Molecular Phylogenetics and Evolution 94 (2016) 492–517
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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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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