Siluriformes, Loricariidae [PDF]

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Molecular Phylogenetics and Evolution 94 (2016) 492–517

Contents lists available at ScienceDirect

Molecular Phylogenetics and Evolution journal homepage: www.elsevier.com/locate/ympev

Molecular phylogeny of the highly diversified catfish subfamily Loricariinae (Siluriformes, Loricariidae) reveals incongruences with morphological classification q Raphaël Covain a,⇑, Sonia Fisch-Muller a, Claudio Oliveira b, Jan H. Mol c, Juan I. Montoya-Burgos d, Stéphane Dray e,f a

Muséum d’histoire naturelle, Département d’herpétologie et d’ichtyologie, route de Malagnou 1, case postale 6434, CH-1211 Genève 6, Switzerland Departamento de Morfologia, Universidade Estadual Paulista Júlio de Mesquita Filho, Instituto de Biociências, Laboratório de Biologia e Genética de Peixes, Rubião Junior 18618-970, Botucatu, SP, Brazil c University of Suriname, Center for Agricultural Research in Suriname, CELOS and Department of Biology, POB 9212, Paramaribo, Suriname d Université de Genève, Département de Génétique et Evolution, Sciences III, quai E. Ansermet 30, CH-1211 Genève 4, Switzerland e Université de Lyon, F-69000 Lyon, France f Université Lyon 1, CNRS, UMR5558, Laboratoire de Biométrie et Biologie Evolutive, F-69622 Villeurbanne, France b

a r t i c l e

i n f o

Article history: Received 24 February 2015 Revised 15 September 2015 Accepted 19 October 2015 Available online 26 October 2015 Keywords: Systematics Neotropics Mitochondrial genes Nuclear genes Freshwaters Amazon basin

a b s t r a c t The Loricariinae belong to the Neotropical mailed catfish family Loricariidae, the most species-rich catfish family. Among loricariids, members of the Loricariinae are united by a long and flattened caudal peduncle and the absence of an adipose fin. Despite numerous studies of the Loricariidae, there is no comprehensive phylogeny of this morphologically highly diversified subfamily. To fill this gap, we present a molecular phylogeny of this group, including 350 representatives, based on the analysis of mitochondrial and nuclear genes (8426 positions). The resulting phylogeny indicates that Loricariinae are distributed into two sister tribes: Harttiini and Loricariini. The Harttiini tribe, as classically defined, constitutes a paraphyletic assemblage and is here restricted to the three genera Harttia, Cteniloricaria, and Harttiella. Two subtribes are distinguished within Loricariini: Farlowellina and Loricariina. Within Farlowellina, the nominal genus formed a paraphyletic group, as did Sturisoma and Sturisomatichthys. Within Loricariina, Loricaria, Crossoloricaria, and Apistoloricaria are also paraphyletic. To solve these issues, and given the lack of clear morphological diagnostic features, we propose here to synonymize several genera (Quiritixys with Harttia; East Andean members of Crossoloricaria, and Apistoloricaria with Rhadinoloricaria; Ixinandria, Hemiloricaria, Fonchiiichthys, and Leliella with Rineloricaria), to restrict others (Crossoloricaria, and Sturisomatichthys to the West Andean members, and Sturisoma to the East Andean species), and to revalidate the genus Proloricaria. Ó 2015 Elsevier Inc. All rights reserved.

1. Introduction The Loricariinae represent a highly diversified subfamily among the large Neotropical catfish family Loricariidae, or suckermouth armored catfish. Loricariids have undergone an evolutionary radiation at a subcontinental scale, from Costa Rica to Argentina, which has been compared to that of the Cichlidae of the Great Lakes of the

q

This paper was edited by the Associate Editor G. Orti.

⇑ Corresponding author.

E-mail addresses: [email protected] (R. Covain), sonia.fisch-muller@ ville-ge.ch (S. Fisch-Muller), [email protected] (C. Oliveira), [email protected] (J.H. Mol), [email protected] (J.I. Montoya-Burgos), stephane.dray@ univ-lyon1.fr (S. Dray). http://dx.doi.org/10.1016/j.ympev.2015.10.018 1055-7903/Ó 2015 Elsevier Inc. All rights reserved.

Rift Valley in Africa (Schaefer and Stewart, 1993). The species core flock Loricariidae (sensu Lecointre et al., 2013), represents the most species rich family of the Siluriformes with 898 valid species and an estimated 300 undescribed species distributed in more than 100 genera (Reis et al., 2003; Ferraris, 2007; Eschmeyer and Fong, 2015). Extremely variable color patterns and body shapes among loricariid taxa reflect their high degree of ecological specialization, and because of their highly specialized morphology loricariids were recognized as a monophyletic assemblage in the earliest classifications of the Siluriformes (de Pinna, 1998). The Loricariidae are characterized by a depressed body covered by bony plates, and above all, by the modification of the mouth into a sucker disk. Within the Loricariidae, members of the subfamily Loricariinae are diagnosed by a long and depressed caudal

R. Covain et al. / Molecular Phylogenetics and Evolution 94 (2016) 492–517

peduncle and by the absence of an adipose fin. They live stuck to the substrate and show marked variations in body shape according to the various habitats colonized, from lotic to lentic systems, on mineral or organic substrates. For example, members of Farlowella resemble a thin stick and blend remarkably among submerged wood and leafs, whereas members of Pseudohemiodon are large and flattened and bury themselves in sandy substrates like flatfishes. Some groups have numerous teeth, pedunculated, and organized in a comblike manner, while other groups have few teeth or even no teeth on the premaxillae. Teeth are often strongly differentiated, and can be bicuspid straight and thick, spoonshaped, reduced in size or very long. An important diversity in lip characteristics, which can be strongly papillose, filamentous or smooth, also characterizes this subfamily (Isbrücker, 1979; Covain and Fisch-Muller, 2007). Different hypotheses have been proposed to classify the Loricariinae (summarized in Table 1). The first attempt was performed by Isbrücker (1979) who distributed them into four tribes and eight subtribes on the basis of external morphology, but without phylogenetic inferences. These included the Loricariini, comprising six subtribes (Loricariina, Planiloricariina, Reganellina, Rineloricariina, Loricariichthyina, and Hemiodontichthyina), the Harttiini, including two subtribes (Harttiina and Metaloricariina), the

493

Farlowellini, and the Acestridiini. The latter were subsequently placed in the subfamily Hypoptopomatinae by Schaefer (1991). In her PhD thesis, Rapp Py-Daniel (1997) proposed a phylogeny of the Loricariinae based on a phylogenetic analysis of morphological characters. She confirmed the monophyly of the subfamily, and split the Loricariinae into two tribes: Loricariini and Harttiini, the latter comprising Farlowellini (sensu Isbrücker, 1979). In a morphological phylogenetic analysis of the family Loricariidae, Armbruster (2004) also obtained a similar splitting based on a restricted sampling of the Loricariinae, with Harttiini (sensu Rapp Py-Daniel, 1997, comprising Harttia, Lamontichthys, Sturisoma, and Sturisomatichthys), forming the sister group of Loricariini (sensu Rapp Py-Daniel, 1997, comprising Crossoloricaria, Loricaria, Loricariichthys, Ixinandria, and Rineloricaria). Covain and FischMuller (2007), based on multivariate analyses of generic diagnostic characters, also split the subfamily into two tribes, the Harttiini and the Loricariini, and proposed four morphological groups within the Loricariini: (1) the Pseudohemiodon group, (2) the Loricaria group, (3) the Rineloricaria group, and (4) the Loricariichthys group. Montoya-Burgos et al. (1998) proposed a first molecular phylogeny of the family Loricariidae using mitochondrial genes. Although, their analysis included only nine representatives of the Loricariinae, they partially confirmed their subdivision into two

Table 1 Alternative classifications of the Loricariinae according to different authors.

The different colors provide limits of the different recognised tribes. These tribes can include different taxa according to the different authors. Salmon: Loricariini; blue: Harttiini; green: Farlowellini; red: Acestridiini.

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R. Covain et al. / Molecular Phylogenetics and Evolution 94 (2016) 492–517

main groups, but with Harttia (nominal genus of Harttiini) forming the sister genus of all other Loricariinae (comprising Farlowellini, part of Harttiini, and Loricariini). Covain et al. (2008) using mitochondrial genes, and Rodriguez et al. (2011) using mitochondrial and nuclear markers performed a molecular phylogeny on a small sampling of the Loricariinae. Both studies restricted Harttiini to Harttia, and included Farlowelliini as a subtribe of Loricariini. Within the latter, the Loricariichthys and Loricaria–Pseudohemiodon morphological groups (sensu Covain and Fisch-Muller, 2007) were confirmed as natural groupings, whereas monophyly of the Rineloricaria group was rejected. Similar results were also obtained using different markers by Cramer et al. (2011) in a molecular phylogeny of the Hypoptopomatinae (including four Loricariinae in the outgroup), and by Lujan et al. (2015) in a molecular phylogeny of the Loricariidae (including 14 Loricariinae). In addition to the conflicting results obtained using either morphological or molecular data, the validity of several genera was regularly questioned by different authors rendering the taxonomy of the group confused. Isbrücker and Isbrücker & Michels (in Isbrücker et al., 2001) described four new genera: Fonchiiichthys, Leliella, Quiritixys and Proloricaria, and revalidated the genus Hemiloricaria Bleeker, 1862 on the basis of a very restricted number of characters. Rapp Py-Daniel and Oliveira (2001) considered Cteniloricaria a junior synonym of Harttia. Ferraris (2003) maintained the validity of Cteniloricaria, and considered junior synonyms of already described genera all the genera described by Isbrücker and Isbrücker & Michels (in Isbrücker et al., 2001). Covain and Fisch-Muller (2007) followed Ferraris (2003) but maintained Cteniloricaria in synonymy with Harttia. Ferraris (2007) modified his previous statement and considered Fonchiiichthys, Proloricaria, and Hemiloricaria valid. Later on, Covain et al. (2012) revalidated Cteniloricaria. There are currently 239 species of Loricariinae considered valid, distributed in 32 genera (for a review see Covain and FischMuller, 2007; also Ghazzi, 2008; Ingenito et al., 2008; Fichberg and Chamon, 2008; Rapp Py-Daniel and Fichberg, 2008; Rodriguez and Miquelarena, 2008; Rodriguez and Reis, 2008; Rodriguez et al., 2008, 2011, 2012; Thomas and Rapp Py-Daniel, 2008; de Carvalho Paixão and Toledo-Piza, 2009; Thomas and Sabaj Pérez, 2010; Covain et al., 2012; Vera-Alcaraz et al., 2012; Oyakawa et al., 2013; Thomas et al., 2013; Ballen and Mojica, 2014; Fichberg et al., 2014; Londoño-Burbano et al., 2014). Given the confused systematics of the Loricariinae, we present a comprehensive and robust molecular phylogeny of this group based on mitochondrial and nuclear genes. The resulting phylogeny, in conjunction with morphological diagnostic characters, will be subsequently used to (1) redefine the tribal and subtribal ranks of the subfamily; (2) evaluate the validity and monophyly of the different genera, and (3) test alternative hypotheses of classification proposed in the literature. 2. Material and methods 2.1. Taxonomic sampling The molecular phylogeny was reconstructed using the taxonomic sampling given in Covain et al. (2008), and Rodriguez et al. (2011) with the addition of 326 representatives of the Loricariinae and 16 outgroup species. The outgroup representatives were chosen in other subfamilies of the Loricariidae. The list of material used for this study is provided in Table 2. The analyzed samples came from the tissue collection of the Muséum d’histoire naturelle de la Ville de Genève (MHNG); Academy of Natural Sciences of Drexel University in Philadelphia (ANSP); Smithsonian Tropical Research Institute (STRI), Panama; Laboratório de Biologia de Peixes, Departamento de Morfologia, Universidade Estadual Paulista, Campus de Botucatu (LBP); Auburn University Museum,

Montgomery (AUM); and Museu de Ciências e Tecnologia of the Pontifícia Universidade Católica do Rio Grande do Sul (MCP), Porto Alegre. The sequences were deposited in GenBank. 2.2. DNA extraction, choice of markers, amplification, and sequencing Tissue samples were preserved in 80% ethanol and stored at 20 °C. Total genomic DNA was extracted with the DNeasy Tissue Kit (Qiagen) following the instructions of the manufacturer. The choice of markers was governed by their ability to resolve inter generic relationships at subfamilial ranks. We thus selected the mitonchondrial genes 12S and 16S for the resolution of phylogenetic relationships between close ralatives (between species to between genera relationships), and the nuclear Fish Reticulon-4 receptor (f-rtn4r) gene composed of two introns and three exons. Exons of this marker are rather conserved and provide information for deeper relationships (intra-familial to inter-ordinal relationships) whereas intronic regions are more variable and offer the possibility to investigate phylogenetic relationships between closely related species. Thus, the selected molecular makers were used to examine a range of taxomonic levels at subfamilial rank, from intra-specific to inter-tribal relationshisps. The PCR amplifications of mitochondrial 12S and 16S, and the nuclear f-rtn4r genes were carried out using the Taq PCR Core Kit (Qiagen). The methodology for PCR amplifications followed Chiachio et al. (2008) for f-rtn4r using the set of primers Freticul4-D, Freticul4-R, Freticul4 D2, and Freticul4 R2 (Roxo et al., 2014). For the complete sequencing of f-rtn4r, three internal primers were designed additionally to Freticul4-iR (Roxo et al., 2014): Freticul4-iD2 50 -CAA CAT CAC YTG GAT TGA GG-30 , Freticul4-LiD 50 -ATG ACC GTG AGC TGC CAG GC-30 , and Freticul4-LiR 50 -GCT CAG TAA TAC GGT TGT TCT GCA-30 . To amplify the almost complete 12S, tRNAval and 16S mitochondrial genes in a single 2500 bp long fragment, a Nested PCR protocol was used. The external round of PCR was performed using the pair of primers Phe-L941 (Roxo et al., 2014) and H3059 (Alves-Gomes et al., 1995). The external amplifications were performed in a total volume of 50 ll, containing 5 ll of 10 reaction buffer, 1 ll of dNTP mix at 10 mM each, 1 ll of each primer at 10 lM, 0.2 ll of Taq DNA Polymerase equivalent to 1 unit of Polymerase per tube, and 1–4 ll of DNA. Cycles of amplification were programmed with the following profile: (1) 3 min. at 94 °C (initial denaturing), (2) 35 s. at 94 °C, (3) 30 s. at 51 °C, (4) 150 s. at 72 °C, and (5) 5 min at 72 °C (final elongation). Steps 2–4 were repeated 35–39 times according to the quality and concentration of DNA. The internal round of PCR was performed using 1 ll of DNA template sampled from external round PCR product, the pair of primers: An12S-1D: 50 -GTA TGA CAC TGA AGA TGT TAA G-30 and iH3059: 50 -GAA CTC AGA TCA CGT AGG-30 , and the same protocol as above except for the annealing temperature that was set to 54 °C. PCR products were sent to Macrogen Inc. (Seoul, Korea) for sequencing. For the complete sequencing of the 2500 bp long mitochondrial fragment, two internal primers were used: Lor1D-1D: 50 -AGG AGC CTG TTC TAG AAC CG-30 and Lor12S-3D (Covain et al., 2008) for a walking sequencing procedure with around 700 bp between each step. 2.3. Sequence alignment, phylogenetic reconstruction, and topological tests The DNA sequences were edited and assembled using BioEdit 7.0.1 (Hall, 1999), aligned using ClustalW (Thompson et al., 1994) and final alignment optimized by eye. Regions with ambiguous alignments in loop regions of mitochondrial ribosomal genes were excluded from the analyses. The fragment of the f-rtn4r gene analyzed here contained relatively long introns, ranging from 489 bp in Rineloricaria altipinnis to 1385 bp in R. cf. latirostris for the first intron, and from 373 bp in R. pentamaculata to 656 bp in

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Table 2 Taxa list, specimen and sequence data for the 350 Loricariinae and 18 outgroup representatives analyzed in this study. The acronyms of institutions follow Fricke and Eschmeyer (2015). Species

Catalog number

Field number

Locality

mt 12S + 16S bases + GenBank No.

Ref.

F-RTN4 bases + GenBank No.

Ref.

Harttia guianensis

MHNG 2643.016

GF00-351

2440 EU310447

2092 FJ013232

Loricaria parnahybae

MHNG 2602.067

BR98-274

French Guiana, Marouini River Brazil, Rio Parnahyba

Crossoloricaria venezuelae Dasyloricaria tuyrensis Farlowella aff. oxyrrynchac Farlowella platorynchus Hemiodontichthys acipenserinus Lamontichthys stibaros Limatulichthys punctatusc Loricaria clavipinna

INHS 35467

VZ 049

2419 EU310444

MHNG 2674.052

PA00-012

Venezuela, Rio Santa Rosa Panama, Rio Ipeti

MHNG 2588.064

PE96-022

Peru, Rio Tambopata

2433 EU310443

MHNG 2588.093

PE96-071

Peru, Rio Ucayali

2432 EU310446

MHNG 2651.012

GY04-015

2422 EU310448

MHNG 2677.039

MUS 208

MHNG 2651.013

GY04-018

MHNG 2640.044

PE98-002

Guyana, Rupununi River Peru, aquarium trade, Rio Itayab Guyana, Rupununi River Peru, Rio Putumayo

MHNG 2621.042

SU01-056

2428 EU310453

MHNG 2650.054

GY04-012

MHNG 2677.086

GF00-083

2438 EU310455

MHNG 2677.038

MUS 211

MHNG 2588.059

PE96-011

Surinam, Sarramacca River Guyana, Rupununi River French Guiana, Marouini River Peru, aquarium trade, Rio Itayab Peru, Rio Tambopata

UFRJ 6-EF4

BR 1114

Brazil, Rio Maranhão

2427 EU310459

MHNG 2651.009

GY04-083

2423 EU310458

1981 KR478422

Chiachio et al. (2008) Chiachio et al. (2008) Rodriguez et al. (2011) Rodriguez et al. (2011) Rodriguez et al. (2011) Rodriguez et al. (2011) Rodriguez et al. (2011) Rodriguez et al. (2011) Rodriguez et al. (2011) Rodriguez et al. (2011) Rodriguez et al. (2011) Rodriguez et al. (2011) Rodriguez et al. (2011) Rodriguez et al. (2011) Rodriguez et al. (2011) Rodriguez et al. (2011) Rodriguez et al. (2011) Rodriguez et al. (2011) Rodriguez et al. (2011) Rodriguez et al. (2011) Rodriguez et al. (2011) Rodriguez et al. (2011) Rodriguez et al. (2011) Rodriguez et al. (2011) This study

MHNG 2651.033

GY04-187

Guyana, Rupununi River Guyana, Sawarab River

c

Sturisoma robustum

MHNG 2588.055

PE96-001

Peru, Rio de las Piedras

2440 EU310460

Sturisomatichthys citurensis Fonchiiloricaria nanodon Fonchiiloricaria nanodon Spatuloricaria aff. caquetaec Spatuloricaria sp. Nanay Apistoloricaria ommation Apistoloricaria ommation Aposturisoma myriodon Aposturisoma myriodon Brochiloricaria macrodon Brochiloricaria sp. Uruguay Crossoloricaria aff. bahuaja Crossoloricaria bahuaja Crossoloricaria cephalaspis Crossoloricaria cephalaspis Crossoloricaria rhami Crossoloricaria variegata Cteniloricaria napova

MHNG 2676.004

PA97-032

Panama, Rio Tuyra

2438 EU310462

MHNG 2710.048

PE08-199

Peru, Rio Monzon

2432 HM592626

MHNG 2710.060

PE08-336

Peru, Rio Aucayacu

2432 HM592627

MHNG 2710.050

PE08-230

Peru, Rio Huallaga

2421 HM592624

MHNG 2677.071

PE05-014

2422 HM592625

ANSP 182331

P6265

Peru, aquarium trade, Rio Nanayb Peru, Rio Amazonas

2417 KR478088

Covain et al. (2008) Covain et al. (2008) Covain et al. (2008) Covain et al. (2008) Covain et al. (2008) Covain et al. (2008) Covain et al. (2008) Covain et al. (2008) Covain et al. (2008) Covain et al. (2008) Covain et al. (2008) Covain et al. (2008) Covain et al. (2008) Covain et al. (2008) Covain et al. (2008) Covain et al. (2008) Covain et al. (2008) Covain et al. (2008) Covain et al. (2008) Covain et al. (2008) Rodriguez et (2011) Rodriguez et (2011) Rodriguez et (2011) Rodriguez et (2011) This study

MHNG 2708.086

MUS 437

2423 KR478089

This study

1982 KR478423

This study

MHNG 2710.035

PE08-004

Peru, aquarium trade, Rio Amazonasb Peru, Rio Huacamayo

2435 KR477910

This study

2289 KR478244

This study

MHNG 2710.043

PE08-131

Peru, Rio Huyhuantal

2435 KR477911

This study

2287 KR478245

This study

LBP 5048

LBPN 24033

Brazil, Rio Paraguay

2425 KR478052

This study

1972 KR478386

This study

MCP 28414

MCP 28414

Brazil, Rio Ibicui-Mirim

2426 KR478053

This study

1986 KR478387

This study

MHNG 2710.072

PE08-714

Peru, Rio Cushabatai

2415 KR478091

This study

1983 KR478425

This study

ANSP 180793

P4078

Peru, Rio Madre de Dios 2417 KR478092

This study

1967 KR478426

This study

Stri-1449

53

Colombia, Rio San Juan

2421 KR478077

This study

2001 KR478411

This study

Stri-1577

22

Colombia, Rio Atrato

2421 KR478076

This study

1997 KR478410

This study

MHNG 2710.041 Stri-6781

PE08-120 36

Peru, Rio Aguaytia Panama, Rio Tuira

2416 KR478083 2422 KR478075

This study This study

1984 KR478417 1986 KR478409

This study This study

MHNG 2704.030

SU07-650

Brazil, Paru de Oeste River

2440 KR477882

This study

2086 KR478216

This study

Loricariichthys maculatus Loricariichthys microdon Metaloricaria paucidens Planiloricaria cryptodon Rineloricaria lanceolata Rineloricaria osvaldoic Rineloricaria platyura Sturisoma monopelte

2423 EU310452

2419 EU310445

2433 EU310449 2426 EU310450 2427 EU310451

2427 EU310454

2418 EU310456 2423 EU310457

2439 EU310461

1967 FJ013231 1994 HM623647 1996 HM623639 2228 HM623650 2292 HM623649 2231 HM623645 2029 HM623648 1950 HM623644 1964 HM623653 2212 HM623642 1934 HM623643 2064 HM623637 1991 HM623646 2211 HM623640 2008 HM623652 2204 HM623641 1965 HM623651 2547 HM623636 2259 HM623635 al.

2006 HM623656

al.

2006 HM623657

al.

1971 HM623654

al.

1980 HM623655

(continued on next page)

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Table 2 (continued) Species

Catalog number

Field number

Locality

mt 12S + 16S bases + GenBank No.

Ref.

F-RTN4 bases + GenBank No.

Ref.

Cteniloricaria platystoma Cteniloricaria platystoma Cteniloricaria platystoma Cteniloricaria platystoma Cteniloricaria platystoma Dasyloricaria latiura Dasyloricaria tuyrensis Farlowella schreitmuelleri Farlowella acus

MHNG 2672.067

SU05-340

2439 KR477888

This study

2091 KR478222

This study

MHNG 2674.003

SU05-039

2441 KR477889

This study

2090 KR478223

This study

MHNG 2650.082

GY04-336

2437 KR477881

This study

2090 KR478215

This study

MHNG 2700.054

GF07-265

2437 KR477902

This study

2089 KR478236

This study

MHNG 2643.015

GF00-352

2439 KR477887

This study

2089 KR478221

This study

Stri-1559 Stri-4140

20 51

Suriname, Corantijn River Suriname, Suriname River Guyana, Essequibo River French Guiana, Mana River French Guiana, Marouini River Panama, Rio Atrato Panama, Rio Tuira

2424 KR477966 2424 KR477965

This study This study

2017 KR478300 2018 KR478299

This study This study

MHNG 2601.087

BR98-106

Brazil, Rio Guamá

2437 KR477943

This study

2241 KR478277

This study

MER95T-22

42

2440 KR477936

This study

2311 KR477936

This study

Farlowella aff. rugosa Farlowella amazona Farlowella curtirostra Farlowella hahni Farlowella knerii Farlowella mariaelenae Farlowella martini Farlowella nattereri

ANSP 179 768 MHNG 2601.065 MER95T-13 MHNG 2678.022 MHNG 2710.052 VZ-59

T2200 BR98-052 43 PR-029 PE08-259 45

Venezuela, Valencia Lake Guyana, Simoni River Brazil, Rio Acara Venezuela, Rio Motatan Argentina, Santa Fé Peru, Rio Aspuzana Venezuela, Rio Caipe

2435 2432 2435 2437 2437 2439

This This This This This This

2298 2299 2301 2235 2234 2309

This This This This This This

VZ-126 MHNG 2650.099

49 GY04-291

2436 KR477940 2439 KR477952

This study This study

2307 KR478274 2305 KR478286

This study This study

Farlowella nattereri

MHNG 2654.067

GY04-306

2438 KR477944

This study

2306 KR478278

This study

Farlowella oxyrryncha Farlowella oxyrryncha Farlowella oxyrryncha Farlowella oxyrryncha Farlowella oxyrryncha Farlowella oxyrryncha Farlowella oxyrryncha Farlowella paraguayensis Farlowella paraguayensis Farlowella platorynchus Farlowella platorynchus Farlowella platorynchus Farlowella reticulata

MHNG 2710.034

PE08-051

Venezuela, Rio Aroa Guyana, Kurupukari cross Guyana, Kurupukari cross Peru, Rio Huacamayo

2437 KR477953

This study

2239 KR478287

This study

MHNG 2613.035

CA 21

Peru, Rio Ucayali

2437 KR477960

This study

2241 KR478294

This study

MHNG 2601.095

BR98-118

Brazil, Rio Guamá

2440 KR477958

This study

2240 KR477958

This study

LBP 2441

LBPN 16200

Brazil, Rio Araguiaia

2436 KR477956

This study

2183 KR478290

This study

MHNG 2710.069

PE08-698

Peru, Rio Neshua

2437 KR477955

This study

2242 KR478289

This study

MHNG 2710.081

PE08-823

Peru, Rio Cushabatai

2437 KR477957

This study

2242 KR478291

This study

LBP4043

LBPN 22907

Brazil, Rio Jurua

2437 KR477959

This study

2228 KR478293

This study

Stri-2205

25

2437 KR477961

This study

2236 KR478295

This study

LBP 5217

LBPN 26396

Paraguay, Arroyo Curuguati Brazil, Rio Paraná

2434 KR477962

This study

2238 KR478296

This study

MHNG 2650.096

GY04-290

2435 KR477949

This study

2296 KR478283

This study

MHNG 2602.021

BR98-163

Guyana, Kurupukari cross Brazil, Rio Peritoro

2435 KR477950

This study

2302 KR478284

This study

MHNG 2710.094

PE08-906

Peru, Rio Ucayali

2432 KR477951

This study

2301 KR478285

This study

MHNG 2683.081

GF06-637

2439 KR477963

This study

2243 KR478297

This study

Farlowella reticulata

MHNG 2683.070

GF06-588

2438 KR477942

This study

2242 KR478276

This study

Farlowella reticulata

MHNG 2681.060

GF06-118

2437 KR477964

This study

2242 KR478298

This study

Farlowella smithi Farlowella taphorni Farlowella vittata Harttia aff. punctata Harttia carvalhoi

ANSP 180541 VZ-89 VZ-63 LBP 5839 MHNG 2587.027

P4099 48 46 LBP 28353 BR 1236

2436 2433 2438 2433 2432

This This This This This

2236 2168 2303 2084 2046

This This This This This

Harttia carvalhoi

LBP 2115

LBP 21352

Harttia Harttia Harttia Harttia

LBP 5859 LBP 5863 LBP 7505 MHNG 2690.013

LBP 28331 LBP 28339 LBP 34804 SU01-445

MHNG 2643.022

GF99-202

French Guiana, Maroni River French Guiana, Mana River French Guiana, Oyapock River Peru, Rio Manuripe Venezuela, Rio Mayupa Venezuela, Rio Caipe Brazil, Rio Tocantins Brazil, Rio Paraíba do Sul Brazil, Rio Paraíba do Sul Brazil, Rio Tapajós Brazil, Rio Tapajós Brazil, Rio Tapajós Suriname, Coppename River French Guiana, Oyapock River

dissidens dissidens duriventris fluminensis

Harttia fowleri

KR477948 KR477937 KR477938 KR477941 KR477954 KR477939

KR477945 KR477946 KR477947 KR477898 KR477891

study study study study study study

study study study study study

KR478282 KR478271 KR478272 KR478275 KR478288 KR478273

KR478279 KR478280 KR478281 KR478232 KR478225

study study study study study study

study study study study study

2433 KR477890

This study

2046 KR478224

This study

2435 2435 2432 2435

This This This This

1955 1954 1951 2092

This This This This

KR477892 KR477914 KR477915 KR477884

2442 KR477880

study study study study

This study

KR478226 KR478248 KR478249 KR478218

2086 KR478214

study study study study

This study

497

R. Covain et al. / Molecular Phylogenetics and Evolution 94 (2016) 492–517 Table 2 (continued) Species

Catalog number

Field number

Locality

mt 12S + 16S bases + GenBank No.

Ref.

F-RTN4 bases + GenBank No.

Ref.

Harttia gracilis Harttia guianensis

LBP 6331 MHNG 2662.091

LBP 29819 GF03-160

2433 KR477916 2438 KR477885

This study This study

2041 KR478250 2092 KR478219

This study This study

Harttia guianensis

MHNG 2680.053

RV-21

2443 KR477886

This study

2092 KR478220

This study

Harttia kronei

MHNG 2586.058

BR 1166

2424 KR477900

This study

2081 KR478234

This study

Harttia kronei

LBP 2661

LBP 17427

2426 KR477894

This study

2083 KR478228

This study

Harttia kronei

LBP 2883

LBP 18609

2425 KR477895

This study

2080 KR478229

This study

Harttia kronei

LBP 1269

LBP 11215

2426 KR477899

This study

2080 KR478233

This study

Harttia Harttia Harttia Harttia

LBP 6847 LBP 6492 DZSJRP 2819 LBP 2121

LBP 31528 LBP 31545 BR98-747 LBP 21362

2435 2436 2429 2435

KR477918 KR477917 KR477903 KR477896

This This This This

study study study study

2068 2068 2072 2041

KR478252 KR478251 KR478237 KR478230

This This This This

study study study study

LBP 5836 MHNG 2645.059 MHNG 2645.053 LBP 5845 LBP 5860 LBP 5861 LBP 5838

LBP 28348 BR 995 BR 1051 LBP 28327 LBP 28333 LBP 28335 LBP 28352

Brazil, Rio Paraná French Guiana, Approuague River French Guiana, Sinnamary River Brazil, Rio Ribeira de Iguape Brazil, Rio Ribeira de Iguape Brazil, Rio Ribeira de Iguape Brazil, Rio Ribeira de Iguape Brazil, Rio São Francisco Brazil, Rio São Francisco Brazil, Rio São Francisco Brazil, Rio Paraíba do Sul Brazil, Rio São Francisco Brazil, Rio Tocantins Brazil, Rio Tocantins Brazil, Rio Xingu Brazil, Rio Xingu Brazil, Rio Xingu Brazil, Rio São Francisco

2429 2431 2430 2433 2432 2436 2429

KR477897 KR477893 KR477905 KR477907 KR478245 KR477908 KR477904

This This This This This This This

study study study study study study study

2060 2084 2084 1971 1973 1973 2061

KR478231 KR478227 KR478239 KR478241 KR478246 KR478242 KR478238

This This This This This This This

study study study study study study study

LBP 6528

LBP 31652

Brazil, Rio São Francisco 2431 KR477919

This study

2061 KR477919

This study

LBP 5857 LBP 5850 LBP 5838

LBP 28329 LBP 28367 LBP 28351

Brazil, Rio Tapajós 2436 KR477906 Brazil, Rio Tocantins 2433 KR477901 Brazil, Rio São Francisco 2429 KR477920

This study This study This study

1968 KR478240 2085 KR478235 2061 KR478254

This study This study This study

MHNG 2674.042

SU05-001

2438 KR477883

This study

2092 KR478217

This study

LBP 5835 MHNG 2704.029

LBP 28346 SU07-644

Suriname, Suriname River Brazil, Rio São Francisco Brazil, Paru de Oeste River Suriname, Nassau Mountains Suriname, Nassau Mountains Suriname, Nassau Mountains French Guiana, Trinité Mountains French Guiana, Trinité Mountains French Guiana, Trinité Mountains French Guiana, Balenfois Mountains French Guiana, Balenfois Mountains French Guiana, Balenfois Mountains French Guiana, Trinité Mountains French Guiana, Trinité Mountains French Guiana, Trinité Mountains French Guiana, Lucifer Mountains French Guiana, Lucifer Mountains French Guiana, Lucifer Mountains French Guiana, Lucifer Mountains French Guiana, Lucifer Mountains French Guiana, Lucifer Mountains French Guiana, Crique Limonade

2433 KR477913 2437 KR477909

This study This study

2054 KR478247 2092 KR478243

This study This study

2418 KR478145

This study

2026 KR478474

This study

2417 KR478146

This study

2026 KR478475

This study

2418 KR478131

This study

2026 KR478460

This study

2418 KR478164

This study

2021 KR478490

This study

2418 KR478165

This study

2022 KR478491

This study

2418 KR478135

This study

2022 KR478464

This study

2418 KR478136

This study

2005 KR478465

This study

2419 KR478159

This study

2005 KR478485

This study

2418 KR478133

This study

2005 KR478462

This study

2418 KR478144

This study

2022 KR478473

This study

2422 KR478134

This study

2022 KR478463

This study

2418 KR478139

This study

2022 KR478468

This study

2414 KR478153

This study

2152 KR478479

This study

2414 KR478154

This study

2149 KR478480

This study

2414 KR478155

This study

2152 KR478481

This study

2414 KR478156

This study

2152 KR478482

This study

2414 KR478158

This study

2152 KR478484

This study

2414 KR478157

This study

2148 KR478483

This study

2414 KR478478

This study

NA



leiopleura leiopleura longipinna loricariformis

Harttia novalimensis Harttia punctata Harttia punctata Harttia sp. 1 Xingu Harttia sp. 2 Xingu Harttia sp. 3 Xingu Harttia sp. Rio São Francisco Harttia sp. Serra do Cipó Harttia sp. Tapajos Harttia sp. Tocantins Harttia sp. Três Marias Harttia surinamensis Harttia torrenticola Harttia tuna

Harttiella crassicauda MHNG 2679.098

MUS 306

Harttiella crassicauda MHNG 2674.051

MUS 221

Harttiella crassicauda MHNG 2674.051

MUS 231

Harttiella intermedia

MHNG 2713.087

MUS 650

Harttiella intermedia

MHNG 2713.087

MUS 651

Harttiella intermedia

MHNG 2713.087

MUS 652

Harttiella longicauda

MHNG 2723.094

MUS 470

Harttiella longicauda

MHNG 2723.094

MUS 463

Harttiella longicauda

MHNG 2723.094

MUS 456

Harttiella longicauda

MHNG 2699.070

GF07-026

Harttiella longicauda

MHNG 2699.070

GF07-082

Harttiella longicauda

MHNG 2699.070

GF07-111

Harttiella lucifer

MHNG 2721.088

GF10-034

Harttiella lucifer

MHNG 2721.088

GF10-043

Harttiella lucifer

MHNG 2721.088

GF10-037

Harttiella lucifer

MHNG 2721.091

GF10-051

Harttiella lucifer

MHNG 2721.091

GF10-053

Harttiella lucifer

MHNG 2721.091

GF10-055

Harttiella lucifer

MHNG 2712.085

MUS 592

(continued on next page)

498

R. Covain et al. / Molecular Phylogenetics and Evolution 94 (2016) 492–517

Table 2 (continued) Species

Catalog number

Field number

Locality

mt 12S + 16S bases + GenBank No.

Ref.

F-RTN4 bases + GenBank No.

Ref.

Harttiella lucifer

MHNG 2712.085

MUS 593

2414 KR478151

This study

NA



Harttiella lucifer

MHNG 2712.085

MUS 594

2413 KR478152

This study

NA



Harttiella parva

MHNG 2723.093

MUS 606

2416 KR478147

This study

2026 KR478476

This study

Harttiella parva

MHNG 2723.093

MUS 607

2416 KR478148

This study

2026 KR478477

This study

Harttiella parva

MHNG 2723.093

MUS 611

2416 KR478477

This study

2026 KR478478

This study

Harttiella pilosa

MHNG 2682.055

GF06-344

2417 KR478132

This study

2026 KR478461

This study

Harttiella pilosa

MHNG 2682.055

GF06-343

2417 KR478137

This study

2026 KR478466

This study

Harttiella pilosa

MHNG 2724.002

GF03-033

2419 KR478138

This study

2026 KR478467

This study

Hemiodontichthys acipenserinus Hemiodontichthys acipenserinus Hemiodontichthys acipenserinus Hemiodontichthys acipenserinus Ixinandria steinbachi Lamontichthys filamentosus Lamontichthys filamentosus Lamontichthys llanero Lamontichthys stibaros Limatulichthys punctatus Limatulichthys punctatus Limatulichthys punctatus Limatulichthys punctatus Limatulichthys punctatus Limatulichthys punctatus Limatulichthys punctatus Loricaria sp. Guyana Loricaria sp. Guyana Loricaria aff. nickeriensis Loricaria aff. parnahybae Loricaria apeltogaster Loricaria cataphracta

MHNG 2588.057

PE96-005

French Guiana, Crique Limonade French Guiana, Crique Limonade French Guiana, Atachi Bakka Mountains French Guiana, Atachi Bakka Mountains French Guiana, Atachi Bakka Mountains French Guiana, Tortue Mountains French Guiana, Tortue Mountains French Guiana, Tortue Mountains Peru, Madre de Dios

2425 KR478140

This study

2259 KR478469

This study

MHNG 2602.007

BR98-138

Brazil, Rio Guamá

2421 KR478141

This study

2217 KR478470

This study

MCP 28819

MCP 28819

Brazil, Rio Purus

2424 KR478142

This study

2238 KR478471

This study

LBP 5524

LBPN 26640

Brazil, Rio Jari

2422 KR478143

This study

2283 KR478472

This study

NA MHNG 2680.009

IXS2 MUS 310

Argentina, Salta Peru, aquarium trade

2427 KR477986 2434 KR478262

This study This study

2513 KR478320 2116 KR478263

This study This study

LBP 162

LBPN 4038

Brazil, Rio Branco

2433 KR477930

This study

2115 KR478264

This study

MHNG 2749.019

MUS 356

2434 KR477928

This study

2089 KR478262

This study

MHNG 2710.049

PE08-224

Colombia, aquarium trade Peru, Rio Huallaga

2433 KR477931

This study

2040 KR478265

This study

ANSP 182707

P6232

Peru, Rio Itaya

2424 KR478095

This study

1957 KR478429

This study

MHNG 2602.009

BR98-140

Brazil, Rio Guamá

2424 KR478094

This study

1963 KR478428

This study

AUM 42223

V5319

Venezuela, Rio Orinoco

2425 KR478097

This study

1960 KR478431

This study

LBP 5055

LBPN 23618

Brazil, Rio Jurua

2422 KR478096

This study

1959 KR478430

This study

MHNG 2710.037

PE08-112

Peru, Rio Agaytia

2427 KR478093

This study

1959 KR478427

This study

LBP 5285

LBPN 26769

Brazil, Rio Jari

2427 KR478183

This study

1956 KR478508

This study

LBP 5249

LBPN 26472

Brazil, Rio Jari

2426 KR478182

This study

1958 KR478507

This study

MHNG 2650.057 MHNG 2651.031 MHNG 2681.009

GY04-110 GY04-191 GF06-044

2424 KR478068 2424 KR478069 2424 KR478061

This study This study This study

1979 KR478402 1983 KR478403 1944 KR478395

This study This study This study

LBP 1615

LBPN 11690

Guyana, Pirara River Guyana, Sawarab bridge French Guiana, Oyapock River Brazil, Rio Araguaia

2434 KR478059

This study

1977 KR478393

This study

NA MHNG 2749.022

NA GF98-044

2427 KR478056 2428 KR478057

This study This study

1973 KR478390 1943 KR478391

This study This study

Loricaria cataphracta MHNG 2683.061

GF06-570

2425 KR478062

This study

1933 KR478396

This study

Loricaria cataphracta MHNG 2744.037

SU08-042

2424 KR478054

This study

1932 KR478388

This study

Loricaria cataphracta MHNG 2749.021

SU08-943

2424 KR478055

This study

1932 KR478389

This study

Loricaria cf. lata Loricaria nickeriensis

LBP 5053 MHNG 2672.080

LBPN 16148 SU05-334

2423 KR478058 2424 KR478060

This study This study

1961 KR478392 1932 KR478394

This study This study

Loricaria prolixa Loricaria prolixa Loricaria simillima

LBP 7511 LBP 7511 MHNG 2677.075

LBPN 34925 LBPN 34924 PE05-030

2429 KR478063 2428 KR478064 2424 KR478065

This study This study This study

1975 KR478397 1975 KR478398 1950 KR478399

This study This study This study

Loricaria sp. Araguaia Loricaria sp. Branco Loricaria sp. Branco Loricaria sp. Mato Grosso

LBP 5049

LBPN 11506

Argentina, Entre Rios French Guiana, Kourou River French Guiana, Mana River Suriname, Suriname River Suriname, Commewijne River Brazil, Rio Araguaia Suriname, Corantijn River Brazil, Rio Paraná Brazil, Rio Paraná Peru, aquarium trade, Rio Amazonasb Brazil, Rio Araguaia

2429 KR478066

This study

2006 KR478400

This study

LBP 169 LBP 223 MCP 36566

LBPN 4032 LBPN 4101 MCP 36566

Brazil, Rio Branco Brazil, Rio Branco Paraguay, Mato Grosso

2424 KR478067 2424 KR478090 2429 KR478070

This study This study This study

1969 KR478401 1967 KR478424 1949 KR478404

This study This study This study

499

R. Covain et al. / Molecular Phylogenetics and Evolution 94 (2016) 492–517 Table 2 (continued) Species

Catalog number

Field number

Locality

mt 12S + 16S bases + GenBank No.

Ref.

F-RTN4 bases + GenBank No.

Ref.

Loricaria sp. Orinoco Loricaria sp. Paraguay Loricaria sp. Rupununi Loricaria tucumanensis Loricariichthys anus

AUM 42224 MHNG 2677.003

V5315 PY9093

Venezuela, Rio Orinoco Paraguay, Rio Paraguay

2426 KR478071 2427 KR478072

This study This study

1961 KR478071 1930 KR478406

This study This study

MHNG 2651.036

GY04-129

2427 KR478074

This study

1967 KR478408

This study

NA

AG06-018

Guyana, Rupununi River Argentina, Ita-Ibate

2423 KR478073

This study

1976 KR478407

This study

MCP 28415

MCP 28415

2430 KR478175

This study

2280 KR478500

This study

Loricariichthys anus

MCP 21317

MCP 21317

2430 KR478174

This study

2276 KR478499

This study

Loricariichthys anus Loricariichthys castaneus Loricariichthys castaneus Loricariichthys castaneus Loricariichthys cf. ucayalensis Loricariichthys derbyi Loricariichthys derbyi Loricariichthys labialis Loricariichthys melanocheilus Loricariichthys platymetopon Loricariichthys sp. Amazonas Loricariichthys sp. Jari Loricariichthys sp. Jari Loricariichthys sp. Orinoco Loricariichthys sp. Rio Baia Metaloricaria nijsseni

LBP 578 MHNG 2583.068

LBPN 7309 BR 162

2429 KR478176 2430 KR478114

This study This study

2272 KR478501 2230 KR478444

This study This study

LBP 7489

LBPN 35548

Brazil, Rio Grande do Sul Brazil, Rio Grande do Sul Brazil, Rio Guiaba Brazil, surroundings of Rio de Janeiro Brazil

2429 KR478115

This study

2275 KR478445

This study

LBP 7490

LBPN 35549

Brazil

2429 KR478116

This study

2279 KR478446

This study

ANSP 182668

P6046

Peru, Rio Nanay

2424 KR478117

This study

2197 KR478447

This study

MHNG 2602.061 LBP 5531 MHNG 2677.001

BR98-250 LBPN 27214 PY9094

Brazil, Rio Parnahyba Brazil, Rio Parnahyba Paraguay, Rio Paraguay

2428 KR478119 2425 KR478171 2429 KR478178

This study This study This study

2240 KR478449 2243 KR478497 1956 KR478503

This study This study This study

MCP 28915

MCP 28915

Brazil, Rio Ibicui-Mirim

2426 KR478120

This study

2271 KR478450

This study

MHNG 2677.004

PY9098

Paraguay, Rio Paraguay

2427 KR478118

This study

2232 KR478448

This study

Stri-531

28

Peru, Rio Amazonas

2426 KR478173

This study

2231 KR478498

This study

LBP 5517

LBPN 26622

Brazil, Rio Jari

2428 KR478112

This study

2228 KR478442

This study

LBP 5420

LBPN 27135

Brazil, Rio Jari

2427 KR478121

This study

2232 KR478451

This study

AUM 42225

V5310

Venezuela, Rio Orinoco

2426 KR478109

This study

NA



LBP 3094

LBPN 19263

Brazil, Rio Baia

2429 KR478113

This study

2226 KR478443

This study

MHNG 2674.025

SU05-012

2435 KR477934

This study

2089 KR478268

This study

Metaloricaria nijsseni MHNG 2672.053

SU05-359

2437 KR477967

This study

2089 KR478301

This study

Metaloricaria nijsseni MHNG 2690.016

SU01-459

2441 KR477933

This study

2089 KR478267

This study

Metaloricaria paucidens Paraloricaria agastor Paraloricaria agastor Paraloricaria vetula Pseudohemiodon aff. apithanos Pseudohemiodon aff. apithanos Pseudohemiodon aff. apithanos Pseudohemiodon apithanos Pseudohemiodon apithanos Pseudohemiodon laminus Pseudohemiodon laticeps Pseudohemiodon laticeps Pseudohemiodon sp.

MHNG 2681.042

GF06-108

2439 KR477932

This study

2073 KR478266

This study

NA NA NA MHNG 2677.070

AG06-017 AG06-019 YC-008 PE05-009

2427 2426 2425 2416

This This This This

1984 1984 1984 2003

This This This This

ANSP 178115

P1759

MHNG 2710.086

PE08-852

Suriname, Suriname River Suriname, Corantijn River Suriname, Coppename River French Guiana, Oyapock River Argentina, Ita-Ibate Argentina, Puerto Abra Argentina, Entre Rios Peru, aquarium trade, Rio Amazonasb Peru, aquarium trade, Rio Itayab Peru, Rio Cushabatai

MHNG 2677.073

PE05-020

MHNG 2677.074

PE05-026

MHNG 2677.077

PE05-035

LBP 4332

Pseudoloricaria laeviuscula Pseudoloricaria laeviuscula Pseudoloricaria laeviuscula Pseudoloricaria laeviuscula

KR478167 KR478168 KR478166 KR478080

study study study study

KR478493 KR478494 KR478492 KR478414

study study study study

2418 KR478078

This study

2003 KR478412

This study

2411 KR478079

This study

2004 KR478413

This study

2414 KR478110

This study

2012 KR478440

This study

2414 KR478081

This study

2012 KR478415

This study

2426 KR478082

This study

2009 KR478416

This study

LBPN 24034

Peru, aquarium trade, Rio Itayab Peru, aquarium trade, Rio Nanayb Peru, aquarium trade, Rio Amazonasb Brazil, Rio Paraguay

2424 KR478169

This study

2003 KR478495

This study

NA

NA

Argentina, Corrientes

2424 KR478170

This study

2004 KR478496

This study

MHNG 2677.076

PE05-034

2406 KR478111

This study

1980 KR478441

This study

AUM 44646

G5231

Peru, aquarium trade, Rio Amazonasb Guyana, Takutu River

2427 KR478099

This study

1990 KR478433

This study

AUM 44646

G5232

Guyana, Takutu River

2427 KR478100

This study

1990 KR478434

This study

AUM 44646

G5233

Guyana, Takutu River

2427 KR478103

This study

1990 KR478436

This study

INPA 28991

MUS 517

Brazil, Rio Madeira

2430 KR478098

This study

1990 KR478432

This study (continued on next page)

500

R. Covain et al. / Molecular Phylogenetics and Evolution 94 (2016) 492–517

Table 2 (continued) Species

Catalog number

Field number

Locality

mt 12S + 16S bases + GenBank No.

Ref.

F-RTN4 bases + GenBank No.

Ref.

Pterosturisoma microps Rhadinoloricaria aff. macromystax Rhadinoloricaria sp. Orinoco Rhadinoloricaria sp. Orinoco Rhadinoloricaria sp. Orinoco Rineloricaria aequalicuspis Rineloricaria aff. cadeae Rineloricaria aff. cadeae Rineloricaria aff. fallax Rineloricaria aff. langei Rineloricaria aff. latirostris Rineloricaria aff. phoxocephala Rineloricaria aff. phoxocephala Rineloricaria aff. phoxocephala Rineloricaria aff. phoxocephala Rineloricaria aff. phoxocephala Rineloricaria aff. phoxocephala Rineloricaria aff. stewarti Rineloricaria aff. stewarti Rineloricaria aff. stewarti Rineloricaria aff. stewarti Rineloricaria aff. stewarti Rineloricaria aff. stewarti Rineloricaria aff. stewarti Rineloricaria aff. strigilata Rineloricaria altipinnis Rineloricaria altipinnis Rineloricaria cadeae

MHNG 2677.072

PE05-016

Peru, aquarium trade

2439 KR477921

This study

2075 KR478255

This study

ANSP 182349

T2364

2414 KR478084

This study

1967 KR478418

This study

ANSP 185044

T4029

Guyana, Rupununi River Venezuela, Rio Orinoco

2415 KR478085

This study

1979 KR478419

This study

AUM 42094

V5507

Venezuela, Rio Orinoco

2414 KR478086

This study

1980 KR478420

This study

AUM 42094

V5508

Venezuela, Rio Orinoco

2415 KR478087

This study

1979 KR478421

This study

MCP 29282

MCP 29282

2427 KR478213

This study

2499 KR478534

This study

LBP 901

LBPN 7359

Brazil, Arroio Molha Coco Brazil, Eldorado do Sul

2424 KR477987

This study

2492 KR478321

This study

LBP4772

LBPN 25580

Brazil, Rio Guiaba

2424 KR477976

This study

2533 KR478310

This study

LBP 4085

LBPN 23512

Brazil, Rio Japim

2420 KR477979

This study

1984 KR478313

This study

LBP 1189

LBPN 10585

Brazil, Rio Iguaçu

2425 KR478323

This study

2501 KR478324

This study

MHNG 2749.014

MUS 491

Brazil, aquarium trade

2425 KR478185

This study

2507 KR478510

This study

MCP 28832

495

Brazil, Rio Purus

2427 KR478104

This study

2243 KR478437

This study

MCP 28832

496

Brazil, Rio Purus

2426 KR478126

This study

2246 KR478455

This study

MCP 28832

NA

Brazil, Rio Purus

2427 KR478125

This study

2243 KR478454

This study

LBP 4123

LBPN 23617

Brazil, Rio Jurua

2431 KR478127

This study

2242 KR478456

This study

MHNG 2749.013

PI 720

Peru, Rio Momon

2431 KR478128

This study

2241 KR478457

This study

ANSP 182368

T2101

2431 KR478038

This study

2244 KR478372

This study

MHNG 2663.003

GF03-196

2425 KR478023

This study

2209 KR478357

This study

MHNG 2681.019

GF06-077

2422 KR478028

This study

2214 KR478362

This study

MHNG 2682.091

GF06-428

2425 KR478025

This study

2209 KR478359

This study

MHNG 2683.049

GF06-538

2425 KR478024

This study

2209 KR478358

This study

MHNG 2617.015

MUS

2425 KR478029

This study

2209 KR478363

This study

MHNG 2704.040

SUJM-064

2429 KR478035

This study

2210 KR478369

This study

MHNG 2749.011

SU08-945

2426 KR478037

This study

2210 KR478371

This study

LBP 2949

LBPN 19534

2417 KR477992

This study

2258 KR478326

This study

Stri-3589

40

2425 KR478026

This study

1866 KR478360

This study

MHNG 2709.086

PA97-045

2423 KR478027

This study

1866 KR478361

This study

MCP 21217

MCP 21217

2427 KR477991

This study

2479 KR478325

This study

NA

RC

Guyana, Essequibo River French Guiana, Approuague River French Guiana, Oyapock River French Guiana, Maroni River French Guiana, Mana River French Guiana, Sinnamary River Suriname, Suriname River Suriname, Commewijne River Brazil, Córrego da batata Panama, Rio Chucunaque Panama, Rio Chucunaque Brazil, Rio Grande do Sul Argentina, Salta

2429 KR477989

This study

2511 KR478323

This study

MHNG 2680.033

NA

Argentina, Rio Sali

2426 KR477988

This study

2511 KR478322

This study

LBP 1248

LBPN 11175

2429 KR478108

This study

2498 KR478439

This study

LBP 771

LBPN 8534

Brazil, Rio Ribeira do Iguape Brazil, Rio Marumbi

2429 KR478347

This study

2802 KR478348

This study

Colombia, aquarium trade Guyana, Takutu River Suriname, Corantijn River Guyana, Rupununi River Guyana, Berbice River Guyana, Demerara River

2428 KR477984

This study

2206 KR478318

This study

2429 KR477980 2427 KR477975

This study This study

2284 KR478314 2280 KR478309

This study This study

2427 KR477978

This study

2281 KR478312

This study

2427 KR477973 2427 KR477977

This study This study

2281 KR478307 2280 KR478311

This study This study

Rineloricaria catamarcensis Rineloricaria catamarcensis Rineloricaria cf. kronei Rineloricaria cf. latirostris Rineloricaria eigenmanni Rineloricaria fallax Rineloricaria fallax

NA

MUS 494

MHNG 2651.054 MHNG 2672.015

GY04-146 SU05-412

Rineloricaria fallax

MHNG 2650.072

GY04-009

Rineloricaria fallax Rineloricaria fallax

MHNG 2651.034 MHNG 2650.067

GY04-396 GY04-384

501

R. Covain et al. / Molecular Phylogenetics and Evolution 94 (2016) 492–517 Table 2 (continued) Species

Catalog number

Field number

Locality

mt 12S + 16S bases + GenBank No.

Ref.

Rineloricaria fallax Rineloricaria formosa Rineloricaria formosa Rineloricaria heteroptera Rineloricaria heteroptera Rineloricaria heteroptera Rineloricaria heteroptera Rineloricaria hoehnei

LBP 4343 ANSP 185291 AUM 43885 AUM 43886

LBPN 24075 V5405 V5531 V5530

Brazil, Boa Vista Venezuela, Rio Orinoco Venezuela, Rio Orinoco Venezuela, Rio Orinoco

2429 2429 2429 2429

This This This This

AUM 43886

V5534

Venezuela, Rio Orinoco

2429 KR477969

This study

2219 KR478303

This study

AUM 43886

V5529

Venezuela, Rio Orinoco

2429 KR477970

This study

2219 KR478304

This study

AUM 43928

V5562

Venezuela, Rio Orinoco

2428 KR477971

This study

2220 KR478305

This study

MHNG 2678.018

PR-018

2424 KR477972

This study

2221 KR478306

This study

LBP 729

LBPN 8268

2426 KR477985

This study

2208 KR478319

This study

MHNG 2613.029

CA-01

Paraguay, Paraguay River Brazil, Jaragua do Sul, Rio Itapocu Peru, Rio Ucayali

2423 KR478203

This study

2232 KR478528

This study

MHNG 2651.029

GY04-172

Guyana, Takutu River

2424 KR477996

This study

2231 KR478330

This study

MHNG 2651.059

GY04-252

2424 KR477995

This study

2232 KR478329

This study

MHNG 2680.008

MUS 244

Guyana, Mauishparu River Brazil, Purus River

2424 KR477997

This study

2232 KR478331

This study

Stri-2422

26

2425 KR478326

This study

2219 KR478327

This study

LBP 1557

LBPN 11505

Argentine Rio Corrientes Brazil, Rio Araguaia

2424 KR477994

This study

2198 KR478328

This study

MHNG 2710.033

PE08-053

Peru, Rio Huacamayo

2423 KR478202

This study

2230 KR478527

This study

MCP 38347

MCP 38347

2426 KR478018

This study

2804 KR478352

This study

LBP 4409

LBPN 24247

2427 KR477983

This study

2204 KR478317

This study

MHNG 2680.011 MCP 21263

MUS 312 MCP 21263

2427 KR478013 2426 KR478212

This study This study

2203 KR478347 2504 KR478533

This study This study

MHNG 2680.034

MUS

2421 KR477999

This study

2214 KR478333

This study

MHNG 2749.015

PI 719

Brazil, Rio Grande do Sul Brazil, Rio Negro, Barcelos Brazil, aquarium trade Brazil, Rio Grande do Sul Argentina, Rio CunaPiru Peru, Rio Momon

2425 GBxxxxx

This study

2280 KR478334

This study

MHNG 2678.014 LBP 5 LBP 1319

PR-009 LBPN 3656 LBPN 11000

Argentina, Santa Fé Brazil, Rio Paraguay Brazil, Rio Tibagi

2433 KR478012 2433 KR478190 2432 KR478040

This study This study This study

2522 KR478346 2506 KR478515 2021 KR478375

This study This study This study

LBP 1731

LBPN 12864

Brazil, Rio Amazonas

2421 KR478036

This study

2220 KR478370

This study

MHNG 2601.081

BR98-088

Brazil, Rio Guamá

2428 KR478123

This study

NA



MHNG 2663.004

GF03-193

2427 KR478102

This study

953 KR478435

This study

NA

MUS 334

French Guiana, Approuague River Brazil, Rio Purus

2426 KR478129

This study

2229 KR478458

This study

MHNG 2650.074

GY04-197

Guyana, Takutu River

2424 KR478122

This study

2220 KR478452

This study

MHNG 2749.012

GF99-009

French Guiana, Kaw

2427 KR478101

This study

NA



MHNG 2601.063

BR98-049

Brazil, Rio Acara

2428 KR478124

This study

949 KR478453

This study

MCP 28832

497

Brazil, Rio Purus

2426 KR478130

This study

931 KR478459

This study

MCP 21195

MCP 21195

Brazil, Lagoa Fortaleza

2427 KR478106

This study

2504 KR478438

This study

Stri-1399

52

Colombia, Rio Baudo

2426 KR478001

This study

2244 KR478335

This study

MHNG 2587.054

BR1253

2426 KR478194

This study

2790 KR478519

This study

MHNG 2587.015

BR1215

2424 KR478191

This study

2507 KR478516

This study

LBP 1750

LBPN 11818

Brazil, Rio Paraíba do Sul Brazil, Rio Paraíba do Sul Brazil, Rio Araguaia

2428 KR478040

This study

2034 KR478040

This study

MHNG 2586.083

BR1190

Brazil, Rio Betari

2429 KR478192

This study

2515 KR478517

This study

MHNG 2586.072

BR1184

Brazil, Rio Betari

2429 KR478172

This study

NA



LBP 2654

LBPN 17410

Brazil, Rio Carombé

2427 KR478034

This study

2208 KR478368

This study

Rineloricaria jaraguensis Rineloricaria lanceolata Rineloricaria lanceolata Rineloricaria lanceolata Rineloricaria lanceolata Rineloricaria lanceolata Rineloricaria lanceolata Rineloricaria lanceolata Rineloricaria longicauda Rineloricaria melini Rineloricaria melini Rineloricaria microlepidogaster Rineloricaria misionera Rineloricaria morrowi Rineloricaria parva Rineloricaria parva Rineloricaria pentamaculata Rineloricaria platyura Rineloricaria platyura Rineloricaria platyura Rineloricaria platyura Rineloricaria platyura Rineloricaria platyura Rineloricaria platyura Rineloricaria platyura Rineloricaria quadrensis Rineloricaria sneiderni Rineloricaria sp. Agua Santa Rineloricaria sp. Ao Itai Rineloricaria sp. Araguaia Rineloricaria sp. Betari Rineloricaria sp. Betari Rineloricaria sp. Carombé

KR477974 KR477981 KR477982 KR477968

study study study study

F-RTN4 bases + GenBank No.

Ref.

2285 2253 2253 2219

This This This This

KR477974 KR478315 KR478316 KR478302

study study study study

(continued on next page)

502

R. Covain et al. / Molecular Phylogenetics and Evolution 94 (2016) 492–517

Table 2 (continued) Species

Catalog number

Field number

Locality

mt 12S + 16S bases + GenBank No.

Ref.

F-RTN4 bases + GenBank No.

Ref.

Rineloricaria sp. Corantijn Rineloricaria sp. Corantijn Rineloricaria sp. Corantijn Rineloricaria sp. Corrego Seco Rineloricaria sp. Guama 4 Rineloricaria sp. Guama 5 Rineloricaria sp. Guama 5 Rineloricaria sp. Guama 5 Rineloricaria sp. Guama 6 Rineloricaria sp. Huacamayo Rineloricaria sp. Huacamayo Rineloricaria sp. Macacu Rineloricaria sp. Maroni 2 Rineloricaria sp. Maroni 2 Rineloricaria sp. Martinso Rineloricaria sp. Mongaguá Rineloricaria sp. Orinoco Rineloricaria sp. Orinoco Rineloricaria sp. Panama Rineloricaria sp. Paraiba do Sul Rineloricaria sp. Parguaza Rineloricaria sp. Piedade Rineloricaria sp. Previsto Rineloricaria sp. Puerto Ayacucho Rineloricaria sp. Ribeira Rineloricaria sp. Rio da Toca Rineloricaria sp. São João Rineloricaria sp. São João 2 Rineloricaria sp. São João 2 Rineloricaria sp. Ucayali Rineloricaria sp. Ucayali 2 Rineloricaria sp. Uruguay Rineloricaria sp. Von Humbolt Rineloricaria stewarti

MHNG 2671.085

SU05-450

MHNG 2704.035

SU07-017

MHNG 2722.048

SU01-417

MHNG 2586.065

BR1176

MHNG 2601.091

BR98-112

Suriname, River Suriname, River Suriname, River Brazil, Rio Iguape Brazil, Rio

Corantijn

2431 KR478005

This study

2188 KR478339

This study

Sipaliwini

2430 KR478002

This study

2188 KR478336

This study

Nickerie

2433 KR478006

This study

2194 KR478340

This study

Ribeira do

2429 KR478184

This study

2716 KR478509

This study

Guamá

2426 KR478199

This study

2474 KR478524

This study

MHNG 2601.044

BR98-010

Brazil, Rio Gurupi

2425 KR478200

This study

2508 KR478525

This study

MHNG 2601.042

BR98-008

Brazil, Rio Gurupi

2425 KR478201

This study

2510 KR478526

This study

MHNG 2602.025

BR98-167

Brazil, Rio Piria

2417 KR478198

This study

2508 KR478523

This study

MHNG 2601.063

BR98-047

Brazil, Rio Acara

2427 KR478501

This study

2285 KR478502

This study

MHNG 2613.032

CA-33

Peru, Rio Pisqui

2431 KR478015

This study

2453 KR478349

This study

MHNG 2710.032

PE08-057

Peru, Rio Huacamayo

2431 KR478016

This study

2528 KR478350

This study

MHNG 2587.082

BR1273

Brazil, Rio da Toca

2425 KR478017

This study

2506 KR478351

This study

MHNG 2749.018

SU08-441

2430 KR478003

This study

2249 KR478337

This study

MHNG 2749.018

SU08-442

2430 KR478004

This study

2249 KR478338

This study

MHNG 2586.089

BR1196

Suriname, Paloemeu River Suriname, Paloemeu River Brazil, Rio Martinso

2429 KR478020

This study

2802 KR478354

This study

LBP 2128

LBPN 21378

2429 KR478019

This study

2786 KR478353

This study

AUM 44067

V5435

Brazil, Riacho Sitio do Meio Venezuela, Rio Orinoco

2428 KR478030

This study

2197 KR478364

This study

AUM 44067

V5437

Venezuela, Rio Orinoco

2428 KR478031

This study

2197 KR478365

This study

MHNG 2749.016

PA00-011

Panama, Rio Ipeti

2427 KR478181

This study

989 KR478506

This study

MHNG 2583.065

BR 156

2427 KR478107

This study

NA



LBP 2308

LBPN 15846

2427 KR478032

This study

2217 KR478366

This study

MHNG 2586.055

BR1163

Brazil, Rio Paraíba do Sul Venezuela, Rio Parguaza Brazil, Rio Piedade

2429 KR478039

This study

2226 KR478373

This study

MHNG 2710.047

PE08-186

Peru, Rio Previsto

2433 KR478195

This study

2528 KR478520

This study

MHNG 2749.017

MUS 489

2427 KR478033

This study

2279 KR478367

This study

MHNG 2586.088

BR1195

2429 KR478193

This study

2493 KR478518

This study

MHNG 2587.078

BR1269

Venezuela, aquarium trade Brazil, Rio Ribeira do Iguape Brazil, Rio Macacu

2423 KR478022

This study

2573 KR478356

This study

LBP 802

LBPN 7954

Brazil, Rio São João

2429 KR478188

This study

2793 KR478513

This study

MHNG 2586.052

BR1155

Brazil, Rio Araraguara

2428 KR478187

This study

2505 KR478512

This study

MHNG 2586.052

BR1156

Brazil, Rio Araraguara

2425 KR478186

This study

2501 KR478511

This study

MHNG 2710.095

PE08-905

Peru, Rio Ucayali

2426 KR478520

This study

2481 KR478521

This study

LBP 3273

LBPN 20081

Peru, Rio Huancabamba 2433 KR478021

This study

2536 KR478355

This study

MCP 21616

MCP 21616

2432 KR478189

This study

2506 KR478514

This study

MHNG 2710.068

PE08-697

2430 KR478197

This study

2532 KR478522

This study

MHNG 2651.057

GY04-257

2424 KR478009

This study

2289 KR478343

This study

Rineloricaria stewarti MHNG 2651.027 Rineloricaria stewarti MHNG 2671.015

GY04-183 SU05-592

2429 KR478010 2427 KR478007

This study This study

2286 KR478344 2289 KR478341

This study This study

Rineloricaria stewarti MHNG 2671.084

SU05-457

Brazil, Rio Grande do Sul Peru, bosque Von Humbolt Guyana, Mauishparu River Guyana, Takutu River Suriname, Coppename River Suriname, Corantijn River

2426 KR478008

This study

2270 KR478342

This study

503

R. Covain et al. / Molecular Phylogenetics and Evolution 94 (2016) 492–517 Table 2 (continued) Species

Catalog number

Field number

Locality

mt 12S + 16S bases + GenBank No.

Ref.

F-RTN4 bases + GenBank No.

Ref.

Rineloricaria strigilata Rineloricaria teffeana Rineloricaria uracantha Rineloricaria uracantha Rineloricaria wolfei Spatuloricaria cf. evansii Spatuloricaria puganensis Spatuloricaria puganensis Spatuloricaria sp. Araguaia Spatuloricaria sp. Ireng Spatuloricaria sp. Magdalena 1 Spatuloricaria sp. Magdalena 2 Spatuloricaria sp. Magdalena 2 Spatuloricaria sp. Magdalena 2 Spatuloricaria sp. Orinoco Sturisoma aureum

MCP 23751

MCP 23751

2426 KR477998

This study

2780 KR478332

This study

NA Stri-1662

NA 23

Brazil, Rio Grande do Sul SR, aquarium specimen Panama, Rio Mandinga

2427 KR478011 2426 KR478180

This study This study

2281 KR478345 2245 KR478505

This study This study

LBP 2762

LBPN 18551

2424 KR478179

This study

2230 KR478504

This study

ANSP 182695 LBP 2385

P6236 LBPN 16145

Panama, Santa Rita Arriba Peru, Rio Itaya Brazil, Rio Araguaia

2424 KR478105 2427 KR478042

This study This study

NA 1958 KR478376

– This study

ANSP 180486

P4743

Peru, Rio Yanatili

2421 KR478043

This study

1957 KR478377

This study

ANSP 180789

P4747

Peru, Rio Urubamba

2421 KR478044

This study

1958 KR478378

This study

LBP 1556

LBPN 11507

Brazil, Rio Araguaia

2427 KR478046

This study

1960 KR478380

This study

ANSP 182372

T2361

Guyana, Ireng River

2423 KR478047

This study

1978 KR478381

This study

MHNG 2722.096

MUS 353

2426 KR478045

This study

1981 KR478379

This study

IAvHP

6635

2418 KR478048

This study

1960 KR478382

This study

IAvHP

6637

2418 KR478049

This study

1961 KR478383

This study

IAvHP

6638

2419 KR478050

This study

1961 KR478384

This study

ANSP 185303

P4006

Colombia, aquarium trade Colombia, Rio Magdalena, Honda Colombia, Rio Magdalena, Honda Colombia, Rio Magdalena, Honda Venezuela, Rio Orinoco

2427 KR478051

This study

1958 KR478385

This study

NA

MUS 286

2438 KR477925

This study

2287 KR478259

This study

Sturisoma aureum

MHNG 2684.019

MUS 357

2442 KR478160

This study

2287 KR478486

This study

Sturisoma cf. guentheri Sturisoma dariense Sturisoma festivum

ANSP 182587

P6330

2446 KR477926

This study

1977 KR478260

This study

MHNG 2674.059 MER95T-20

PA97-019 44

2440 KR477922 2443 KR477923

This study This study

2302 KR478256 2295 KR478257

This study This study

Sturisoma frenatum Sturisoma nigrirostrum Sturisoma panamense Sturisoma robustum Sturisoma sp. Rio Branco Sturisomatichthys leightoni Ancistrus cirrhosusa

Stri-872 ANSP 178322

47 P1593

Panama, Darien Venezuela, Maracaibo Lake Colombia, Rio San Juan Peru, Rio Amazonas

2440 KR477924 2444 KR478162

This study This study

2304 KR478258 2589 KR478488

This study This study

MHNG 2674.058

PA00-013

Panama, Rio Ipeti

2443 KR478163

This study

2302 KR478489

This study

MHNG 2677.002 LBP 1615

PY9091 LBPN 4044

Paraguay, Rio Paraguay Brazil, Rio Branco

2443 KR478161 2442 KR477935

This study This study

2540 KR478487 2583 KR478269

This study This study

NA

MUS 327

2440 KR477927

This study

2307 KR478261

This study

MHNG 2645.037

MUS 202

Colombia, aquarium specimen Argentina, Rio Uruguay

2425 EU310442

Pseudorinelepis genibarbisa Guyanancistrus brevispinisa Guyanancistrus longispinisa Guyanancistrus nigera Hypostomus gymnorhynchusa Lasiancistrus heteracanthusa Lithoxus lithoidesa

MHNG 2588.079

PE96-040

Peru, Rio Ucayali

2436 HM592623

MHNG 2725.099

GF00-103

2439 JN855735

MHNG 2725.100

GF99-204

MHNG 2722.089

GF99-185

MHNG 2621.098

SU01-160

MHNG 2613.037

CA 13

French Guiana, Maroni River French Guiana, Oyapock River French Guiana, Oyapock River French Guiana, Approuague River Peru, Rio Pauya

MHNG 2651.087

GY04-136

2428 JN855740

Pseudancistrus barbatusa Hemiancistrus mediansa Peckoltia oligospilaa

MHNG 2653.059

GF00-074

MHNG 2664.078

GF00-084

MHNG 2602.017

BR98-154

Guyana, Essequibo River French Guiana, Maroni River Suriname, Tapanahony River Brazil, Rio Guamá

2439 KR478207

Covain et al. (2008) Rodriguez et al. (2011) Covain and FischMuller (2012) Covain and FischMuller (2012) Covain and FischMuller (2012) Covain and FischMuller (2012) Covain and FischMuller (2012) Covain and FischMuller (2012) Covain and FischMuller (2012) Covain and FischMuller (2012) This study

Peckoltia sabajia

MHNG 2651.016

GY04-029

2437 KR478206

This study

MHNG 2651.020

GY04-030

2441 KR478205

This study

MNHN 2011-0013

GF00-115

Guyana, Rupununi River Guyana, Rupununi River French Guiana, Maroni River

2435 KR478204

This study

1809 HM623638 Rodriguez et al. (2011) 1925 HM623634 Rodriguez et al. (2011) 1807 JN855772 Covain and FischMuller (2012) 1808 JN855757 Covain and FischMuller (2012) 1809 JN855759 Covain and FischMuller (2012) 1818 JN855789 Covain and FischMuller (2012) 1790 JN855787 Covain and FischMuller (2012) 1715 JN855777 Covain and FischMuller (2012) 1809 JN855761 Covain and FischMuller (2012) 1820 JF747011 Fisch-Muller et al. (2012) 1814 JF747020 Fisch-Muller et al. (2012) 1815 JF747019 Fisch-Muller et al. (2012) 1808 JF747017 Fisch-Muller et al. (2012) 1814 JF747016 Fisch-Muller et al. (2012)

Peckoltia cavatica Panaqolus koko

a

a

Colombia, aquarium trade Colombia, aquarium trade Peru, Rio Nanay

2439 JN855720 2438 JN855722 2442 JN855752 2432 JN855750

2442 JN855724 2437 JN855719

(continued on next page)

504

R. Covain et al. / Molecular Phylogenetics and Evolution 94 (2016) 492–517

Table 2 (continued)

a b c

Species

Catalog number

Field number

Locality

mt 12S + 16S bases + GenBank No.

Ref.

F-RTN4 bases + GenBank No.

Ref.

Scobinancistrus aureatusa Hypancistrus zebraa

MHNG 2684.020

MUS 358

2442 KR478210

This study

1816 KR478531

This study

MHNG 2708.072

MUS 420

2435 KR478209

This study

1790 KR478530

This study

Megalancistrus cf. parananusa Neoplecostomus micropsa

MHNG 2711.048

MUS 332

Brazil, aquarium trade, Rio Xingub Brazil, aquarium trade, Rio Xingub Brazil, aquarium trade

2442 KR478208

This study

1816 KR478529

This study

MHNG 2588.002

BR 1283

Brazil, Rio dos Frades

2442 KR478211

This study

1816 KR478532

This study

Outgroup. According to the exporter. Specimen reidentified after publication.

Harttiella lucifer for the second, with several species dependent indels that locally challenged the alignment process. To reduce the misleading effects of misaligned regions, we used the model alignment for this marker given by Rodriguez et al. (2011) that produced good assessment statistics according to SOAP 1.2a4 (Löytynoja and Milinkovitch, 2001), better than automatic alignments produced by CLUSTAL-X 1.83 under various parameter values (i.e. increase in mean nodal support, model adequacy, and tree balance). Moreover, and despite the presence of indels in its intronic regions, this same marker has proven to be efficient in solving the phylogenetic relationships among other catfish subfamilies (Chiachio et al., 2008; Cardoso and Montoya-Burgos, 2009; Alexandrou et al., 2011; Cramer et al., 2011; Covain and Fisch-Muller, 2012; Roxo et al., 2012, 2014; Costa e Silva et al., 2014). Additionally, Fisch-Muller et al. (2012) demonstrated that in Ancistrinae, the two introns of f-rtn4r were rather conserved, and displayed less variation than coding mitochondrial genes, making easier detection of homologous regions. Gaps were considered as missing data, and regions impossible to amplify or to sequence were coded as ambiguities (N). The final alignment of f-rtn4r marker is accessible on Dryad (http://datadryad.org/) using accession number XXXX. Since mitochondrial DNA is presumably transmitted through maternal lineage as a single non recombining genetic unit (Meyer, 1993), a first partition corresponding to the mitochondrial genes was created. With the mutational patterns in intronic and exonic regions of f-rtn4r being rather characterized by insertions/deletions and transitions/transversions respectively, two other partitions were created for introns and exons. Congruence in phylogenetic signals contained in mitochondrial and nuclear markers was secondarily assessed using the Congruence Among Distance Matrices (CADM) test (Legendre and Lapointe, 2004) as implemented in ape 2.6.2 (Paradis et al., 2004; Paradis, 2006) in R 2.12.1 (R Development Core Team, 2009). Patristic pairwise maximum likelihood (ML) (Felsenstein, 1981) distances were computed as estimates of tree topologies with Treefinder (Jobb et al., 2004) version of October 2008 for each partition using a likelihood model under which the distances are optimized. Appropriate substitution models corresponding to each potential partition were accordingly determined with the Akaike Information Criterion (Akaike, 1974) as implemented in Treefinder. The CADM test was computed using 9999 permutations of the three ML distances matrices. Two phylogenetic reconstruction methods allowing the analysis of partitioned data were used. First, a ML reconstruction was performed with Treefinder, and robustness of the results was estimated by resampling the data set with the nonparametric bootstrap (Efron, 1979) following Felsenstein’s (1985) methodology with 2,000 pseudoreplicates. Second, a Bayesian inference analysis was conducted in MrBayes 3.1.2 (Huelsenbeck and Ronquist, 2001; Ronquist and Huelsenbeck, 2003). Two runs of eight chains (one cold, seven heated) were conducted simultane-

ously for 2  107 generations, with the tree space sampled each 1000th generation. Convergence between chains occurred after 2  106 generations (average standard deviation of split frequencies

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