A new species of Loricaria (Loricariidae: Loricariinae) from the upper Amazon River basin, Colombia

Alejandro Londoño-Burbano¹ , Alexander Urbano-Bonilla², Matthew R. Thomas³ and Marcelo R. Britto¹

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Abstract​

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Introduction​

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Loricaria is the type genus of Loricariidae, described by Linnaeus (1758), with L. cataphracta Linnaeus, 1758 as the type species; as currently known, the genus is monophyletic based on morphological evidence (Rapp Py-Daniel, 1997; Thomas, 2011). Through molecular data, Covain et al. (2016) found the genus to be paraphyletic, however, maintaining the validity of Brochiloricaria Isbrücker & Nijssen, 1979 and Paraloricaria Isbrücker, 1979, and revalidating the genus Proloricaria Isbrücker, 2001 to render Loricaria as monophyletic. The latter hypothesis places the genus in the “Loricaria – Pseudohemiodon group” along with Brochiloricaria, Crossoloricaria Isbrücker, 1979, Dentectus Martín Salazar, Isbrücker & Nijssen, 1982, Paraloricaria, Planiloricaria Isbrücker, 1971, Proloricaria, Pseudohemiodon Bleeker, 1862, Pyxiloricaria Isbrücker & Nijssen, 1984, Reganella Eigenmann, 1905, Ricola Isbrücker & Nijssen, 1978, Rhadinoloricaria Isbrücker & Nijssen, 1974, and Spatuloricaria Schultz, 1944. Several synonyms of the genus were proposed, as well as the revalidation of genera previously synonymized with Loricaria (see Covain et al., 2016 for comments on the synonyms). Loricaria is diagnosed from other loricariin genera by the following: presence of long, slender (filiform) papillae on the upper and lower lips, and low number of bicuspid premaxillary teeth (usually 3–4 per side) that are twice the length of the dentary teeth(Isbrücker, 1981; Thomas, Rapp Py-Daniel, 2008).

During the last 17 years eight new species of Loricaria have been described (Londoño-Burbano et al., 2020; Saraiva et al., 2021), but an updated taxonomic revision of Loricaria has not been published since Isbrücker (1981), who restricted the genus to include 11 valid species. As stated by Londoño-Burbano et al. (2020), the discovery and description of additional species expands our knowledge and understanding of the diversity and distribution of Loricaria, but it also demonstrates the need for additional collecting in areas that have been inaccessible and poorly surveyed.

Currently Loricaria includes 18 valid species (Fricke et al., 2023) distributed in the Amazon, Orinoco, Paraguay, Paraná, and small coastal drainages of Guiana and Brazil (Thomas et al., 2013). However, species richness within the genus is poorly known in the upper Amazonas River basin, including several remote areas in Bolivia, Colombia, Ecuador, and Peru; these localities are not easily accessible and few specimens of Loricaria have been collected there. Morphological and molecular analyses of specimens recently collected from the Orteguaza River drainage, Putumayo River (upper Amazon River, Colombia), and examination of museum material revealed a new species described herein. We assign the new species to Loricaria based on external morphological characters traditionally proposed as diagnostic for the genus.

Material and methods

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Measurements and counts follow Thomas, Sabaj Pérez (2010). Composition of species groups within Loricaria follow Thomas, Rapp Py-Daniel (2008) and Thomas, Sabaj Pérez (2010). Measurements were taken point to point with digital calipers (0.1 mm) and were included in tables as percentages of standard length (SL) or head length (HL); holotype data is presented in millimeters (mm). Counts and measurements were taken from the left side of the specimens except when the structure being measured or counted was damaged, in which case data were obtained from the right side. Plate series nomenclature followed Thomas, Rapp Py-Daniel (2008), Thomas, Sabaj Pérez (2010), and Londoño-Burbano, Reis (2019). Posterior lateral plates were examined here as the median series beginning with the first plate on which the dorsal and ventral odontode keels meet and continue parallel to each other to the end of the caudal peduncle. Sexual dimorphism was analyzed following Rapp Py-Daniel, Cox Fernandes (2005). The terms “main cusp” and “lateral cusp” follow Müller, Weber (1992). Characters used to diagnose the new species from congeners not included in “Comparative material examined” were analyzed and compared using original and subsequent descriptions of each species. In the description, counts are followed by their frequency in parentheses, and an asterisk (*) indicates the count of the holotype. Institutional abbreviations follow Sabaj (2020).

Molecular protocols for extraction, amplification, and sequencing of fragments of the cytochrome C oxidase subunit 1 gene (COI) from mitochondrial DNA, editing of sequences, codon visualization, and genetic distances analyses, followed Londoño-Burbano, Britto (2022). Three different species delimitation analyses were carried out. For a Bayesian implementation of the poisson tree processes analysis (bPTP) a Maximum Likelihood (ML) tree was estimated with RAxML PTHREADS-SSE3 implemented in RAxML v. 8.019 (Stamatakis, 2014), with parameters following the autoMRE initialization criteria (as indicated by Pattengale et al., 2009) to identify clades (species) by populations. The best-fit evolutionary model (GTR+G) was calculated using the corrected Akaike Information Criterion (AICc) determined by Partition Finder v. 2.1.1 (Lanfear et al., 2012). Finally, the best ML tree was used as the input file on the PTP web server (http://species.hits.org) for delimitation of each operational taxonomic unit (OTU) from each population; the analysis included default parameters. For the General mixed Yule coalescent (GMYC) analysis, an ultrametric tree was estimated using BEAST v. 2.5 (Bouckaert et al., 2019). To estimate such tree, a .xml file was created in BEAUti with HKY + G as the best-fit model, a strict molecular clock with clock rate of 1, and the Yule model set as prior for the speciation process; remaining parameters were left as default. Markov Monte Carlo Chains (MCMC) were run for 100 million generations and sampled every 10000th generation. Convergence (ESS value > 200), stability, and appropriate mixing of parameters were verified with Tracer v. 1.7.1 (Rambaut et al., 2018); afterwards, a consensus tree was generated with Tree Annotator v. 2.6.7 (Drummond, Rambaut, 2007), with 25% of the trees discarded as burn-in and visualized on FigTree v. 1.4.4 (Rambaut, 2018). GMYC species delimitation was performed with standard parameters [interval = c(0, 10)] and a single threshold, which indicates transition time between to within species branching. This analysis was done through the package splits (Species Limits by Threshold Statistics; http://r-forge.rproject.org/projects/splits) in R v. 4.2.2 (R Development Core Team, 2021). Finally, an Automatic Barcode Gap Discovery (ABGD) analysis was carried out, which according to Puillandre et al. (2012) identifies different sequences into potential species based on limits of divergence. Genetic distances were calculated using MEGA 11 (Tamura et al., 2021) under Kimura 2-parameter model (Kimura, 1980), to estimate the pairwise genetic distances between species, with 1,000 pseudoreps; that matrix was used as input into the ABGD webserver (https://bioinfo.mnhn.fr/abi/public/abgd/abgdweb.html) and ran using the default parameters set by the portal.

The estimated Extent of Occurrence (EOO) of the species was calculated using the web portal of the Geospatial Conservation Assessment Tool (GeoCAT), defining 1 km² grids proposed by Bachman et al. (2011). This analysis is focused on the geospatial aspect of Red Listing and the metric is included as part of the categories and criteria of the IUCN (IUCN Standards and Petitions Subcommittee, 2022).

Results​

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Loricaria nimairaco, new species

urn:lsid:zoobank.org:act:227B959E-CC92-49D0-B5C9-90783CA57C4F

(Figs. 1, 2, 6A, 7, 8, 10; Tabs. 1-4)

Holotype. ICN-MHN 24389, 185.8 mm SL, Colombia, Amazonas, Leticia, río Amazonas, 04°13’29”S 69°56’49”W, 26 Oct 2000, M. Arce.

Paratypes. All from Colombia: ICN-MHN 4492, 6, 115.5–153.1 mm SL, Amazonas, Leticia, Sistema río Amazonas, Laguna Yahuarcaca, Lago 4, 04°11’17”S 69°57’39”W, 13 Jun 1999; ICN-MHN 5212, 4, 123.9–154.5 mm SL, Amazonas, Leticia, km 8 via Leticia-Tarapacá, Yaguarcaca Stream, 04°08’05”S 69°56’36”W, 1 Apr 1999, G Aricari; ICN-MHN 6001, 1, 130.8 mm SL, Amazonas, Leticia, río Amazonas, 04°13’29”S 69°56’49”W, 1 Jul 2000, M. Arce & P. Sánchez; ICN-MHN 9150, 1, 141.5 mm SL, Caquetá, La Montañita, Niña María Stream, tributary of Orteguaza River, 01°22’24”N 75°24’02”W; ICN-MHN 6003, 2, 182.0–182.2 mm SL, same data as holotype; ICN-MHN 9156, 1, 190.9 mm SL, Amazonas, Leticia, sistema río Amazonas, Laguna Yahuarcaca, 04°11’33”S 69°57’28”W, 12 Oct 1999, S. Vejarano; MPUJ 17396, 1, 170.6 mm SL, Putumayo, Puerto Asís, Vereda El Quebradón, río Putumayo, 00°29’43”N 76°21’11”W, 8 Nov 2021, A. Méndez-López, P. Tombé & R. Villota; MPUJ 17397, 1, 155.9 mm SL, Putumayo, Puerto Asís, Vereda Sinaí-Hachapos, Quebrada El Puma, 00°29’48”N 76°22’56”W, 22 Nov 2021, A. Méndez-López, P. Tombé & R. Villota; MPUJ 17398, 1, 104.5 mm SL, Putumayo, Puerto Asís, Vereda Sinaí-Hachapos, Caño Chufiya, 00°29’05”N 76°22’17”W, 26 Aug 2021, A. Méndez-López, P. Tombé & R. Villota; MPUJ 17399, 1, 180.4 mm SL, Putumayo, Puerto Asis, río Putumayo, 00°33’51”N 76°34’31”W, 28 Aug 2021, A. Urbano-Bonilla, A. Méndez-López, G. López Ríos, J. Vásquez, K. Chalial, O. Camacho, R. Villota & W. C. P. Castro; MPUJ 17400, 1, 164.9 mm SL, Putumayo, Puerto Asis, río Putumayo, 00°33’51”N 76°34’31”W, 16 Nov 2021, A. Urbano-Bonilla, A. Méndez-López, G. López Ríos, J. Vásquez, K. Chalial, O. Camacho, R. Villota & W. C. P. Castro; MPUJ 17401, 1, 160.2 mm SL, Putumayo, Villa Garzón, río Guineo, 00°29’22”N 76°31’05”W, 2 Sep 2021, A. Urbano-Bonilla, A. Méndez-López, G. López Ríos, J. Vásquez, K. Chalial, O. Camacho, R. Villota & W. C. P. Castro; MPUJ 17402, 1, 173.1 mm SL, Putumayo, Villa Garzón, río Guineo, 01°01’04”N 76°38’43”W, 1 Mar 2022, A. Urbano-Bonilla, A. Méndez-López, G. López Ríos, J. Vásquez, K. Chalial, O. Camacho, R. Villota & W. C. P. Castro; ROM 107225, 1, 169.6 mm SL, Amazonas, Caquetá, Orteguaza River, 11.4 km SE of Florencia, 01°31’09”N 75°32’19”W, 249 m asl, 7 Aug 2017, N. K. Lujan, A. Ortega-Lara, G. C. Sanchez, C. Conde & V. Meza-Vargas; ROM 107265, 1, 74.8 mm SL, Caquetá, Amazonas River basin, Orteguaza River, 9 km NE of Florencia, 01°39’29”N 75°32’31”W, 272 m asl, 5 Aug 2017, N. K. Lujan, A. Ortega-Lara, G. C. Sanchez, C. Conde & V. Meza-Vargas.

FIGURE 1| Holotype of Loricaria nimairaco, ICN-MHN 24398, 185.8 mm SL, Colombia, Amazonas, Leticia, Amazonas River. Scale bar = 10 mm. Photos: Gabriel Cortés.

FIGURE 2| Loricaria nimairaco, paratype, MPUJ 17399, 180.4 mm SL, Colombia, Putumayo, Puerto Asís, Putumayo River. Scale bar = 10 mm. Photos: Omar E. Melo-Ortiz.

Diagnosis. Loricaria nimairaco can be distinguished from all congeners by the following combination of characters: dorsal portion of head to origin of dorsal fin with uniform black or dark brown coloration or the presence of two longitudinal stripes from tips of the snout to origin of dorsal fin, without transversal bands or spots (Figs. 1–2) (vs. dorsal portion without coloration, with spots, with transversal bars, or with dark transverse bar reaching nares and snout tip; Figs. 3–5); abdominal plates tightly joined and completely covering the median abdominal space and pectoral girdle (Figs. 1–2) (vs. loosely joined, isolated or incompletely covering the pectoral girdle, except species from the Loricaria cataphracta group; Fig. 4); and by having dorsal and pectoral fins totally black or dark brown, without bands, spots, or blotches (Figs. 1–2) (vs. dorsal and pectoral fins hyaline or with dark bands, spots, or blotches (Fig. 4), except L. simillima). The new species is morphologically most similar to L. simillima, from which it can be differentiated by counts on total lateral plates 31–33 (modally 32) (vs. 34–35, modally 34); anterior lateral plates 17–18 (modally 18) (vs. 18–22, modally 20); body width at post-cleithral tip (14.3–17.5% SL vs. 10.6–14.7% SL), and presence of a dark vertical band at distal portion of caudal fin occupying less than half of the fin (Figs. 1–2) (vs. presence of a solid dark vertical band in posterior portion of caudal fin occupying almost the entire fin). Loricaria nimairaco can be diagnosed from L. nickeriensis, which is currently reported as present in the Amazon River, Colombia, by having a broad median abdominal space (Figs. 1–2) (vs. abdominal space narrower than width of each adjacent lateral abdominal plate; Fig. 4), presence of plates on cleithral region (Figs. 1–2) (vs. absence of plates on cleithral region; Fig. 4), post-orbital notch deep and angular (Fig. 6A) (vs. post-orbital notch shallow and rounded; Fig. 6B) and absence of dark blotches on dorsal and ventral portion of body (Figs. 1–2) (vs. presence of dark blotches on dorsal and ventral portion of body; Fig. 4).

FIGURE 3| Lectotype of Loricaria simillima, BMNH 1880.12.8.77, 163.1 mm SL, Ecuador, Canelos. Photos: Claudio Zawadski, ACSImagebase.

FIGURE 4| Holotype of Loricaria nickeriensis, ZMA-PISC 107561, 116.4 mm SL, Suriname, Nickerie District, Fallawatra River, 5 km south-southwest of Stondansie falls. Photos: Mark Allen, ACSImagebase.

FIGURE 5| Dorsal, ventral, and lateral view showing coloration and characteristics of Loricaria simillima, BMNH 1997.6.26.1-2, 202.3 mm SL. Aquarium specimens. Photos: Lucie Goodayle.

FIGURE 6| Lateral view of head showing size of post-orbital notch in: A. Loricaria nimairaco, holotype, ICN-MHN 24398, 185.8 mm SL; and B. Loricaria nickeriensis, holotype, ZMA-PISC 107561, 116.4 mm SL.

Description. Measurements are presented in Tab. 1, and general body form is depicted in Figs. 1–2. A medium- to large-sized Loricaria, with the largest examined specimen 190.9 mmSL. Head and body depressed; maximum body depth at dorsal fin origin, widest at cleithrum, and becoming attenuate posteriorly. Ventral profile of body straight. Head triangular in dorsal view, with lateral margin from snout tip to opercle straight; dorsum entirely covered with plates, including tip of snout. Postorbital notch well developed and large.

TABLE 1 | Morphometrics of Loricaria nimairaco as percentages of standard length or head length; holotype data in mm. Range includes the holotype. N = 23; SD = Standard deviation.

Upper and lower lip covered by long, simple marginal fringe barbels. Filiform papillae on upper lip cover premaxillary teeth. Lower lip with fewer filaments than observed on upper lip. Rictal barbel long and thin, not reaching gill opening, and without secondary branches. Buccal papillae behind premaxillary teeth broader than filaments on lips and longer than premaxillary teeth. Teeth bilobed and slender; main cusp longer than lateral cusp in both premaxillary and dentary teeth; premaxillary teeth longer than dentary teeth. Premaxillary teeth 3(12) or 4*(11), modally 3, and dentary teeth 5(1), 6(6), 7*(8), 8(3), 9(3) or 10(1), modally 7 (see Tab. 2 for meristic comparisons among congeners).

TABLE 2 | Meristic frequencies of Loricaria nimairaco compared to congeners. N = number of specimens included.

Abdomen completely covered with small- to medium-sized irregular plates, without any organization in series or rows. Anterior abdominal plates are smaller, almost rounded, and as numerous as central abdominal plates; anterior border of abdominal plates straight to slightly curved, almost reaching the margin of lower lip, and with or without a shallow median notch (Figs. 1–2). Plates absent at pectoral fin insertion. Predorsal region with two closely aligned, well-developed keels, including supraoccipital tip (Figs. 1–2). Three predorsal plates.

Plates in lateral series 31(5), 32*(16) or 33(2). Anterior lateral plates 17(1) or 18*(22) with well-developed keels, with upper and lower series separated. Posterior lateral plates 13(5), 14*(16), 15(1) or 16(1) with series of keels almost joined. Post-anal plates 20(9) or 21*(14). Thoracic plates 8(13) or 9*(10), elongated, and differentiated from those on the rest of abdomen.

Dorsal-fin rays I,7, spine and two first branched rays longest when adpressed; posterior margin of fin straight when extended. Pectoral-fin rays I,6; posterior margin of pectoral fin slightly concave when extended, with spine and first branched ray longer than other rays; most distal tip reaching to almost half the length of pelvic fin when adpressed. Pelvic-fin rays i,5; first ray prolonged, longer than branched rays; posterior margin of fin straight when extended. Anal-fin rays i,5; anal-fin origin is vertically aligned with dorsal fin insertion; posterior margin of fin straight when extended. Principal caudal-fin rays i,10,i; distal margin of caudal fin concave, with upper and lower rays thickened; upper ray is produced into a long trailing filament, which was broken in most specimens examined.

Coloration in alcohol. Ground color tan to dark brown on dorsum and lateral surfaces; ventral unplated surfaces pale; ventral plated surfaces dark yellow; sides of caudal peduncle with subtle dark spots. Dorsum of head and trunk, extending to three or four plates along the dorsal-fin base, dark brown, without spots or bands (Fig. 1); or, with two longitudinal stripes from tips of the snout to origin of dorsal fin, without transversal bands or spots (Fig. 2). Dorsum of trunk posterior to dorsal-fin insertion marked with three or four dark brown transverse bands: just posterior to end of base of dorsal fin, the following band about five plates posterior to the first one, following band about four plates posterior from it, and the last one not reaching caudal-fin origin (Figs. 1–2). Sides of head anterior to opercular opening dark, same as coloration on dorsal portion of head.

Dorsal and pectoral fins entirely black or dark brown, without spots or bands (Figs. 1–2). Pelvic fins either entirely black or dark brown, without spots or bands (Figs. 1–2) or mostly hyaline, with distal tips of rays dark (Figs. 1–2). Anal fin with irregular dark gray or black blotch or band on basal portion of fin (Fig. 1), or blotch absent (Fig. 2; see below for variation in coloration among populations). Caudal fin with dark pigment covering post-ural plates and distal tips of fin, interrupted by pale vertical band (Fig. 1).

Sexual dimorphism. Male specimens exhibited thickened pectoral spines (Fig. 7); however, contrary to what is reported in other Loricaria species, modifications to lip and barbel morphology (Isbrücker, 1981) were not observed in specimens examined.

FIGURE 7| Dorsal view of Loricaria nimairaco male, showing a slightly hypertrophied pectoral spine indicating sexual dimorphism, paratype, ICN-MHN 9156, 190.9 mm SL, Colombia, Amazonas, Leticia, Amazonas River system, Laguna Yahuarcaca. Photo: Alexander Urbano-Bonilla.

Geographical distribution and habitat. Loricaria nimairaco is known from the Orteguaza River, the main tributary of the Caquetá River basin, an Andean River draining into the upper portion of the Amazon River, the Putumayo River, and from the Amazon River at Leticia, Colombia (Fig. 8). According to field notes from ROM archives (obtained thanks to N. K. Lujan), one of the specimens (ROM 107225) was captured in high current, over predominantly mud substrate with organic matter. In contrast, a small specimen (ROM 107265) was collected in a presumably lower gradient stream in slow current, where the bottom was predominantly cobble mixed with sand, with organic matter.

FIGURE 8| Distribution map of Loricaria nimairaco. Red star indicate holotype locality, and white circles indicate paratype localities. Each symbol may represent more than one lot or locality. FIGURE 9 | Environment at Putumayo River basin. A. Piedmont drainages “río Guineo”; B. Main channel of the Putumayo River in the lower part; and C. Streams of Terra-firme. Photos: Alexander Urbano-Bonilla.

Etymology. The specific name nimairaco [nɨmáìraco] in the Uitoto-Muinane language from Peru, means “house of a wise man” (Minor, Hendrich-Minor, 2008:86). In tribute to our friend and colleague, José Iván Mojica, late professor of the Instituto de Ciencias Naturales de la Universidad Nacional de Colombia. His contributions to Colombian ichthyology (biology, ecology, systematics, and biogeography of freshwater fishes) have made it possible to advance in the conservation of the country’s fishes and rivers, such as the Amazon, the river that was always the home of the wise. A noun in apposition.

Conservation status. Loricaria nimairaco is found in drainages of the Andean piedmont of the Amazon and upper Amazon (Fig. 8) at nine localities in three basins of Colombia, in the Orteguaza (3), Putumayo (1), and Amazon River (5). Aspects such as increasing rate of deforestation of the watersheds, gold mining activities, cattle ranching, and oil exploitation projects occur in the region where the species is recorded (Ayram et al., 2020; Clerici et al., 2020) representing a threat to the species; thus, monitoring of the populations should be implemented. Such monitoring programs and decision-making by environmental authorities (i.e.,Corporaciones Autónomas Regionales-CAR) are currently advancing in the ordering and management of the country’s hydrographic basins, established by decree 1729 of 2002. The geographic distribution (83,689.5 km²) represented as EOO (EOO = B1) categorizes the species as Least Concern (LC) according to the IUCN Subcommittee on Standards and Applications (IUCN 2022).

Color variation within Loricaria nimairaco from the Putumayo River. Specimens were collected in the Piedmont and lowland ecoregions of the Putumayo River basin from main river channels, floodplain forest, and Terra-firme streams (Figs. 9A–C). Specimens captured at those localities showed some differences from populations present at the Orteguaza River, and along the upper Amazon River (Colombia). The main difference was the coloration of the dorsal portion of the head (Fig. 2) from specimens from the Orteguaza and Amazon River (at Leticia); individuals from the Putumayo River have two dark longitudinal stripes from the tip of the snout to the predorsal plates (Fig. 2). Furthermore, the anal fin lacked dark pigmentation (Fig. 2) in contrast to populations of the Orteguaza River and around Leticia, which exhibits a dark spot near the base of the anal fin (Fig. 1). Meristic counts and measurements show some overlap with those of Loricaria simillima Regan, 1904 and totally overlap with what was identified as the new species here(Tab. 2); however, the new species and L. simillima can be differentiated by external morphology (see Diagnosis), meristic counts (Tab. 2), and molecular evidence (see Tab. 3; S1, S2, S3). At present, molecular data are unavailable to assess the identity of populations in the Putumayo River, and further efforts should be made to include samples from that locality in future molecular analyses of the species.

TABLE 3 | Pairwise mtDNA genetic distance values for COI gene between and within species using a Kimura 2 Parameter. Bold values indicate distances > 2% between new species and congeners.

FIGURE 9| Environment at Putumayo River basin. A. Piedmont drainages “río Guineo”; B. Main channel of the Putumayo River in the lower part; and C. Streams of Terra-firme. Photos: Alexander Urbano-Bonilla.

Genetic differentiation and species delimitation. Genetic distances (Tab. 3) were calculated between Loricaria nimairaco and morphologically similar, and geographically closely related species, which were used for the ABGD analysis (see below). Loricaria nimairaco is most closely related to Loricaria cf. simillima from the upper Amazon River in Peru (Fig. 10) and form a cluster as the next divergent branch to the remaining Loricaria species included here (Genbank records from Pereira et al., 2013; Tab. 4). Rhadinoloricaria is divergent from Loricaria, followed by Spatuloricaria caquetae (Fowler, 1943) as the next divergent node to that cluster, and Rineloricaria cf. lanceolata (Günther, 1868) as divergent from (Spatuloricaria (Rhadinoloricaria + Loricaria))(Fig. 10).

TABLE 4 | Vouchers used in DNA extractions, amplification, and sequencing for genetic distances of COI mtDNA and species delimitation analyses. N/A = Not applicable.