Neotropical Ichthyology
Original article
https://doi.org/10.1590/1982-0224-2021-0095
Cryptic speciation in populations of the
genus Aphyocharax (Characiformes:
Characidae) from eastern Amazon
coastal river drainages and surroundings
revealed by single locus species
delimitation methods
Correspondence:
Pâmella Silva de Brito
pamellabrito@hotmail.com
Submitted May 26, 2021
Accepted August 18, 2021
by Carlos DoNascimiento
Epub December 10, 2021
Pâmella S. Brito1,2, Erick C. Guimarães1,2, Karen L. A. Guimarães2,
Luís R. R. Rodrigues2, Marcelo R. Anjos3, Axel M. Katz4,
Luis F. Carvalho-Costa1 and Felipe P. Ottoni5
Recent studies in eastern Amazon coastal drainages and their surroundings have
revealed new fish species that sometimes exhibit little morphological differentiation
(cryptic species). Thus, we used a DNA-based species delimitation approach to
test if populations showing the morphotype and typical character states of the
Aphyocharax avary holotype correspond either to A. avary or A. brevicaudatus, two
known species from the region, or if they form independent lineages, indicating
cryptic speciation. WP and GMYC analyses recovered five lineages (species) in
the ingroup, while a bPTP analysis delimited three lineages. ABGD analyses
produced two possible results: one corroborating the WP and GMYC methods
and another corroborating the bPTP method. All methods indicate undescribed
cryptic species in the region and show variation from at least 1 to 4 species in
the ingroup, depending on the approach, corroborating previous studies, and
revealing this region as a possible hotspot for discovering undescribed fish species.
Keywords: ABGD, Aphyocharacinae, bPTP, Cryptic speciation, GMYC.
1 Universidade Federal do Maranhão, Departamento de Biologia, Laboratório de Genética e Biologia Molecular, Av. dos
Portugueses 1966, Cidade Universitária do Bacanga, 65080-805 São Luís, MA, Brazil. (PSB) pamellabrito@hotmail.com
(corresponding author), (ECG) erick.ictio@yahoo.com.br, (LFCC) lfecc@yahoo.com.br.
Online version ISSN 1982-0224
Print version ISSN 1679-6225
Neotrop. Ichthyol.
vol. 19, no. 4, Maringá 2021
2 Universidade Federal do Oeste do Pará, Laboratório de Genética & Biodiversidade, Instituto de Ciências da Educação,
Campus Tapajós, Rua Vera Paz S/N, 68040-255 Santarém, PA, Brazil. (KLA) karen.guimaraes.bio@gmail.com, (LRRR)
luisreginaldo.ufpa@hotmail.com.
3 Universidade Federal do Amazonas, Laboratório de Ictiologia e Ordenamento Pesqueiro do Vale do Rio Madeira, R. Vinte Nove
de Agosto 786, Centro, 69800-000 Humaitá, AM, Brazil. anjos@ufam.edu.br.
4 Universidade Federal do Rio de Janeiro, Laboratório de Sistemática e Evolução de Peixes Teleósteos, Departamento de Zoologia,
Instituto de Biologia, Cidade Universitária, 21941-599 Rio de Janeiro, RJ, Brazil. axelmk@gmail.com.
5 Universidade Federal do Maranhão, Centro de Ciências Agrárias e Ambientais, Laboratório de Sistemática e Ecologia de
Organismos Aquáticos, BR-222, Km 04, S/N, Boa Vista, 65500-000 Chapadinha, MA, Brazil. felipe.ottoni@ufma.br.
Neotropical Ichthyology, 19(4): e210095, 2021
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Cryptic speciation of the genus Aphyocharax
Estudos recentes nas drenagens costeiras da Amazônia oriental e seus arredores
revelaram novas espécies de peixes que às vezes exibem pouca diferenciação
morfológica (espécies crípticas). Assim, usamos uma abordagem de delimitação de
espécies baseada em DNA para testar se as populações que apresentam o morfotipo
e os estados de caráter típicos do holótipo Aphyocharax avary correspondem a
A. avary ou A. brevicaudatus, duas espécies conhecidas da região, ou se formam
linhagens independentes, indicando especiação críptica. As análises de WP e
GMYC recuperaram cinco linhagens (espécies) no grupo interno, enquanto
uma análise de bPTP delimitou três linhagens. As análises ABGD produziram
dois resultados possíveis: um corroborando os métodos WP e GMYC e outro
corroborando o método bPTP. Todos os métodos indicam espécies crípticas não
descritas na região e apresentam variação de pelo menos uma a quatro espécies
no grupo interno, dependendo da abordagem, corroborando estudos anteriores, e
revelando esta região como um possível “hotspot” para descoberta de espécies de
peixes não descritas.
Palavras-chave: ABGD, Aphyocharacinae, bPTP, Especiação críptica, GMYC.
INTRODUCTION
Speciation is not always accompanied by changes in morphology (= cryptic speciation),
making it difficult to identify species using superficial morphological differentiation
(Bickford et al., 2006; Adams et al., 2014; Ottoni et al., 2019). However, DNA-based
tools help to identify cryptic speciation events and have been increasingly used in
species descriptions and diagnoses (Goldstein, DeSalle, 2010; Pante et al., 2015; Souza
et al., 2018; Ottoni et al., 2019; Ochoa et al., 2020; Souza et al., 2020). In this case,
DNA lineages that diverged from an ancestral branch and evolved independently, as
observed in differentiated species, must be named according to specific nomenclature
codes used by the scientific community.
Aphyocharax Günther, 1868 (Aphyocharacinae) is a monophyletic, small-sized fish
genus that comprises 12 valid species (Tagliacollo et al., 2012; Betancur-R. et al., 2018;
Mirande, 2018; Brito et al., 2019) distributed in the Orinoco, Amazonas and La Plata
river basins, as well as in coastal rivers that drain the Guiana Shield (Tagliacollo et al.,
2012; Brito et al., 2018, 2019). Aphyocharax brevicaudatus Brito, Guimarães, CarvalhoCosta & Ottoni, 2019 is the most recently described species (Brito et al., 2019) that
inhabits the Maracaçumé River basin, an eastern Amazon costal drainage in the state
of Maranhão, in northeastern Brazil. The phylogenetic status of Aphyocharax is well
established, but its internal relationships are not fully resolved (e.g., Tagliacollo et al.,
2012; Brito et al., 2019). There are at least four putative species in the genus that are
not yet described (see Buckup et al., 2007; Brito et al., 2019), and the identification
and taxonomic status of several populations and species are still unclear (Lima et al.,
2013; Ohara et al., 2017; Brito et al., 2018, 2019).
In the last decades, most publications about Aphyocharax have focused on ecology
or distribution (e.g., Gonçalves et al., 2005; Corrêa et al., 2009; Terán et al., 2016),
cytogenetic characterization (e.g., Souza et al., 1995) or phylogeny (e.g., Tagliacollo
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Pâmella S.Brito, Erick C. Guimarães, Karen L.A. Guimarães, Luís R.R. Rodrigues, Marcelo R. Anjos, Axel M.Katz, Luis F. Carvalho-Costa and Felipe P. Ottoni
et al., 2012). However, few studies have focused on the species-level taxonomy of
Aphyocharax, such as the single taxonomic revision of the genus (an unpublished
thesis, Souza-Lima, 2003), some species descriptions (e.g., Taphorn, Thomerson, 1991;
Willink et al., 2003; Brito et al., 2019), and some taxonomic works (e.g., Souza-Lima,
2003; Brito et al., 2018). Moreover, the taxonomic status of some Aphyocharax species
is questionable and problematic. The imprecise definition of the type locality of several
species, old, and change, to and brief morphological descriptions and diagnoses, and
confusing taxonomic histories contribute to the problematic taxonomy of this group
(Brito et al., 2018).
Previous studies indicate the occurrence of several populations of Aphyocharax in
the coastal basins of the eastern Amazon and surroundings at the state limits of Pará
and Maranhão (see Souza-Lima, 2003; Barros et al., 2011; Guimarães et al., 2020a).
These populations have the morphotype and typical character states of the holotype
of Aphyocharax avary Fowler, 1913, as described and discussed by Brito et al. (2018).
However, A. avary is a species with an imprecise type locality in the Madeira River
drainage of the Amazon River basin, with vague distribution records (Brito et al.,
2018; Dagosta, de Pinna, 2019), and requires a comprehensive taxonomic revision.
According to Guimarães et al. (2018a) the river systems in northeastern Brazil,
particularly the river basins of the occidental portion (including the region between
Rio Gurupi and the Parnaíba basin), exhibit a diversified but poorly explored
freshwater fish fauna that is interpreted in different ways in studies based on the
distribution patterns of species (e.g., Hubert, Renno, 2006; Abell et al., 2008; Abreu et
al., 2019). This region is herein termed “eastern Amazon coastal river basins”. Recent
studies exemplify the great diversification between coastal basins of Maranhão State,
as well as the lack of knowledge about the fish in these areas (e.g., Guimarães et al.,
2018a,b; Abreu et al., 2019; Brito et al., 2019; Guimarães et al., 2019; Abreu et al.,
2020; Guimarães et al., 2020a).
In the river drainages of the state of Maranhão (Itapecuru, Mearim, Munim, and
Tocantins River draineages), there are several populations with superficial morphology
similar to A. avary. In this context, we combined newly generated mitochondrial
sequences with those generated by Oliveira et al. (2011) and Tagliacollo et al. (2012)
to study species diversity and delimit species boundaries within Aphyocharax from
several coastal basins in the eastern Amazon coastal river basins and surroundings.
MATERIAL AND METHODS
Study area. The study was carried out in the coastal basins and drainages in the state
of Maranhão, including a region between the Gurupi and Parnaíba river basins, in
addition to the Tocantins River basin in the state (Fig. 1). The study area consists of
10 hydrographic basins, seven of which are state owned (Mearim, Itapecuru, Munim,
Turiaçú, Maracaçumé, Preguiças and Periá basins) and three are federally owned
(Parnaíba, Tocantins, Gurupi). Together, these occupy an area of 113,068.15 km2
(34.6% of the state of Maranhão) that is subdivided into three Brazilian hydrographic
regions (Tocantins-Araguaia, Western Northeast Atlantic and Parnaíba) (MMA,
2006; NUGEO, 2016).
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Cryptic speciation of the genus Aphyocharax
Maranhão is the westernmost state in the Northeast Region of Brazil and borders
the eastern side of Pará State in the North Region of the country. It has an area of about
320,000 km2 and occupies about 3.9% of Brazil (Rebêlo et al., 2003). The state harbors
three of the main Brazilian biomes, and transition ecotone areas between Amazonian
tropical forests and open shrubby and dry forests of Cerrado and Caatinga. Therefore,
this region is considered very important for ecological services and biodiversity
conservation (Guimarães et al., 2018a).
Ethical statement, specimen collection and preservation. Specimens selected
for molecular data analysis (Tab. 1) were fixed and preserved in absolute ethanol.
FIGURE 1 | Map of the sampling localities of Aphyocharax specimens in eastern Amazon coastal river drainages and surroundings in
Brazil. Black circle = Aphyocharax brevicaudatus, Rio Maracaçumé/Maracaçumé/MA; orange circle = Aphyocharax sp. “Munim”, Riacho
Fundo/Rio Munim/Chapadinha/MA; white circle = Aphyocharax sp. (Itapecuru), Riacho Primavera/Rio Itapecuru/Caxias/MA; green circle =
Aphyocharax sp. (Itapecuru), Rio Saco/Rio Itapecuru/Codó/MA; yellow circle = Aphyocharax sp. (Mearim), Bacia 464/Rio Mearim/Arari/MA;
blue circle = Aphyocharax sp. (Mearim), Rio Zutíua/Rio Pindaré/Rio Mearim/Pindaré-Mirim/MA; red circle = Aphyocharax sp. (Mearim), Rio
Zutíua/Rio Pindaré/Rio Mearim/Pindaré-Mirim/MA; pink circle = Aphyocharax sp. (Mearim), Rio Pindaré/Rio Mearim/Bom Jesus das Selvas/
MA; salmon-pink circle = Aphyocharax avary, Rio Sororó/Rio Tocantins/Marabá/PA.
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Pâmella S.Brito, Erick C. Guimarães, Karen L.A. Guimarães, Luís R.R. Rodrigues, Marcelo R. Anjos, Axel M.Katz, Luis F. Carvalho-Costa and Felipe P. Ottoni
DNA extraction, amplification, and sequencing. DNA extraction was
carried out with a Wizard Genomic DNA Purification Kit (Promega) following
the manufacturer’s protocol. The DNA quality was evaluated using 0.8% agarose
gel electrophoresis stained with GelRed (Biotium). The DNA was stored at -20 °C
until further procedures. The partial Cytochrome B mitochondrial gene (CytB) was
amplified using standard PCR (polymerase chain reaction) and primers developed by
Kocher et al. (1989) (L14841 5’ – AAATCAAAGCATAACACTGAAGATG – 3’)
and Irwin et al. (1991) (H15915 5’ – CCAATTTGCATGGATGTCTTCTCGG –
3’).
Amplification reactions were performed at a total volume of 15 μl comprising 10×
buffer, 1.5 mM MgCl2, 400 μM dNTP, 0.2 μM of each primer, 1 U of Taq Polymerase
(Invitrogen), 100 ηg of DNA template and ultrapure water. The amplification
program consisted of a denaturation of 94 °C for 3 min, followed by 35 cycles of 94
°C for 30 s, 46–48 °C for 45 s, and 72 °C for 80 s, and an extension phase of 5 min at
72 °C. Amplicons were visualized using 1% agarose gel electrophoresis stained with
GelRed (Biotium) and purified with Illustra GFX PCR DNA and a Gel Purification
Kit (GE Healthcare). Samples were sequenced using both forward and reverse primers
with a BigDye Terminator 3.1 Cycle Sequencing Kit in an ABI 3730 DNA Analyzer
(Thermo Fisher Scientific).
Data analyses. The dataset included the partial CytB (678 base pairs, bp) and
sequences from other species of Aphyocharax and allied genera from the National
Center for Biotechnology Information (NCBI) databases (Tab. 1). Sequences were
aligned using ClustalW (Chenna et al., 2003) and translated into amino acid residues
using the program MEGA 7 (Kumar et al., 2016) to test if the sequences came from
NUMTs (nuclear mitochondrial DNA sequences), in which case premature stop
codons or indels are expected. The best-fit evolutionary model (GTR+I+G) was
selected using the Akaike information criterion (AIC) and jModelTest 2.1.7 (Darriba
et al., 2012), and used in all analyses, except for Automatic Barcode Gap Discovery
(ABGD).
Species concept, species delimitation, and diagnoses. The unified species
concept was adopted, considering that “species are (segments of) separately evolving
metapopulation lineages” (de Queiroz, 2005, 2007). According to this concept, species
are treated as hypothetical units that could be tested (detected) by applying distinct
criteria (i.e., species delimitation methods), allowing for any method to independently
provide evidence about species limits and identities (de Queiroz, 2005, 2007). Four
distinct and independent single locus species delimitation methods relying on different
operational criteria for species delimitation were implemented: ABGD, Automatic
Barcode Gap Discovery (Puillandre et al., 2012); WP, a tree-based method proposed
by Wiens, Penkrot (2002) (following Sites, Marshall, 2003); and two coalescentbased species delimitation methods termed bPTP, the Bayesian implementation
of the Poisson tree processes (Zhang et al., 2013), and GMYC, the General Mixed
Yule Coalescent method, single-threshold version (Fujisawa, Barraclough, 2013). All
species delimitation methods were performed using the Cytb sequences, which is
widely used for single locus species delimitation approaches (Avise, 2000).
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Cryptic speciation of the genus Aphyocharax
TABLE 1 | List of species, specimens and their respective GenBank sequence accession numbers. Sequences made available by this study are
in bold.
Species
Catalog
number
Genbank
accession
Locality
(Country/River/River drainage/Municipality/State)
Aphyocharacidium bolivianum
LBP 9055
HQ289710
Brazil/Arara/RO
Aphyocharax anisitsi
LBP 4750
JQ820081
Brazil
Aphyocharax anisitsi
LBP 3764
HQ289581
Brazil/Rio Negro/Aquidauana/MS
Aphyocharax avary
CICCAA02344.1
MK409660
Brazil/Rio Sororó/Rio Tocantins/Marabá/PA
Aphyocharax avary
CICCAA 02344.2
MZ558446
Brazil/Rio Sororó/Rio Tocantins/Marabá/PA
Aphyocharax avary
CICCAA02344.3
MK409661
Brazil/Rio Sororó/Rio Tocantins/Marabá/PA
Aphyocharax brevicaudatus (female)
CICCAA 02306
MK409668
Brazil/Rio Maracaçumé/Maracaçumé/MA
Aphyocharax brevicaudatus (male)
CICCAA 02308
MK409669
Brazil/Rio Maracaçumé/Maracaçumé/MA
Aphyocharax brevicaudatus (male)
CICCAA 02310
MK409670
Brazil/Rio Maracaçumé/Maracaçumé/MA
Aphyocharax dentatus
LBP 5112
JQ820082
Brazil/Rio Paraguai/Cáceres/MT
Aphyocharax dentatus
LBP 20
JQ820083
Brazil/Rio Paraguai/Rio Miranda/Corumbá/MT
Aphyocharax cf. erythrurus
LBP 15819
JQ820076
Venezuela
Aphyocharax cf. erythrurus
LBP 15820
JQ820077
Venezuela
Aphyocharax nattereri
LBP 3786
JQ820070
Brazil/Rio Paraguai/lagoa marginal do Rio Negro/Aquidauana/MS
Aphyocharax nattereri
LBP 3734
JQ820071
Brazil
Aphyocharax pusillus
LBP 23546
JQ820078
Brazil
Aphyocharax pusillus
LBP 4046
HQ289590
Brazil/Rio Moa/Cruzeiro do Sul/AC
Aphyocharax rathbuni
LBP 7608
JQ820079
Brazil/La Plata basin /Lagoa marginal do rio Cuiabá/Barão de Melgaço/MT
Aphyocharax rathbuni
LBP 8457
JQ820080
Brazil
Aphyocharax sp.
LBP 1587
HQ289533
Brazil/Rio das Garças/Rio Araguaia/Barra do Garças/MT
Aphyocharax sp.
LBP 2480
JQ820084
Brazil/Rio Araguaia/Aragarças/GO
Aphyocharax sp. “Tapajós”
CICCAA 04851.1
MZ558447
Brazil/Lago Papucu/Rio Tapajós/Santarém/PA
Aphyocharax sp. “Tapajós”
CICCAA 04851.3
MZ558448
Brazil/Lago Papucu/Rio Tapajós/Santarém/PA
Aphyocharax sp. “Tapajós”
CICCAA 04851.4
MZ558449
Brazil/Lago Papucu/Rio Tapajós/Santarém/PA
Aphyocharax sp. “Tapajós”
CICCAA 04851.6
MZ558450
Brazil/Lago Papucu/Rio Tapajós/Santarém/PA
Aphyocharax sp. “Solimões”
CICCAA 04836.1
MZ558451
Brazil/Ilha Cuera/Rio Solimões/Tefé/AM
Aphyocharax sp. “Solimões”
CICCAA 04836.3
MZ558452
Brazil/Ilha Cuera/Rio Solimões/Tefé/AM
Aphyocharax sp. “Solimões”
CICCAA 04840.1
MZ558453
Brazil/Lago Amanã/Rio Solimões/Maraã/AM
Aphyocharax sp. “Solimões”
CICCAA 04840.2
MZ5584534
Brazil/Lago Amanã/Rio Solimões/Maraã/AM
Aphyocharax sp. “Solimões”
CICCAA 04840.3
MZ5584535
Brazil/Lago Amanã/Rio Solimões/Maraã/AM
Aphyocharax sp. “Mearim”
CICCAA 02107.1
MZ558436
Brazil/Bacia 464/Rio Mearim/Arari/MA
Aphyocharax sp. “Mearim”
CICCAA 02107.2
MZ558437
Brazil/Bacia 464/Rio Mearim/Arari/MA
Aphyocharax sp. “Mearim”
CICCAA 02107.3
MZ558438
Brazil/Bacia 464/Rio Mearim/Arari/MA
Aphyocharax sp. “Mearim”
CICCAA 02107.4
MZ558439
Brazil/Bacia 464/Rio Mearim/Arari/MA
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TABLE 1 | (Continued)
Species
Catalog
number
Genbank
accession
Locality
(Country/River/River drainage/Municipality/State)
Aphyocharax sp. “Mearim”
CICCAA 02107.5
MZ558440
Brazil/Bacia 464/Rio Mearim/Arari/MA
Aphyocharax sp. “Pindaré”
CICCAA 02320
MZ558441
Brazil/Igarapé Jenipapo/Rio Pindaré/Rio Mearim/Alto Alegre do Pindaré/MA
Aphyocharax sp. “Pindaré”
CICCAA 02323
MZ558442
Brazil/Rio Zutíua/Rio Pindaré/Rio Mearim/Pindaré-Mirim/MA
Aphyocharax sp. “Pindaré”
CICCAA 02033
MK409665
Brazil/Rio Pindaré/Rio Mearim/Bom Jesus das Selvas/MA
Aphyocharax sp. “Itapecuru”
CICCAA 02034
MK409666
Brazil/Riacho Primavera/Rio Itapecuru/Caxias/MA
Aphyocharax sp. “Itapecuru”
CICCAA 02357
MK409667
Brazil/Riacho Primavera/Rio Itapecuru/Caxias/MA
Aphyocharax sp. “Itapecuru”
CICCAA 02315.1
MZ558443
Brazil/Rio Saco/Rio Itapecuru/Codó/MA
Aphyocharax sp. “Itapecuru”
CICCAA 02315.2
MZ558444
Brazil/Rio Saco/Rio Itapecuru/Codó/MA
Aphyocharax sp. “Itapecuru”
CICCAA 02316
MZ558445
Brazil/Rio Saco/Rio Itapecuru/Codó/MA
Aphyocharax sp. “Munim”
CICCAA02345.1
MK409662
Brazil/Riacho Fundo/Rio Munim/Chapadinha/MA
Aphyocharax sp. “Munim”
CICCAA02345.2
MK409663
Brazil/Riacho Fundo/Rio Munim/Chapadinha/MA
Aphyocharax sp. “Munim”
CICCAA02345.3
MK409664
Brazil/Riacho Fundo/Rio Munim/Chapadinha/MA
Prionobrama paraguayensis
LBP 3230
JQ820073
Brazil/Lagoa marginal/Rio Cuiabazinho/Nobre/MT
Prionobrama paraguayensis
LBP 3230
JQ820072
Brazil/Lagoa marginal/Rio Cuiabazinho/Nobre/MT
Prionobrama filigera
LBP 4139
JQ820075
Brazil/Rio Juruá/Rio Moa/Mâncio Lima/AC
Prionobrama filigera
LBP 4139
JQ820074
Brazil/Rio Juruá/Rio Moa/Mâncio Lima/AC
Leptagoniates steindachneri
LBP 4137
HQ289600
Brazil/ Rio Moa/Mâncio Lima/AC
Paragoniates alburnus
LBP 9208
HQ289712
Venezuela/Rio Manapire/Cabruta/Guárico
Phenagoniates macrolepis
LBP 6105
HQ289678
Venezuela/Rio Apon Medio/Machiques de Perijá/Zulia
Xenagoniates bondi
LBP 3074
HQ289563
Venezuela/Rio Orinoco/Caicara del Orinoco/Bolivar
Wiens and Penkrot analysis (WP). WP is based on the direct inspection of
haplotype trees generated by a phylogenetic analysis with at least two individuals
(haplotypes) of each focal species as terminals. In this method, the term “exclusive”
is used instead of monophyletic since the term monophyly is considered inapplicable
below the species level (Wiens, Penkrot, 2002). Clustered haplotypes with a
concordant geographic distribution that form mutual and well supported clades
(exclusive lineages) are strong evidence for species discrimination (absence of gene
flow with other lineages). When haplotypes from the same locality fail to cluster
together, there is potential evidence for gene flow with other populations (Wiens,
Penkrot, 2002). Statistical support for the haplotypic tree was assessed by the posterior
probability, with about 0.95 or higher considered significant (Alfaro, Holder, 2006).
When only one haplotype (specimen) from one putative population was available,
the species delimitation was based on the exclusivity of the sister clade of this single
haplotype supported by significant values (Wiens, Penkrot, 2002). In addition, the
method recognizes non-exclusive lineages as species since their sister clades are
exclusive and supported by significant values (Wiens, Penkrot, 2002).
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A Bayesian inference (BI) phylogenetic tree was estimated with the software
MrBayes 3.2 (Ronquist et al., 2012) to reconstruct the evolutionary relationships among
terminals using the general time reversible (GTR+I+G) evolutionary model. The BI
analysis was conducted with the following parameters: two independent Markov
chain Monte Carlo (MCMC) runs of two chains each for 10 million generations, with
a tree sampling frequency every 1,000 generations. The convergence of the MCMC
chains and the proper burn-in value were assessed by evaluating the stationary phase
of the chains using Tracer v. 1.6 (Rambaut et al., 2014). After removing the first 25%
of the samples (burn-in), the final consensus tree and its posterior probabilities were
generated with the remaining tree samples.
The ingroup included species and populations with the morphotype and typical
characters of A. avary in the eastern Amazon coastal river drainages and surroundings:
Aphyocharax brevicaudatus (from the Maracaçumé River basin), A. avary (from the
Tocantins River basin), Aphyocharax sp. “Itapecuru” (from the Itapecuru River
basin), Aphyocharax sp. “Mearim” (from the Mearim River basin), and Aphyocharax
sp. “Munim” (from the Munim River basin) (colored haplotypes in Fig. 2; Tab. 1).
As the outgroup, we used sequences of Aphyocharacidium bolivianum Géry, 1973,
Leptagoniates steindachneri Boulenger, 1887, Paragoniates alburnus Steindachner, 1876,
Phenagoniates macrolepis (Meek & Hildebrand, 1913), Prionobrama filigera (Cope,
1870), Prionobrama paraguayensis (Eigenmann, 1914), Xenagoniates bondi Myers, 1942,
and other species and populations of Aphyocharax (excluding those of the ingroup)
(uncolored haplotypes in Fig. 2; Tab. 1).
General Mixed Yule Coalescent (GMYC). The GMYC is a single locus
coalescent-based species delimitation approach that relies on branch lengths to establish
a threshold between speciation and coalescent processes (Fujisawa, Barraclough,
2013). Here we applied the single-threshold version of the method, which usually
outperforms the multiple-threshold version (Fujisawa, Barraclough, 2013). A new
dataset was created for this analysis, including only the ingroup (see WP section) and
the clade with Aphyocharax cf. erythrurus, A. pusillus, Aphyocharax sp. “Solimões” +
Aphyocharax sp. “Tapajós” (see Tab. 1) as the outgroup, which has the geographically
closest populations to the ingroup. This new dataset was reduced to include only
unique haplotypes using DAMBE5 (Xia, 2013) and the requirements of this method.
The input ultrametric phylogenetic tree was made in BEAST v.1.8.4 (Drummond et
al., 2012) with the following parameters: an uncorrelated relaxed clock with lognormal
distribution, a Yule process as the tree prior with 10 million generations and sampling
frequency of 1000. The GMYC analysis was performed using the Exelixis Lab’s server
(https://species.h-its.org/gmyc/). We also performed a GMYC test analysis with the
same parameters but included all the available species of Aphyocharax (see Fig. S1).
Bayesian implementation of the Poisson tree processes (bPTP). The bPTP
is another single locus coalescent-based species delimitation method, but it differs
from other similar approaches, such as GMYC, since an ultrametric tree is not needed
(not relying on branch lengths to delimit species), thus avoiding errors and computer
intensive processes (Zhang et al., 2013). The method assumes that more molecular
variability (number of nucleotide substitutions) is expected between haplotypes from
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Pâmella S.Brito, Erick C. Guimarães, Karen L.A. Guimarães, Luís R.R. Rodrigues, Marcelo R. Anjos, Axel M.Katz, Luis F. Carvalho-Costa and Felipe P. Ottoni
different species than within a species (Zhang et al., 2013), establishing a threshold
between speciation and coalescent processes. The reduced dataset for performing the
bPTP was the same used in the GMYC, following the requirements of this method.
The input phylogenetic tree was estimated with the software Mrbayes 3.2 (Ronquist
et al., 2012) following the same parameters used in the WP. The bPTP analysis was
performed using the Exelixis Lab’s web server (http://species.h-its.org/ptp/), following
the default parameters except for a 20% burn-in. Aphyocharax cf. erythrurus was chosen
as the outgroup since it is the most geographically distant species from the ingroup in
this reduced dataset. We also performed a bPTP test analysis with the same parameters
but included all the available species of Aphyocharax (see Fig. S2).
Automatic Barcode Gap Discovery (ABGD). The ABGD is a barcode species
delimitation method that aims to establish a minimum gap that probably corresponds
to the threshold between interspecific and intraspecific processes (Puillandre et
al., 2012). The major advantage of ABGD compared to the other barcode species
delimitation methods is that the inference of the limit between interspecific and
intraspecific processes (gap detection) is recursively applied to previously obtained
groups to get finer partitions until there is no further partitioning, allowing a more
refined search. Basically, the ABGD analysis indicates the number of groups (species)
estimated relative to a large spectrum of p values (prior intraspecific values). For this, a
0.1 value assumes the maximum intraspecific variability, indicating that all sequences
belong to only one species, and a 0.001 value assumes very low intraspecific variability,
indicating that each distinct haplotype represents a different species. After running the
ABGD, additional molecular, morphological, or ecological characters are needed to
infer the correct number of species, following an integrative taxonomic perspective.
The reduced dataset for performing the ABGD was the same used in the GMYC and
bPTP. The analysis was conducted using the ABGD server website (https://bioinfo.
mnhn.fr/abi/public/abgd/abgdweb.html) following the default parameters.
RESULTS
Phylogenetic analysis. The topology of our phylogenetic analysis (Fig. 2) recovered
Aphyocharax as monophyletic but supported by a low posterior probability value (0.88),
with A. nattereri as sister to all other Aphyocharax. However, all the other lineages sister
to A. nattereri formed a large clade supported with the maximum posterior probability
value (1) (Fig. 2). Within this large clade, three other clades formed: 1– comprising
A. anisitsi, A. dentatus, A. rathbuni and a species not identified to the species level, but
with low node support (0.59); 2– comprising Aphyocharax cf. erythrurus and several
haplotypes considered here as A. pusillus, supported by the maximum support value
(1); and 3– comprising our ingroup (populations occurring in the eastern Amazon
coastal river drainages and surroundings, i.e., Aphyocharax brevicaudatus [from the
Maracaçumé River basin], A. avary [from the Tocantins River basin], Aphyocharax
sp. “Itapecuru” [from the Itapecuru River basin], Aphyocharax sp. “Mearim” [from the
Mearim River basin] and Aphyocharax sp. “Munim” [from the Munim River basin])
supported by the maximum support value (1). The last two clades are probably sister
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Cryptic speciation of the genus Aphyocharax
groups; however, they are supported by low posterior probability (0.55) (Fig. 2).
Species delimitation. WP. The BI phylogenetic analysis delimited five species
within our ingroup: 1– Aphyocharax brevicaudatus (yellow colored); 2– A. avary (grey
colored); 3–Aphyocharax sp. “Itapecuru” (blue colored); 4– Aphyocharax sp. “Mearim”
(red colored); and 5– Aphyocharax sp. “Munim” (green colored). The haplotypes of
each species formed exclusive clades with the maximum posterior probability value
(1) (Fig. 2).
FIGURE 2 | Bayesian inference phylogenetic tree used in the WP species delimitation method. Numbers above and below branches are
posterior probability values. The colored haplotypes indicate the ingroup. Each group of haplotypes in the ingroup delimitated by WP as
an exclusive lineage (species) has a different coloration. Species delimitated in our ingroup by WP: 1– Aphyocharax brevicaudatus (yellow
colored); 2– A. avary (grey colored); 3– A. sp. “Itapecuru” (blue colored); 4– A. sp. “Mearim” (red colored); and 5– A. sp. “Munim” (green
colored).
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Pâmella S.Brito, Erick C. Guimarães, Karen L.A. Guimarães, Luís R.R. Rodrigues, Marcelo R. Anjos, Axel M.Katz, Luis F. Carvalho-Costa and Felipe P. Ottoni
GMYC and bPTP. Both single locus coalescent species delimitation methods
delimited different lineages (species). The GMYC delimitated the following species:
Aphyocharax brevicaudatus, A. avary, Aphyocharax sp. “Itapecuru,” Aphyocharax
sp. “Mearim,” and Aphyocharax sp. “Munim” (Fig. 2). The bPTP delimitated the
following species: Aphyocharax brevicaudatus, A. avary, and one single lineage including
Aphyocharax sp. “Itapecuru” + Aphyocharax sp. “Mearim” + Aphyocharax sp. “Munim”
(Fig. 3).
ABDG. This method had two possible results. Result 1 delimited three species
within our ingroup: Aphyocharax brevicaudatus, A. avary, and one single lineage
including Aphyocharax sp. “Itapecuru” + Aphyocharax sp. “Mearim” + Aphyocharax sp.
“Munim” (Fig. 3). These same three groups (species) were delimited between p values
ranging from 0.0077 and 0.0028. Result 2 delimited five species within our ingroup:
Aphyocharax brevicaudatus, A. avary, Aphyocharax sp. “Itapecuru,” Aphyocharax sp.
“Mearim” and Aphyocharax sp. “Munim.” Initially, result 2 delimited the same groups
as result 1, but a “recursive partition” later delimited the five groups listed above (Fig.
3) with a p value of 0.0017.
FIGURE 3 | Ultrametric tree (Bayesian inference) including unique haplotypes summarizing the results of the GMYC, bPTP and ABGD
(results 1 and 2). Numbers above and below branches are posterior probability values. Red values: posterior probabilities calculated by the
software Beast; black values: posterior probabilities calculated by the software Mr. Bayes. Values below 50 are indicated as “- “. The stars
indicate the ingroup.
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Cryptic speciation of the genus Aphyocharax
DISCUSSION
Besides our phylogenetic approach to delimit lineages using species delimitation
methods, we can state the following about the Aphyocharax phylogeny. The topology
of our phylogenetic analysis (Fig. 2) recovered Aphyocharax as monophyletic but
supported by a low posterior probability value - pp (0.88), with A. nattereri as sister to all
other Aphyocharax species. The reason for the low support is probably because the fast
evolutionary rate of Cytochrome b (Cytb) is more suitable for species delimitation or to
reconstruct the relationships of closely related species (Avise, 2000). However, besides
A. nattereri, the other remaining OTU form a robust clade supported by the maximum
posterior probability value.
The last clade also includes two smaller clades supported by low posterior probability
values, which demonstrates that the gene used is not suitable for recovering older and the
most basal branch and node relationships (Fig. 2). The first clade (pp = 0.59) includes A.
rathbuni, A. anisitsi, a putative undescribed species (Aphyocharax sp.) and A. dentatus. The
second clade (node support = 0.55) includes two other clades. Clade 1 comprises several
haplotypes considered here as A. pusillus and Aphyocharax cf. erythrurus (with maximum
node support). Clade 2 contains our ingroup (with maximum node support) that
comprises species and populations occurring along the coastal river basins of the eastern
Amazon region and surroundings: Aphyocharax brevicaudatus (from the Maracaçumé
River basin), A. avary (from the Tocantins River basin), Aphyocharax sp. “Itapecuru”
(from the Itapecuru River basin), Aphyocharax sp. “Mearim” (from the Mearim River
basin) and Aphyocharax sp. “Munim” (from the Munim River basin) (colored haplotypes
in Fig. 2; Tab. 1).
The species and populations of the latter clade (colored clade) have the morphotype
and typical character states of the type material of A. avary (as described and discussed
by Brito et al., 2018), a species with an imprecise type locality in the Madeira River
drainage of the Amazon River basin (Brito et al., 2018). Aphyocharax brevicaudatus is
easily distinguished from the populations of our ingroup by unambiguous character
states (see Brito et al., 2019). It is the most basal taxon in the ingroup clade. Aphyocharax
avary was recovered as the sister group of all the other lineages from the coastal river
basins in the eastern Amazon region. This clade has a moderate node support value
(0.88). The monophyly of the lineages from these coastal river basins is supported by the
maximum node support value (Fig. 2). Within this latter group, the lineage Aphyocharax
sp. “Munim” is the sister group to the clade Aphyocharax sp. “Itapecuru” and Aphyocharax
sp. “Mearim.” This last clade has a high node support value (0.98) (Fig. 2).
The WP method recovered five lineages (i.e., species) in our ingroup that are all
supported by the maximum node support value: 1– Aphyocharax brevicaudatus (yellow
colored); 2– A. avary (grey colored); 3– Aphyocharax sp. “Itapecuru” (blue colored);
4– Aphyocharax sp. “Mearim” (red colored); and 5– Aphyocharax sp. “Munim” (green
colored) (Fig. 2). Three of these lineages are possible undescribed cryptic species.
Aphyocharax avary from the Tocantins River basin might be another one due to its
disjunct geographical distribution to the type locality of A. avary. However, resolving
this issue depends on the inclusion of haplotypes from the type locality of A. avary.
Therefore, this species delimitation method recovered at least three undescribed species.
The GMYC single-threshold version delimited the same lineages (i.e., species) as the
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Pâmella S.Brito, Erick C. Guimarães, Karen L.A. Guimarães, Luís R.R. Rodrigues, Marcelo R. Anjos, Axel M.Katz, Luis F. Carvalho-Costa and Felipe P. Ottoni
WP (Fig. 3) in our ingroup. On the other hand, the bPTP delimited three lineages in our
ingroup: Aphyocharax brevicaudatus, A. avary, and a single lineage including Aphyocharax
sp. “Itapecuru” + Aphyocharax sp. “Mearim” + Aphyocharax sp. “Munim” (Fig. 3).
Thus, according to the bPTP, we have at least one undescribed cryptic species in the
region. The situation for Aphyocharax avary from the Tocantins River is the same here
compared to the WP and GMYC. The ABGD analyses produced two possible results:
one corroborating the same result from the bPTP (ABGD result 1) in our ingroup, and
another (ABGD result 2) corroborating the results from the WP and GMYC analyses
(Fig. 2) in our ingroup. Therefore, the number of species depends on the method
used, although all of them pointed to undescribed cryptic species in the region. Some
studies argue that in some cases GMYC can lead to an overestimation of the number of
species (e.g., Talavera et al., 2013; García-Melo et al., 2019). Despite that in our study the
GMYC analysis delimited the highest number of species, the results of this method were
corroborated by the WP and ABGD result 2. Therefore, we cannot state that the GMYC
analysis overestimated the number of delimited species in our study.
Although molecular taxonomy studies involving fishes from the coastal river basins
of the Eastern Amazon region are still scarce, some studies have been published in recent
years, especially for the Characidae, which corroborate that this region has endemic
characid species (e.g., Guimarães et al., 2018b, 2019, 2020b; Brito et al., 2019). Along
with these studies, we show the usefulness of molecular approaches for revealing cryptic
lineages (species) in the region and opportunities for new discoveries to enhance our
knowledge of neotropical freshwater fishes.
Based on our data obtained here, it is clear that the Cytb gene is very effective at
delimiting lineages (species) due to its rapid evolutionary rate. Another conclusion
is that there is one or more cryptic undescribed species of Aphyocharax, depending
on the operational criterium used to delimit species, in the coastal river basins of the
Eastern Amazon region. This is not limited to Aphyocharax, since other published and
unpublished studies have found similar results for other characin groups (e.g., Guimarães
et al., 2018b, 2019, 2020) and Characidae genera (E. C. Guimarães, 2021, pers. comm.).
If similar approaches are applied, the same results might be found for other freshwater
fish groups in the studied region. Thus, further studies using molecular approaches
in the study area are needed to unravel hidden species and accurately estimate the
freshwater fish diversity of the region.
ACKNOWLEDGMENTS
We are grateful to CAPES (Coordenação de Aperfeiçoamento de Pessoal de Nível
Superior – Finance Code 001) and FAPEMA (Fundação de Amparo à Pesquisa e ao
Desenvolvimento Científico e Tecnológico do Maranhão) for providing the financial
and infrastructure support to carry out this work. AMK thanks Fundação Carlos
Chagas Filho de Amparo à Pesquisa do Estado do Rio de Janeiro (FAPERJ: grant
e–26/202.005/2020). Part of the examined material was collected by Elisabeth Henschel,
which was funded by the National Geographic Society (Early Career Grant Number
EC–316R–18). The English in this paper was reviewed by Nathan Smith.
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Cryptic speciation of the genus Aphyocharax
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AUTHORS’ CONTRIBUTION
Pâmella Silva de Brito: Conceptualization, Data curation, Formal analysis, Funding acquisition,
Investigation, Methodology, Project administration, Resources, Software, Supervision, Validation,
Visualization, Writing-original draft, Writing-review and editing.
Erick Cristofore Guimarães: Conceptualization, Data curation, Formal analysis, Funding acquisition,
Investigation, Methodology, Project administration, Resources, Software, Supervision, Validation,
Visualization, Writing-original draft, Writing-review and editing.
Karen Larissa Auzier Guimarães: Formal analysis, Investigation, Methodology, Writing-original draft,
Writing-review and editing.
Luís Reginaldo Ribeiro Rodrigues: Formal analysis, Investigation, Methodology, Writing-original draft,
Writing-review and editing.
Marcelo Rodrigues dos Anjos: Conceptualization, Data curation, Writing-original draft, Writing-review
and editing.
Axel Makay Katz: Formal analysis, Investigation, Methodology, Writing-original draft, Writing-review
and editing.
Luis Fernando Carvalho-Costa: Conceptualization, Data curation, Formal analysis, Funding acquisition,
Investigation, Methodology, Project administration, Resources, Software, Supervision, Writing-original
draft, Writing-review and editing.
Felipe Polivanov Ottoni: Conceptualization, Data curation, Formal analysis, Funding acquisition,
Investigation, Methodology, Project administration, Resources, Software, Supervision, Validation,
Visualization, Writing-original draft, Writing-review and editing.
ETHICAL STATEMENTS
Individuals collected for this study were euthanized with a buffered solution of Tricaine methanesulfonate
MS–222 (250 mg/L) for 10 min or more, until the opercular movements completely ceased, according to
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Neotropical Ichthyology, 19(4): e210095, 2021
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Cryptic speciation of the genus Aphyocharax
animal welfare laws and guidelines (Close et al., 1996, 1997; Leary et al., 2013). Sampling was authorized by
IBAMA and SISBIO through the documents Nº 02001.007241/2004–37 and Nº 42415, respectively.
COMPETING INTERESTS
The authors declare no competing interests.
This is an open access article under the terms of the
Creative Commons Attribution License, which permits
use, distribution and reproduction in any medium,
provided the original work is properly cited.
Distributed under
Creative Commons CC-BY 4.0
© 2021 The Authors.
Diversity and Distributions Published by SBI
HOW TO CITE THIS ARTICLE
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Brito PS, Guimarães EC, Guimarães KLA, Rodrigues LRR, Anjos MR, Katz AM,
Carvalho-Costa LF, Ottoni FP. Cryptic speciation in populations of the genus Aphyocharax
(Characiformes: Characidae) from eastern Amazon coastal river drainages and
surroundings revealed by single locus species delimitation methods. Neotrop Ichthyol. 2021;
19(4):e210095. https://doi.org/10.1590/1982-0224-2021-0095
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