006.docx (20.8KB, docx)

    Data Availability Statement

    All relevant data are within the manuscript and its Supporting Information files. All DNA sequences generated during this study have been deposited in GenBank under the accession numbers OR992015–OR992035 for rag2 and OR981620–OR064739 for COI (see Table 3 for details).


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