Molecular identification of Brachygenys and Haemulon species (Perciformes: Haemulidae) from the Brazilian coast

Najila Nolie Catarine Dantas Cerqueira Matheus Marcos Rotundo Alexandre Pires Marceniuk Vanessa Paes da Cruz Fausto Foresti Claudio Oliveira About the authors

Abstract

The fishes of the Haemulidae family are currently allocated to 19 genera with a worldwide distribution in the tropical and subtropical waters of the world’s oceans. Brachygenys and Haemulon are important genera of reef fish in Brazil, as they occur in large shoals, which are both ecologically and commercially valuable. This study identified the Brazilian species of the genera Brachygenys and Haemulon using DNA barcodes. While we found only a single lineage in Brachygenys chrysargyrea, Haemulon melanurum, H. parra, and H. squamipinna, more than one molecular operational taxonomic unit (MOTU) was identified in H. atlanticus, H. aurolineatum, and H. plumieri, indicating the possible existence of discrete populations or cryptic species.

Keywords:
Barriers; DNA barcoding; Marine fish; Species delimitation; Western Atlantic

Resumo

Os peixes da família Haemulidae estão atualmente distribuídos em 19 gêneros, com distribuição mundial em águas oceânicas tropicais e subtropicais. Brachygenys e Haemulon são importantes gêneros de peixes recifais do Brasil, visto que ocorrem em grandes cardumes, de valores ecológicos e comerciais. Este estudo identificou as espécies brasileiras dos gêneros Brachygenys e Haemulon usando o código de barras de DNA. Embora apenas uma única linhagem de Brachygenys chrysargyrea, Haemulon melanurum, H. parra e H. squamipinna tenha sido encontrada em nosso conjunto de dados, mais de uma unidade taxonômica operacional molecular (MOTU) foi identificada em H. atlanticus, H. aurolineatum e H. plumieri, indicando a possível existência de populações discretas ou espécies crípticas.

Palavras-chave:
Barreiras; DNA barcoding; Peixes marinhos; Delimitação de espécies; Atlântico Ocidental

INTRODUCTION

Haemulidae is composed of 136 fish species in 19 genera (Fricke et al., 2021Fricke R, Eschmeyer WN, Fong JD. Eschmeyer’s catalog of fishes: Genera/Species By Family/Subfamily [Internet]. San Francisco: California Academy of Science; 2021. Available from: https://researcharchive.calacademy.org/research/ichthyology/catalog/SpeciesByFamily.asp
https://researcharchive.calacademy.org/r...
). Two of these genera, Brachygenys Poey, 1868 and Haemulon Cuvier, 1829, are considered important groups of reef fish found in Brazil, given that they occur in large shoals, which are ecologically and commercially valuable (Rocha et al., 2008Rocha LA, Lindeman KC, Rocha CR, Lessios HA. Historical biogeography and speciation in the reef fish genus Haemulon (Teleostei: Haemulidae). Mol Phylogenet Evol. 2008; 48(3):918–28. https://doi.org/10.1016/j.ympev.2008.05.024
https://doi.org/10.1016/j.ympev.2008.05....
). The most recent review of the Haemulidae identified 21 species in the genus Haemulon (scaled-fin grunts), of which, 16 occur in the western Atlantic, while five species are found in the eastern Pacific (Tavera, Wainwright, 2019Tavera JJ, Wainwright PC. Geography of speciation affects rate of trait divergence in haemulid fishes. Proc R Soc Lond B Biol Sci. 2019; 286(1896):20182852. https://doi.org/10.1098/rspb.2018.2852
https://doi.org/10.1098/rspb.2018.2852...
; Fricke et al., 2021Fricke R, Eschmeyer WN, Fong JD. Eschmeyer’s catalog of fishes: Genera/Species By Family/Subfamily [Internet]. San Francisco: California Academy of Science; 2021. Available from: https://researcharchive.calacademy.org/research/ichthyology/catalog/SpeciesByFamily.asp
https://researcharchive.calacademy.org/r...
). Menezes et al., (2003)Menezes NA, Buckup PA, Figueiredo JL, Moura RL, editors. Catálogo das espécies de peixes marinhos do Brasil. São Paulo: Museu de Zoologia USP; 2003. recorded the occurrence of nine Haemulon species on the Brazilian coast: Haemulon aurolineatum Cuvier, 1830, H. chrysargyreum (Günther, 1859), H. melanurum (Linnaeus, 1758), H. parra (Demarest, 1823), H. plumieri (Lacepède, 1801), H. sciurus (Shaw, 1803), H. squamipinna Rocha & Rosa, 1999, H. steindachneri (Jordan & Gilbert, 1882) (currently identified as Haemulon atlanticus Carvalho, Marceniuk, Oliveira & Wosiacki, 2021 by (Carvalho et al., 2020Carvalho CO, Marceniuk AP, Oliveira C, Wosiacki WB. Integrative taxonomy of the species complex Haemulon steindachneri (Jordan and Gilbert, 1882) (Eupercaria; Haemulidae) with a description of a new species from the Western Atlantic. Zoology. 2020; 141:125782. https://doi.org/10.1016/j.zool.2020.125782
https://doi.org/10.1016/j.zool.2020.1257...
), and H. striatum (Linnaeus, 1758).

Tavera, Wainwright, (2019)Tavera JJ, Wainwright PC. Geography of speciation affects rate of trait divergence in haemulid fishes. Proc R Soc Lond B Biol Sci. 2019; 286(1896):20182852. https://doi.org/10.1098/rspb.2018.2852
https://doi.org/10.1098/rspb.2018.2852...
reassigned Haemulon chrysargyreum to the genus Brachygenys, based on morphological and molecular evidence, with the current valid name Brachygenys chrysargyrea (Günther, 1859) (Fricke et al., 2021Fricke R, Eschmeyer WN, Fong JD. Eschmeyer’s catalog of fishes: Genera/Species By Family/Subfamily [Internet]. San Francisco: California Academy of Science; 2021. Available from: https://researcharchive.calacademy.org/research/ichthyology/catalog/SpeciesByFamily.asp
https://researcharchive.calacademy.org/r...
). The genus Brachygenys (smallmouth grunts) includes only three species, Brachygenys californiensis (Steindachner, 1875) and B. jessiae (Jordan & Bollman, 1890), which are found in the eastern Pacific (Tavera, Wainwright, 2019Tavera JJ, Wainwright PC. Geography of speciation affects rate of trait divergence in haemulid fishes. Proc R Soc Lond B Biol Sci. 2019; 286(1896):20182852. https://doi.org/10.1098/rspb.2018.2852
https://doi.org/10.1098/rspb.2018.2852...
), and B. chrysargyrea which occurs in the Western Atlantic, where it is restricted to the oceanic islands of Brazil, the Fernando de Noronha and Atol das Rocas archipelagos (Rocha, Rosa, 1999Rocha LA, Rosa IL. New species of Haemulon (Teleostei: Haemulidae) from the Northeastern Brazilian coast. Copeia. 1999; 1999(2):447–52. https://doi.org/10.2307/1447491
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; Fricke et al., 2021Fricke R, Eschmeyer WN, Fong JD. Eschmeyer’s catalog of fishes: Genera/Species By Family/Subfamily [Internet]. San Francisco: California Academy of Science; 2021. Available from: https://researcharchive.calacademy.org/research/ichthyology/catalog/SpeciesByFamily.asp
https://researcharchive.calacademy.org/r...
).

The biological characteristics of the Brachygenys and Haemulon species, including their ample geographic ranges, ecological features, genetic patterns, and speciation mechanisms, has been the subject of many taxonomic, evolutionary, and phylogenetic studies (e.g., Rocha et al., 2008Rocha LA, Lindeman KC, Rocha CR, Lessios HA. Historical biogeography and speciation in the reef fish genus Haemulon (Teleostei: Haemulidae). Mol Phylogenet Evol. 2008; 48(3):918–28. https://doi.org/10.1016/j.ympev.2008.05.024
https://doi.org/10.1016/j.ympev.2008.05....
; Motta-Neto et al., 2011aMotta-Neto CC, Cioffi MB, Bertollo LAC, Molina WF. Extensive chromosomal homologies and evidence of karyotypic stasis in Atlantic grunts of the genus Haemulon (Perciformes). J Exp Mar Biol Ecol. 2011a; 401(1–2):75–79. https://doi.org/10.1016/j.jembe.2011.02.044
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, bMotta-Neto CC, Cioffi MB, Bertollo LAC, Molina WF. Molecular cytogenetic analysis of Haemulidae fish (Perciformes): Evidence of evolutionary conservation. J Exp Mar Biol Ecol. 2011b; 407(1):97–100. https://doi.org/10.1016/j.jembe.2011.07.014
https://doi.org/10.1016/j.jembe.2011.07....
; Sanciangco et al., 2011Sanciangco MD, Rocha LA, Carpenter KE. A molecular phylogeny of the grunts (Perciformes: Haemulidae) inferred using mitochondrial and nuclear genes. Zootaxa. 2011; 2966(1):37–50. https://doi.org/10.11646/zootaxa.2966.1.4
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; Liang et al., 2012Liang R, Zhuo X, Yang G, Luo D, Zhong S, Zou J. Molecular phylogenetic relationships of family Haemulidae (Perciformes: Percoidei) and the related species based on mitochondrial and nuclear genes. Mitochondrial DNA. 2012; 23(4):264–77. https://doi.org/10.3109/19401736.2012.690746
https://doi.org/10.3109/19401736.2012.69...
; Tavera et al., 2012Tavera JJ, Acero PA, Balart EF, Bernardi G. Molecular phylogeny of grunts (Teleostei, Haemulidae), with an emphasis on the ecology, evolution, and speciation history of New World species. BMC Evol Biol. 2012; 12(1):57. https://doi.org/10.1186/1471-2148-12-57
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, 2018Tavera J, Acero PA, Wainwright PC. Multilocus phylogeny, divergence times, and a major role for the benthic-to-pelagic axis in the diversification of grunts (Haemulidae). Mol Phylogenet Evol. 2018; 121:212–23. https://doi.org/10.1016/j.ympev.2017.12.032
https://doi.org/10.1016/j.ympev.2017.12....
; Bernal et al., 2017Bernal MA, Gaither MR, Simison WB, Rocha LA. Introgression and selection shaped the evolutionary history of sympatric sister-species of coral reef fishes (genus: Haemulon). Mol Ecol. 2017; 26(2):639–52. https://doi.org/10.1111/mec.13937
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; Tavera, Wainwright, 2019Tavera JJ, Wainwright PC. Geography of speciation affects rate of trait divergence in haemulid fishes. Proc R Soc Lond B Biol Sci. 2019; 286(1896):20182852. https://doi.org/10.1098/rspb.2018.2852
https://doi.org/10.1098/rspb.2018.2852...
). The formation of marine biogeographic barriers, in particular, the Isthmus of Panama, resulted in the establishment of geminal species (Jordan, 1908Jordan DS. The law of the geminate species. Am Nat. 1908; 42(494):73–80. https://doi.org/10.1086/278905
https://doi.org/10.1086/278905...
), that is, allopatric twin species in the eastern Pacific and western Atlantic oceans, as in the case of H. steindachneri from the eastern Pacific and H. atlanticus from the western Atlantic (Carvalho et al., 2020Carvalho CO, Marceniuk AP, Oliveira C, Wosiacki WB. Integrative taxonomy of the species complex Haemulon steindachneri (Jordan and Gilbert, 1882) (Eupercaria; Haemulidae) with a description of a new species from the Western Atlantic. Zoology. 2020; 141:125782. https://doi.org/10.1016/j.zool.2020.125782
https://doi.org/10.1016/j.zool.2020.1257...
).

The principal objective of this study was to identify the Brachygenys and Haemulon species from Brazil based on the DNA barcode method. We also evaluated the influence of oceanic barriers on the dispersal of the study species.

MATERIAL AND METHODS

Sample collection. Three specimens of Brachygenys chrysargyrea and 47 specimens of Haemulon (H. atlanticus = 15 specimens; H. aurolineatum = 17 specimens; H. melanurum = 4 specimens; H. parra = 5 specimens; H. plumieri = 5 specimens; and H. squamipinna = 1 specimen) were collected between 2006 and 2019 off the coasts of Brazil, between the northern extreme of the country and the southeastern state of São Paulo (Fig. 1; S1).

FIGURE 1 |
Species of the genera Haemulon and Brachygenys collected off the coast of Brazil during this study. A. Haemulon aurolineatum (16.2 cm of Total Length, TL); B. H. melanurum (18.3 cm of TL); C. H. parra (21.7 cm of TL); D. H. squamipinna (15.9 cm of TL); E. H. plumieri (23.5 cm of TL); F. H. atlanticus (16.1 cm of TL); G. Brachygenys chrysargyrea (16.0 cm of TL).

The species collected were identified based on their morphological characteristics (Lindeman, Toxey, 2002Lindeman KC, Toxey CS. Haemulidae: Grunts. In: Carpenter KE, editor. The living marine resources of the Western Central Atlantic – Volume 3: Bony fishes part 2 (Opistognathidae to Molidae), sea turtles and marine mammals. Rome: Food and Agriculture Organization of the United nations (FAO); 2002. p.1522–50.; Marceniuk et al., 2017Marceniuk AP, Caires RA, Rotundo MM, Alcântara RAK, Wosiacki WB. The ichthyofauna (Teleostei) of the Rio Caeté estuary, northeast Pará, Brazil, with a species identification key from northern Brazilian coast. Pan-Am J Aquat Sci. 2017; 12(1):31–79.). Barcode sequences of 149 specimens were obtained from the GenBank and BOLD databases (S1), and were inserted in the distribution map of the study species, in order to obtain a more ample sample of the different coastal regions of the Atlantic.

A small fragment of muscle tissue was removed from each specimen collected during this study and preserved in 95% ethanol at -20°C, before being deposited in the collection of the Fish Genetics and Biology Laboratory (Laboratório de Biologia e Genética de Peixes, LBP) at UNESP, in Botucatu, São Paulo, and the zoological collection of the Universidade Santa Cecília (AZUSC), in Santos, São Paulo (S2).

The species were sampled in accordance with Brazilian legislation, as regulated by the National Council for the Control of Animal Experimentation (CONCEA) and authorized by the Ethics Committee on the Use of Animals (CEUA) of the Biosciences Institute at UNESP through its (protocol 1057/2017).

Extraction of DNA, PCR amplification, and sequencing. The total DNA was extracted from the muscle tissue samples following the protocol proposed by Ivanova et al., (2006)Ivanova NV, Dewaard JR, Hebert PDN. An inexpensive, automation-friendly protocol for recovering high-quality DNA. Mol Ecol Notes. 2006; 6(4):998–1002. https://doi.org/10.1111/j.1471-8286.2006.01428.x
https://doi.org/10.1111/j.1471-8286.2006...
. Partial sequences of approximately 650 base pairs (bps) of the COI gene were obtained by PCR amplification using the FishF2 and FishR2 primers (Ward et al., 2005Ward RD, Zemlak TS, Innes BH, Last PR, Hebert PDN. DNA barcode Australia’s fish species. Philos Trans R Soc Lond B Biol Sci. 2005; 360(1462):1847–57. https://doi.org/10.1098/rstb.2005.1716
https://doi.org/10.1098/rstb.2005.1716...
). The PCR reactions were run in a Veriti® 96-well Thermal Cycler (Applied BiosystemsTM or Mastercycler® EPGradient, Eppendorf) using the following temperature cycle: initial denaturation at 94°C for 4 min, followed by 30 cycles of denaturation at 94°C for 30 sec, annealing at 52°C for 30 sec, and extension at 68°C for 1 min, with a final extension at 68°C for 10 min. Each PCR solution comprised of: 7.55 μl of ultrapure water (milli-Q); 1.15 μl of (10X) buffer; 0.5 μl of MgCl2 (50 mM), 0.5 μl of dNTPs (2 mM); 0.25 μl of each primer (5 mM); 0.2 μl of (5 U/μl) Taq DNA polymerase PHT (Phoneutria Biotechnologies and Services Ltda., Brazil), and 2 μl of the DNA template (50 – 100 ng/ul), for a final volume of 12.5 μl.

The amplification of the target sequence was confirmed by electrophoresis in 1% agarose gel using Blue Green Loading dye I (LGC Biotecnologia). The amplified PCR products were purified with an ExoSap-IT® (USB Corporation) solution, and the purified products were sequenced using the BigDye Terminator v3.1 Cycle Sequencing Ready Reaction kit (Applied Biosystems). This reaction solution consisted of: 3.9 μl of ultrapure water; 1.05 μl of 5X buffer; 0.7 μl of BigDye Terminator mix; 0.35 μl of the FishF2 or FishR2 primers (10 mM), and 1.0 μl of the purified PCR product (50 ng/μl). The amplification cycle was: 2 min at 96°C, and 35 cycles of 30 sec at 96°C, 15 sec at 54°C, and 4 min at 60°C. The purified PCR products were then precipitated in EDTA 125 nM/sodium acetate/alcohol, and the samples were sequenced automatically using an ABI 3130X1 Genetic Analyzer sequencer (Applied BiosystemsTM).

Data analysis. The sequences were edited and aligned using the Geneious Pro 4.8.5 software (Kearse et al., 2012Kearse M, Moir R, Wilson A, Stones-Havas S, Cheung M, Sturrock S, Buxton S, Cooper A, Markowitz S, Duran C, Thierer T, Ashton B, Meintjes P, Drummond A. Geneious basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics. 2012; 28(12):1647–49. https://doi.org/10.1093/bioinformatics/bts199
https://doi.org/10.1093/bioinformatics/b...
). The edited sequences were compared with those deposited in the National Center for Biotechnology Information (NCBI) GenBank using the BLASTn tool (Johnson et al., 2008Johnson M, Zaretskaya I, Raytselis Y, Merezhuk Y, McGinnis S, Madden TL. NCBI BLAST: A better web interface. Nucleic Acids Res. 2008; 36(Suppl. 2):W5–W9. https://doi.org/10.1093/nar/gkn201
https://doi.org/10.1093/nar/gkn201...
). The final matrix had 199 sequences, including 50 obtained in the present study and 149 extracted from GenBank (ncbi.nlm.nih.gov/genbank) or BOLD (boldsystems.org) (S1). The end alignment was exported and analyzed to generate trees in the MEGA v 7.0 software (Kumar et al., 2018Kumar S, Stecher G, Li M, Knyaz C, Tamura K. MEGA X: Molecular Evolutionary Genetics Analysis across computing platforms. Mol Biol Evol. 2018; 35(6):1547–49. https://doi.org/10.1093/molbev/msy096
https://doi.org/10.1093/molbev/msy096...
), based on the neighbor-joining (NJ) method using the Kimura -2- Parameter model (K2P) (Kimura, 1980Kimura M. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol. 1980; 16(2):111–20. https://doi.org/10.1007/BF01731581
https://doi.org/10.1007/BF01731581...
) and the maximum likelihood (ML) method with the best Tamura-Nei model (Kumar et al., 2018Kumar S, Stecher G, Li M, Knyaz C, Tamura K. MEGA X: Molecular Evolutionary Genetics Analysis across computing platforms. Mol Biol Evol. 2018; 35(6):1547–49. https://doi.org/10.1093/molbev/msy096
https://doi.org/10.1093/molbev/msy096...
) and gamma distribution (TRN+G) identified by the PartitionFinder software (Lanfear et al., 2012Lanfear R, Calcott B, Ho SYW, Guindon S. Partitionfinder: Combined selection of partitioning schemes and substitution models for phylogenetic analyses. Mol Biol Evol. 2012; 29(6):1695–701. https://doi.org/10.1093/molbev/mss020
https://doi.org/10.1093/molbev/mss020...
). All trees were tested by bootstrap, with 1000 pseudoreplicates (Felsenstein, 1985Felsenstein J. Confidence limits on phylogenies: An approach using the bootstrap. Evolution. 1985; 39(4):783–91. https://doi.org/10.1111/j.1558-5646.1985.tb00420.x
https://doi.org/10.1111/j.1558-5646.1985...
).

Species delimitation analyses. Three methods of species delimitation were used: (1) The Automatic Barcode Gap Discovery, ABGD (Puillandre et al., 2012Puillandre N, Lambert A, Brouillet S, Achaz G. ABGD, Automatic Barcode Gap Discovery for primary species delimitation. Mol Ecol. 2012; 21(8);1864–77. https://doi.org/10.1111/j.1365-294X.2011.05239.x
https://doi.org/10.1111/j.1365-294X.2011...
) which is based on a pairwise genetic distance matrix (generated in MEGA V7.0) run on the ABGD web server (https://bioinfo.mnhn.fr/abi/public/abgd/abgdweb.html) with the Kimura distance model (K2P) and other parameters at default (Pmin = 0.001; Pmax = 0.1); (2) the Bayesian Poisson Tree Process PTP (Zhang et al., 2013Zhang J, Kapli P, Pavlidis P, Stamatakis A. A general species delimitation method with applications to phylogenetic placements. Bioinformatics. 2013; 29(22):2869–76. https://doi.org/10.1093/bioinformatics/btt499
https://doi.org/10.1093/bioinformatics/b...
) run on the PTP web server (species.h-its.org/ptp), using the best Maximum Likelihood (ML) tree, 10,000 MCMC generations, and a 0.1 burn-in rate as the default settings, and (3) the general mixed Yule-coalescent GMYC (Pons et al., 2006Pons J, Barraclough TG, Gomez Zurita J, Cardoso A, Duran DP, Hazell S, Kamoun S, Sumlin WD, Vogler AP. Sequence based species delimitation for the DNA taxonomy of undescribed insects. Syst Biol. 2006; 55(4):595–609. https://doi.org/10.1080/10635150600852011
https://doi.org/10.1080/1063515060085201...
; Fujisawa, Barraclough, 2013Fujisawa T, Barraclough TG. Delimiting species using single locus data and the generalized mixed yule coalescent approach: A revised method and evaluation on simulated data sets. Syst Biol. 2013; 62(5):707–24. https://doi.org/10.1093/sysbio/syt033
https://doi.org/10.1093/sysbio/syt033...
), run on the GMYC web server (https://species.h-its.org/gmyc/).

This analysis was conducted using the ultrametric gene tree estimated from the birth-death prior and the relaxed lognormal parameters. The number of polymorphic sites, the number of haplotypes, and the haplotype (HD) and nucleotide diversity (Pi) were estimated using DnaSP v5 (Librado, Rozas, 2009Librado P, Rozas J. DnaSP v5: A software for comprehensive analysis of DNA polymorphism data. Bioinformatics. 2009; 25(11):1451–52. https://doi.org/10.1093/bioinformatics/btp187
https://doi.org/10.1093/bioinformatics/b...
), with the median-joining network being produced using the PopArt program (Leigh, Bryant, 2015Leigh JW, Bryant D. POPART: Full feature software for haplotype network construction. Methods Ecol Evol. 2015; 6(9):1110–16. https://doi.org/10.1111/2041-210X.12410
https://doi.org/10.1111/2041-210X.12410...
), for mutational analyses.

RESULTS

Barcode sequences were obtained from 50 specimens, which were complemented with 149 sequences obtained from GenBank and BOLD (S1), totaling 199 sequences in the final matrix (184 for Haemulon and 15 for Brachygenys) representing the different regions of the western Atlantic and eastern Pacific. The barcode sequences obtained here ranged in length from 440 to 558 bps. The overall mean nucleotide frequencies were 23.1% adenine, 26.6% cytosine, 19.6% guanine, and 30.6% thymine. No stop codons, deletions or insertions were found in any of the sequences.

The intraspecific genetic distances (based on the K2P model) ranged from 0.001±0.001, in both H. melanurum and H. parra, to 0.027±0.005 in H. plumieri (Tab. 1). The interspecific values ranged from 0.0746±0.0121 between H. steindachneri and H. atlanticus to 0.1645±0.0212 between B. jessiae and H. atlanticus (Tab. 1).

TABLE 1 |
Pairwise K2P genetic distances between the Brachygenys and Haemulon species (below the diagonal) and standard errors (above the diagonal). The numbers in bold type represent the intraspecific K2P genetic distances and their standard errors.

The results of the Maximum Likelihood (ML) analyses and the GMYC species delimitation method indicated the presence of 15 MOTUs in the database, while the ABGD and PTP species delimitation methods identified 13 MOTUs (Fig. 2; S3).

FIGURE 2 |
The Maximum Likelihood tree of the Haemulon and Brachygenys specimens, based on the sequences of the mitochondrial cytochrome c oxidase subunit I gene under the TRN+G model. The numbers at each branch indicate the bootstrap values (1000 pseudoreplicates) and those between parentheses are the number of specimens analyzed. The species delimitation methods were ABGD, PTP, and GMYC (see Material and Methods section).

A single MOTU was found in B. californiensis, B. chrysargyrea, B. jessiae, H. atlanticus, H. melanurum, H. parra, H. squamipinna, and H. steindachneri in all analyses. Three MOTUs were identified in H. aurolineatum based on to the PTP and ABGD approaches, while the ML and GMYC methods identified four units in the samples of this species. In H. plumieri, the PTP and ABGD approaches identified two MOTUs, while the ML and GMYC methods identified three (Fig. 2; S3). Given these results, we decided to calculate the genetic distances between these MOTUs using the K2P model (Tab. 2), as described below.

TABLE 2 |
Pairwise K2P distances between Brachygenys and Haemulon genetic lineages (below the diagonal) and standard errors (above the diagonal). The numbers in bold type represent the intraspecific K2P genetic distances. + Only one sample available. The species identified by letters correspond to the distribution of the specimens as described in the article.

The three species delimitation methods used in the present study (PTP, ABGD, and GMYC) identified only one H. atlanticus MOTU in all the samples analyzed (Fig. 2). However, the ML tree included two lineages, H. atlanticus A, with 19 specimens from the Brazilian states of Pará, Ceará, Alagoas, and São Paulo, as well as Colombia, and H. atlanticus B (5 specimens from Colombia, Guatemala, and Venezuela). The genetic distance between the H. atlanticus A and B lineages was 0.012±0.004. The comparative network analysis of H. steindachneri, H. atlanticus A, and H. atlanticus B further reinforced the presence of three groups (Fig. 3), with 30 mutations separating H. steindachneri (Pi = 0.00271; HD = 0.81667) from H. atlanticus (Pi = 0.00567; HD = 0.65217), and nine mutations between H. atlanticus A Pi = 0.00177; HD = 0.45614) and H. atlanticus B (Pi = 0.00155; HD = 0.70000).

In the case of H. aurolineatum, the ML and GMYC identified four MOTUs, denominated here as H. aurolineatum A (four specimens from Bermuda), H. aurolineatum B (one specimen from Bermuda), H. aurolineatum C (four specimens from the Gulf of Mexico), and H. aurolineatum D, with 49 specimens from Belize, Brazil, Colombia, Jamaica, Venezuela, and the Gulf of Mexico (Fig. 2; S3).

The genetic distances between the pairs of these MOTUs ranged from 0.0183±0.049 between H. aurolineatum lineages C and D to 0.1382±0.0172 between H. aurolineatum lineages A and B (Tab. 2). When the PTP and ABGD methods were applied, however, only three MOTUs were observed - H. aurolineatum A, H. aurolineatum B, and H. aurolineatum C+D (Fig. 2; S3). The genetic distances between these MOTUs were 0.1382±0.0173 between H. aurolineatum A and B, 0.1089±0.0147 between H. aurolineatum A and C+D, and 0.1059±0.0150 between H. aurolineatum B and C+D.

There were 37 mutations between H. aurolineatum A (Pi = 0.00000; HD = 0.00000) and H. aurolineatum D (Pi = 0.00389; HD = 0.72364), five between H. aurolineatum C and H. aurolineatum D (Pi = 0.00281; HD = 0.83333), and 34 mutations between H. aurolineatum B and H. aurolineatum C (Pi = 0.00000; HD = 0.00000) (Fig. 3).

FIGURE 3 |
Haplotype networks of the three Haemulon species in which multiple MOTUs were identified. The dashes represent mutational steps. The size of the circle representing each haplotype is proportional to the number of individuals with that haplotype. The black dots represent missing haplotypes. A. H. steindachneri = Haemulon steindachneri (eastern Pacific); H. atlanticus B = specimens from Colombia, Guatemala, and Venezuela; H. atlanticus A = specimens from Brazil and Colombia; B. H. aurolineatum A = specimens from Bermuda; H. aurolineatum B = specimens from Bermuda; H. aurolineatum C = specimens from the United States; H. aurolineatum D = specimens from Belize, Brazil, Colombia, Jamaica, Venezuela, and the United States; and C. H. plumieri C = specimens from Brazil and Puerto Rico; H. plumieri B = specimens from the United States; H. plumieri A = specimens from the Bahamas, Belize, Haiti, Mexico, Puerto Rico, and the United States.

The ML and GMYC analyses identified three MOTUs in H. plumieri, identified here as H. plumieri A (20 specimens from the Caribbean and Gulf of Mexico), H. plumieri B (five specimens from the Gulf of Mexico), and H. plumieri C, with 10 specimens from Brazil and the Caribbean (Fig 2; S3). The genetic distances between these MOTUs were 0.064±0.011 between H. plumieri lineages A and B, 0.048±0.010 between H. plumieri A and C, and 0.024±0.006 between H. plumieri B and C (Tab. 2). When the PTP and ABGD methods were considered, however, only two MOTUs were observed, one containing H. plumieri A+B and the other, H. plumieri C (Fig. 2; S3). The genetic distance between H. plumieri A+B and H. plumieri C was 0.052±0.009. There were 11 mutations between H. plumieri C (Pi = 0.00194; HD = 0.20000) and H. plumieri B (Pi = 0.00097; HD = 0.40000) and 19 mutations between H. plumieri C and H. plumieri A (Pi = 0.00394; HD = 0.87368) (Fig. 3).

DISCUSSION

Four of the species analyzed, B. chrysargyrea, H. melanurum, H. parra, and H. squamipinna, presented extremely low intraspecific distances, and all the different analytical approaches indicated that they represented a single MOTU. In the specific case of H. squamipinna, the evidence that the samples represented a single species was expected, given the very restricted distribution of the species off the northeastern coast of Brazil (Rocha, Rosa, 1999Rocha LA, Rosa IL. New species of Haemulon (Teleostei: Haemulidae) from the Northeastern Brazilian coast. Copeia. 1999; 1999(2):447–52. https://doi.org/10.2307/1447491
https://doi.org/10.2307/1447491...
). In the other cases, however, the species are much more amply distributed, with H. melanurum being found from southeastern Florida to northern Brazil, including the whole of the Caribbean (Menezes et al., 2003Menezes NA, Buckup PA, Figueiredo JL, Moura RL, editors. Catálogo das espécies de peixes marinhos do Brasil. São Paulo: Museu de Zoologia USP; 2003. ), while H. parra and B. chrysargyrea are distributed from southeastern Florida to southeastern Brazil (Menezes et al., 2003Menezes NA, Buckup PA, Figueiredo JL, Moura RL, editors. Catálogo das espécies de peixes marinhos do Brasil. São Paulo: Museu de Zoologia USP; 2003. ).

In all three cases, the distribution of the species straddles the potential barrier formed by the Amazon-Orinoco Plume. In addition, the southern limit of the distribution of H. parra in Brazil was originally described as being São Paulo (Menezes et al., 2003Menezes NA, Buckup PA, Figueiredo JL, Moura RL, editors. Catálogo das espécies de peixes marinhos do Brasil. São Paulo: Museu de Zoologia USP; 2003. ), and we collected samples in São Paulo during the present study, which indicates that this species also traverses the Vitória Trindade seamount chain, off the eastern coast of Brazil, which was a potential biogeographic barrier during periods of marine regression, in the Quaternary and Tertiary, as observed in other genera and species, such as Orthopristis ruber (Cuvier, 1830) (Marceniuk et al., 2019Marceniuk AP, Caires RA, Machado L, Cerqueira NNCD, Serra RRMS, Oliveira C. Redescription of Orthopristis ruber and Orthopristis scapularis (Haemulidae: Perciformes), with a hybridization zone off the Atlantic coast of South America. Zootaxa. 2019; 4576(1):109–26. https://doi.org/10.11646/zootaxa.4576.1.5
https://doi.org/10.11646/zootaxa.4576.1....
), Macrodon ancylodon (Bloch & Schneider, 1801) (Santos et al., 2006Santos S, Hrbek T, Farias IP, Schneider H, Sampaio I. Population genetic structuring of the king weakfish, Macrodon ancylodon (Sciaenidae), in the Atlantic coastal waters of South America: Deep genetic divergence without morphological change. Mol Ecol. 2006; 15(14):4361–73. https://doi.org/10.1111/j.1365-294X.2006.03108.x
https://doi.org/10.1111/j.1365-294X.2006...
), and Chaetodipterus faber (Broussonet, 1782) (Machado et al., 2017Machado LF, Damasceno JS, Bertoncini AA, Tosta VC, Farro APC, Hostim-Silva M, Oliveira C. Population genetic structure and demographic history of the spadefish, Chaetodipterus faber (Ephippidae) from Southwestern Atlantic. J Exp Mar Biol Ecol. 2017; 487:45–52. https://doi.org/10.1016/j.jembe.2016.11.005
https://doi.org/10.1016/j.jembe.2016.11....
).

Some of the haemulids from the western Atlantic have ample geographic distributions and have larvae that are able to disperse rapidly on oceanic currents, as well as the ability to migrate vertically in the water column (Majoris et al., 2019Majoris JE, Catalano KA, Scolaro D, Atema J, Buston PM. Ontogeny of larval swimming abilities in three species of coral reef fishes and a hypothesis for their impact on the spatial scale of dispersal. Mar Biol. 2019; 166(12):159. https://doi.org/10.1007/s00227-019-3605-2
https://doi.org/10.1007/s00227-019-3605-...
). These characteristics would maximize the potential for gene flow between the northern and southern populations of these species in the Western Atlantic, which would minimizing the chances of forming isolated groups (Rocha, 2003Rocha LA. Patterns of distribution and processes of speciation in Brazilian reef fishes. J Biogeogr. 2003; 30(8):1161–71. https://doi.org/10.1046/j.1365-2699.2003.00900.x
https://doi.org/10.1046/j.1365-2699.2003...
; Rocha et al., 2002Rocha LA, Bass AL, Robertson DR, Bowen BW. Adult habitat preferences, larval dispersal, and the comparative phylogeography of three Atlantic surgeonfishes (Teleostei: Acanthuridae). Mol Ecol. 2002; 11(2):243–51. https://doi.org/10.1046/j.0962-1083.2001.01431.x
https://doi.org/10.1046/j.0962-1083.2001...
, 2005Rocha LA, Robertson DR, Roman J, Bowen BW. Ecological speciation in tropical reef fishes. Proc R Soc Lond B Biol Sci. 2005; 272(1563):573–79. https://doi.org/10.1098/2004.3005
https://doi.org/10.1098/2004.3005...
, 2007Rocha LA, Craig MT, Bowen BW. Phylogeography and the conservation of reef fishes. Coral Reefs. 2007; 26(3):501–12. https://doi.org/10.1007/s00338-007-0280-4
https://doi.org/10.1007/s00338-007-0280-...
, 2008Rocha LA, Lindeman KC, Rocha CR, Lessios HA. Historical biogeography and speciation in the reef fish genus Haemulon (Teleostei: Haemulidae). Mol Phylogenet Evol. 2008; 48(3):918–28. https://doi.org/10.1016/j.ympev.2008.05.024
https://doi.org/10.1016/j.ympev.2008.05....
). The ample geographic ranges and genetic homogeneity detected here in H. melanurum, H. parra, and B. chrysargyrea may thus also be at least partially due to the swimming capabilities of these fishes.

Some Haemulon species have dispersed from the Pacific Ocean to the western Atlantic (Tavera et al., 2012Tavera JJ, Acero PA, Balart EF, Bernardi G. Molecular phylogeny of grunts (Teleostei, Haemulidae), with an emphasis on the ecology, evolution, and speciation history of New World species. BMC Evol Biol. 2012; 12(1):57. https://doi.org/10.1186/1471-2148-12-57
https://doi.org/10.1186/1471-2148-12-57...
), followed by reverse invasions during the occurrence of vicarious events and the formation of the Isthmus of Panama (Stange et al., 2018Stange M, Sánchez-Villagra MR, Salzburger W, Matschiner M. Bayesian divergence-time estimation with genome-wide single-nucleotide polymorphism data of sea catfishes (Ariidae) supports Miocene closure of the Panamanian Isthmus. Syst Biol. 2018; 67(4):681–99. https://doi.org/10.1093/sysbio/syy006
https://doi.org/10.1093/sysbio/syy006...
). These historical processes resulted in allopatric speciation, which has given rise to twin species (Jordan, 1908Jordan DS. The law of the geminate species. Am Nat. 1908; 42(494):73–80. https://doi.org/10.1086/278905
https://doi.org/10.1086/278905...
), and both sister and novel lineages (Rocha et al., 2007Rocha LA, Craig MT, Bowen BW. Phylogeography and the conservation of reef fishes. Coral Reefs. 2007; 26(3):501–12. https://doi.org/10.1007/s00338-007-0280-4
https://doi.org/10.1007/s00338-007-0280-...
; Luiz et al., 2012Luiz OJ, Madin JS, Robertson DR, Rocha LA, Wirtz P, Floeter SR. Ecological traits influencing range expansion across large oceanic dispersal barriers: Insights from tropical Atlantic reef fishes. Proc R Soc Lond B Biol Sci. 2012; 279(1730):1033–40. https://doi.org/10.1098/rspb.2011.1525
https://doi.org/10.1098/rspb.2011.1525...
; Tavera et al., 2018Tavera J, Acero PA, Wainwright PC. Multilocus phylogeny, divergence times, and a major role for the benthic-to-pelagic axis in the diversification of grunts (Haemulidae). Mol Phylogenet Evol. 2018; 121:212–23. https://doi.org/10.1016/j.ympev.2017.12.032
https://doi.org/10.1016/j.ympev.2017.12....
; Tavera, Wainwright, 2019Tavera JJ, Wainwright PC. Geography of speciation affects rate of trait divergence in haemulid fishes. Proc R Soc Lond B Biol Sci. 2019; 286(1896):20182852. https://doi.org/10.1098/rspb.2018.2852
https://doi.org/10.1098/rspb.2018.2852...
). In contrast with the species represented by a single lineage in the western Atlantic, as discussed above, the presence of multiple MOTUs in H. atlanticus, H. aurolineatum, and H. plumieri is an intriguing phenomenon, which cannot be accounted for by either the current barriers to gene flow (such as the Amazon-Orinoco Plume) or ancient processes, such as the isolation of the fauna of the Gulf of Mexico and the southern coast of Brazil (Victoria Trindade seamount chain) during the Quaternary and Tertiary glacial cycles.

Until recently, H. steindachneri was believed to occur in both the Pacific and Atlantic oceans, but an ample taxonomic review, supported by cytogenetic and molecular data (Rocha et al., 2008Rocha LA, Lindeman KC, Rocha CR, Lessios HA. Historical biogeography and speciation in the reef fish genus Haemulon (Teleostei: Haemulidae). Mol Phylogenet Evol. 2008; 48(3):918–28. https://doi.org/10.1016/j.ympev.2008.05.024
https://doi.org/10.1016/j.ympev.2008.05....
; Tavera et al., 2012Tavera JJ, Acero PA, Balart EF, Bernardi G. Molecular phylogeny of grunts (Teleostei, Haemulidae), with an emphasis on the ecology, evolution, and speciation history of New World species. BMC Evol Biol. 2012; 12(1):57. https://doi.org/10.1186/1471-2148-12-57
https://doi.org/10.1186/1471-2148-12-57...
, 2018Tavera J, Acero PA, Wainwright PC. Multilocus phylogeny, divergence times, and a major role for the benthic-to-pelagic axis in the diversification of grunts (Haemulidae). Mol Phylogenet Evol. 2018; 121:212–23. https://doi.org/10.1016/j.ympev.2017.12.032
https://doi.org/10.1016/j.ympev.2017.12....
; Bernal et al., 2017Bernal MA, Gaither MR, Simison WB, Rocha LA. Introgression and selection shaped the evolutionary history of sympatric sister-species of coral reef fishes (genus: Haemulon). Mol Ecol. 2017; 26(2):639–52. https://doi.org/10.1111/mec.13937
https://doi.org/10.1111/mec.13937...
, 2019Bernal MA, Dixon GB, Matz MV, Rocha LA. Comparative transcriptomics of sympatric species of coral reef fishes (genus: Haemulon). PeerJ. 2019; 7:e6541. https://doi.org/10.7717/peerj.6541
https://doi.org/10.7717/peerj.6541...
; Motta-Neto et al., 2012Motta-Neto CC, Lima-Filho PA, Araújo WC, Bertollo LAC, Molina WF. Differentiated evolutionary pathways in Haemulidae (Perciformes): Karyotype stasis versus morphological differentiation. Rev Fish Biol Fish. 2012; 22(2):457–65. https://doi.org/10.1007/s11160-011-9236-4
https://doi.org/10.1007/s11160-011-9236-...
, 2019Motta-Neto CC, Cioffi MB, Costa GWWF, Amorim KDJ, Bertollo LAC, Artoni RF, Molina WF. Overview on karyotype stasis in Atlantic grunts (Eupercaria, Haemulidae) and the evolutionary extensions for other marine fish groups. Front Mar Sci. 2019; 6:628. ; Tavera, Wainwright, 2019Tavera JJ, Wainwright PC. Geography of speciation affects rate of trait divergence in haemulid fishes. Proc R Soc Lond B Biol Sci. 2019; 286(1896):20182852. https://doi.org/10.1098/rspb.2018.2852
https://doi.org/10.1098/rspb.2018.2852...
), confirmed that H. steindachneri is restricted to the Pacific, while a new species, H. atlanticus, was described for the Atlantic (Carvalho et al., 2020Carvalho CO, Marceniuk AP, Oliveira C, Wosiacki WB. Integrative taxonomy of the species complex Haemulon steindachneri (Jordan and Gilbert, 1882) (Eupercaria; Haemulidae) with a description of a new species from the Western Atlantic. Zoology. 2020; 141:125782. https://doi.org/10.1016/j.zool.2020.125782
https://doi.org/10.1016/j.zool.2020.1257...
). Ours results also support the separation of the eastern Pacific H. steindachneri from H. atlanticus, which is found in the western Atlantic (Carvalho et al., 2020Carvalho CO, Marceniuk AP, Oliveira C, Wosiacki WB. Integrative taxonomy of the species complex Haemulon steindachneri (Jordan and Gilbert, 1882) (Eupercaria; Haemulidae) with a description of a new species from the Western Atlantic. Zoology. 2020; 141:125782. https://doi.org/10.1016/j.zool.2020.125782
https://doi.org/10.1016/j.zool.2020.1257...
), with a genetic distance of 0.0746±0.0121 (Tab. 1), and the two species were separated clearly in all analyses.

However, while all three species delimitation methods used here (PTP, ABGD, and GMYC) indicated that only one MOTU was present in the H. atlanticus samples, the ML tree identified two groups, denominated here as H. atlanticus A (specimens from the Caribbean and the Atlantic coast of South America) and H. atlanticus B (specimens from the Caribbean). The genetic distance between these two MOTUs was 0.012±0.004, which is lower than that usually found between valid marine fish species, i.e., around 2% (Ward, 2009Ward RD. DNA barcode divergence among species and genera of birds and fishes. Mol Ecol Resour. 2009; 9(4):1077–85. https://doi.org/10.1111/j.1755-0998.2009.02541.x
https://doi.org/10.1111/j.1755-0998.2009...
), although it was consistent with that found by Rocha et al., (2008)Rocha LA, Lindeman KC, Rocha CR, Lessios HA. Historical biogeography and speciation in the reef fish genus Haemulon (Teleostei: Haemulidae). Mol Phylogenet Evol. 2008; 48(3):918–28. https://doi.org/10.1016/j.ympev.2008.05.024
https://doi.org/10.1016/j.ympev.2008.05....
and Carvalho et al., (2020)Carvalho CO, Marceniuk AP, Oliveira C, Wosiacki WB. Integrative taxonomy of the species complex Haemulon steindachneri (Jordan and Gilbert, 1882) (Eupercaria; Haemulidae) with a description of a new species from the Western Atlantic. Zoology. 2020; 141:125782. https://doi.org/10.1016/j.zool.2020.125782
https://doi.org/10.1016/j.zool.2020.1257...
, which supports the need for further studies to determine whether this difference is due to the simple isolation of populations or the existence of a cryptic species derived from a recent speciation process (Rocha et al., 2007Rocha LA, Craig MT, Bowen BW. Phylogeography and the conservation of reef fishes. Coral Reefs. 2007; 26(3):501–12. https://doi.org/10.1007/s00338-007-0280-4
https://doi.org/10.1007/s00338-007-0280-...
; Motta-Neto et al., 2011aMotta-Neto CC, Cioffi MB, Bertollo LAC, Molina WF. Extensive chromosomal homologies and evidence of karyotypic stasis in Atlantic grunts of the genus Haemulon (Perciformes). J Exp Mar Biol Ecol. 2011a; 401(1–2):75–79. https://doi.org/10.1016/j.jembe.2011.02.044
https://doi.org/10.1016/j.jembe.2011.02....
).

In H. aurolineatum, by contrast, some of the analyses identified four MOTUs, that is, H. aurolineatum A and B (specimens from Bermuda), H. aurolineatum C (specimens from the United States), and H. aurolineatum D (specimens from the Gulf of Mexico, Caribbean, and the Atlantic coast of South America), while the other analyses indicated that H. aurolineatum C and D constitute a single MOTU (C+D). In H. plumieri, some of the analyses identified three MOTUs, that is, H. plumieri A (specimens from the Gulf of Mexico and the Caribbean), H. plumieri B (specimens from the Gulf of Mexico), and H. plumieri C (specimens from the Caribbean and the Atlantic coast of South America), while the other analyses indicated that H. plumieri A and B constitute a single MOTU (A+B). Although the genetic distances between some of these MOTU pairs were lower than 2%, many were higher, and reached up to 13%.

In recent years, advances in sequencing technology have supported a substantial increase in the DNA sequences available in databases, such as GenBank, for biodiversity studies. This includes fish, and these advances have contributed to the identification of species from groups with major taxonomic disagreements (Porter, Hajibabaei, 2018Porter TM, Hajibabaei M. Over 2.5 milion COI sequences in GenBank and growing. PLOS ONE. 2018; 13(9):e0200177. https://doi.org/10.1371/journal.pone.0200177
https://doi.org/10.1371/journal.pone.020...
; Leray et al., 2019Leray M, Knowlton N, Ho SL, Nguyen BN, Machida RJ. GenBank is a reliable resource for 21st century biodiversity research. Proc Natl Acad Sci USA. 2019; 116(45):22651–56. https://doi.org/10.1073/pnas.1911714116
https://doi.org/10.1073/pnas.1911714116...
).

However, some authors have questioned the validity of the discrimination of fish species based on DNA sequences, given the frequent misidentification of the sequences available in these databases due to taxonomic inconsistencies, sampling errors, contamination, and hybridization, which reduces their reliability for comparison with other sequences (Locatelli et al., 2020Locatelli NS, McIntyre PB, Therkildsen NO, Baetscher DS. GenBank’s reliability is uncertain for biodiversity researchers seeking species-level assignment for eDNA. Proc Natl Acad Sci USA. 2020; 117(51):32211–12. https://doi.org/10.1073/pnas.2007421117
https://doi.org/10.1073/pnas.2007421117...
; Pentinsaari et al., 2020Pentinsaari M, Ratnasingham S, Miller SE, Hebert PDN. BOLD and GenBank revisited – Do identification errors arise in the lab or in the sequence libraries? PLoS ONE. 2020; 15(4):e0231814. https://doi.org/10.1371/journal.pone.0231814
https://doi.org/10.1371/journal.pone.023...
). This problem was identified in the case of the five H. aurolineatum GenBank sequences from Bermuda, which we believe have been identified mistakenly as H. aurolineatum, given their considerable genetic distance from the other specimens analyzed, as well as the lack of published reports of this species in the region of the Bermuda archipelago.

Studies of reef fish have identified a number of processes that may have influenced the present-day intra- and inter-specific structuring observed in some groups found in the western Atlantic (Santos et al., 2006Santos S, Hrbek T, Farias IP, Schneider H, Sampaio I. Population genetic structuring of the king weakfish, Macrodon ancylodon (Sciaenidae), in the Atlantic coastal waters of South America: Deep genetic divergence without morphological change. Mol Ecol. 2006; 15(14):4361–73. https://doi.org/10.1111/j.1365-294X.2006.03108.x
https://doi.org/10.1111/j.1365-294X.2006...
; Rodríguez-Rey et al., 2014Rodríguez-Rey GT, Solé-Cava AM, Lazoski C. Genetic homogeneity and historical expansions of the slipper lobster, Scyllarides brasiliensis, in the south-west Atlantic. Mar Freshw Res. 2014; 65(1):59–69. https://doi.org/10.1071/MF12359
https://doi.org/10.1071/MF12359...
; Silva et al., 2014Silva G, Horne JB, Castilho R. Anchovies go north and west without losing diversity: Post glacial range expansions in a small pelagic fish. J Biogeogr. 2014; 41(6):1171–82. https://doi.org/10.1111/jbi.12275
https://doi.org/10.1111/jbi.12275...
, 2015Silva R, Veneza I, Sampaio I, Araripe J, Schneider H, Gomes G. High levels of genetic connectivity among populations of yellowtail snapper, Ocyurus chrysurus (Lutjanidae – Perciformes), in the Western South Atlantic revealed through multilocus analysis. PLoS ONE. 2015; 10(3):e0122173. https://doi.org/10.1371/journal.pone.0122173
https://doi.org/10.1371/journal.pone.012...
; Ashe et al., 2015Ashe JL, Feldheim KA, Fields AT, Reyier EA, Brooks EJ, O’Connell MT, Skomal G, Gruber SH, Chapman DD. Local population structure and context-dependent isolation by distance in a large coastal shark. Mar Ecol Prog Ser. 2015; 520:203–16. https://doi.org/10.3354/meps11069
https://doi.org/10.3354/meps11069...
; Souza et al., 2015Souza AS, Júnior EAD, Galetti Jr PM, Machado EG, Pichorim M, Molina WF. Wide-range genetic connectivity of coney, Cephalopholis fulva (Epinephelidae), through oceanic islands and continental Brazilian coast. An Acad Bras Cienc. 2015; 87(1):121–36. https://doi.org/10.1590/0001-3765201520130411
https://doi.org/10.1590/0001-37652015201...
; Bernal et al., 2018Bernal MA, Donelson JM, Veilleux HD, Ryu T, Munday PL, Ravasi T. Phenotypic and molecular consequences of stepwise temperature increase across generations in a coral reef fish. Mol Ecol. 2018; 27(22):4516–28. https://doi.org/10.1111/mec.14884
https://doi.org/10.1111/mec.14884...
, 2019Bernal MA, Dixon GB, Matz MV, Rocha LA. Comparative transcriptomics of sympatric species of coral reef fishes (genus: Haemulon). PeerJ. 2019; 7:e6541. https://doi.org/10.7717/peerj.6541
https://doi.org/10.7717/peerj.6541...
).

These processes include the glacial cycles of the Pleistocene and Miocene, when the Vitória Trindade seamount chain, off the eastern coast of Brazil, isolated the fish fauna of southern Brazil, with a similar process of isolation occurring in the Gulf of Mexico. Another important event was the uplifting of the Andes, around 8 million years ago, which reconfigured the continental drainages of South America, establishing the transcontinental flow of the Amazon River to the Atlantic Ocean.

All these processes may have caused alterations in the gene flow of reef fish populations. In the specific cases of H. atlanticus, H. aurolineatum, and H. plumieri, however, the well-known barriers, such as the Amazon-Orinoco plume and the Victoria Trindade seamount chain would not account for the differentiation of the MOTUs found herein, which implies the influence of alternative phenomena, such as other paleogeographical events or even parametric or sympatric speciation events resulting from processes of ecological specialization.

The DNA barcode method contributed to the identification of the Brazilian reef fish fauna of the genera Brachygenys and Haemulon, and how barriers and ocean currents may influence the population dynamics of these species in the Western Atlantic. Our results indicated that some Haemulon species have been able to traverse the barrier of the Amazon plume and that the action of ocean currents may contribute to the dispersion of these species. However, the evolution of the populations of H. plumieri, H. atlanticus, H. steindachneri, and H. aurolineatum may have been influenced by variations in oceanographic conditions and barriers resulting in the formation of distinct MOTUs, as identified here, that have enriched the diversity of the reef fish species found off Brazil.

ACKNOWLEDGEMENTS

This study was supported by grants from the Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq, grants 306054/2006 to CO and 300462/2016–6 to APM), the Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP, 2016/09204–6 to CO), the Fundação Amazônia Paraense de Amparo a Estudos e Pesquisas (FAPESPA grant ICAAF 017/2016 to APM), and the Programa de Treinamento Institutional (MCTIC/CNPq, process 444338/2018–7 and 300675/2019–4 to APM). The authors thank all the fishermen from the institutional project “Pró-Pesca: pescando o conhecimento”.

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ADDITIONAL NOTES

  • HOW TO CITE THIS ARTICLE

    Cerqueira NNCD, Rotundo MM, Marceniuk AP, Cruz VP, Foresti F, Oliveira C. Molecular identification of Brachygenys and Haemulon species (Perciformes: Haemulidae) from the Brazilian coast. Neotrop Ichthyol. 2021; 19(2):e200109. https://doi.org/10.1590/1982-0224-2020-0109

Publication Dates

  • Publication in this collection
    09 July 2021
  • Date of issue
    2021

History

  • Received
    5 Oct 2020
  • Accepted
    2 June 2021
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E-mail: neoichth@nupelia.uem.br
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