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Research Article
A new species of Caecilia (Gymnophiona, Caeciliidae) from the Magdalena valley region of Colombia
expand article infoAndrés R. Acosta-Galvis, Mauricio Torres, Paola Pulido-Santacruz
‡ Instituto de Investigación de Recursos Biológicos Alexander von Humboldt, Bogotá, Colombia
Open Access

Abstract

A new species of the genus Caecilia (Caeciliidae) from the western foothills of the Serranía de los Yariguíes in Colombia is described. Caecilia pulchraserrana sp. nov. is similar to C. degenerata and C. corpulenta but differs from these species in having fewer primary annular grooves and a shorter body length. With this new species, the currently recognized species in the genus are increased to 35. Mitochondrial DNA sequences, including newly sequenced terminals representing two additional, previously unanalyzed species, corroborate the phylogenetic position of the new species within Caecilia and the monophyly of the genus. This analysis also included newly sequenced terminals of Epicrionops aff. parkeri (Rhinatrematidae) and trans-Andean Microcaecilia nicefori (Siphonopidae). Evidence was found for the non-monophyly of the family Siphonopidae and the siphonopid genera Microcaecilia and Siphonops. The implications of these results for caecilian systematics are discussed and the status of the trans-Andean populations of Caecilia degenerata is commented upon.

Keywords

Amphibia, Caecilia degenerata, Epicrionops, Microcaecilia, paraphyly, phylogeny, Siphonopidae, South America, taxonomy, tropical humid forest

Introduction

The Neotropical caecilian amphibian genus Caecilia Linnaeus, 1758 (Gymnophiona: Caeciliidae) currently comprises 34 nominal species (Wilkinson et al. 2011; Frost 2018; Maciel and Hoogmoed 2018), 18 of which occur in Colombia, with eight being endemic to this country. Seven species occur in the Magdalena valley region of Colombia (Dunn 1942; Lynch 1999) and external morphology segregates them into two groups. A first group comprises four species that lack secondary annular grooves: C. caribea Dunn, 1942, endemic to Colombia, from the eastern slope of the Cordillera Central, Caldas Department, between 10–1700 m above sea level (a.s.l); C. corpulenta Taylor, 1968, from the type locality in Peru, with a Colombian record from the Andean forests on the 1750 m a.s.l., Santander Department; C. subdermalis Taylor, 1968, from northern Ecuador and eastern slopes of the Cordillera Central, Huila and Caldas Departments in Colombia, between 850–2320 m a.s.l.; and C. degenerata Dunn, 1942, endemic to Colombia, from both flanks of the Cordillera Oriental, between 800–2100 m a.s.l., Boyacá, Cundinamarca, and Santander Departments (Dunn 1942; Taylor 1968; Ruiz-Carranza et al. 1996; Lynch 1999; Acosta-Galvis 2000; Rivera-Correa 2006; Castro-Herrera et al. 2007; Frost 2018; Appendix 1).

A second group includes three species that have secondary annular grooves: C. guntheri Dunn, 1942, with a wide distribution from northern Ecuador to Colombia, where the records are discontinuous and include the sub-Andean forests of the Cordillera Occidental and the region of Muzo at Quípama Municipality, Boyacá Department, western slope of the Cordillera Oriental, 1000 m a.s.l.; C. subnigricans Dunn, 1942, from northern Venezuela and lowlands of the Caribbean and Magdalena Valley regions of Colombia, with a record from Mariquita Municipality, Tolima Department; and C. thompsoni Boulenger, 1902b, endemic to the middle Magdalena valley in Colombia, 240–1571 m a.s.l. (Dunn 1942; Taylor 1968; Ruiz-Carranza et al. 1996; Lynch 1999; Acosta-Galvis 2000; Bernal et al. 2005 Acosta-Galvis et al. 2006; Lynch and Romero 2012; Mueses-Cisneros and Moreno-Quintero 2012; Paternina-H et al. 2013; Acevedo-Rincón et al. 2014; Angarita-M et al. 2015; Restrepo et al. 2017; Frost 2018; Appendix 1).

During a recent herpetological survey in wet tropical forests of the Serranía de los Yariguíes, in the Department of Santander, Colombia (Fig. 1), we collected several specimens of a small Caecilia that lack secondary annular grooves and dermal scale pockets, suggesting that they correspond to either C. degenerata or C. corpulenta. However, a low number of primary annular grooves and a combination of morphometric characters indicate instead that these specimens belong to a new species, which we describe herein. To test the generic placement of the new species and to explore the relationships of other Neotropical caecilians, we perform a phylogenetic analysis of DNA sequences. We discuss the implications of our results for caecilian systematics and comment on the status of the trans-Andean populations of C. degenerata.

Figure 1. 

A Map of Colombia showing the known localities of the species of Caecilia that occur in the Magdalena valley region. Key: C. caribea (blue triangle), C. corpulenta (black dot), C. degenerata (black cross), C. guntheri (violet asterisk), C. subnigricans (yellow triangle), C. subdermalis (green star), C. thompsoni (black star), Caecilia pulchraserrana sp. nov. (red triangle) B Type locality of Caecilia pulchraserrana sp. nov. (red triangle) at Serranía de los Yariguíes, Santander Department, Colombia.

Materials and methods

Fieldwork and reference collections

The new species was collected during fieldwork carried out in the Serranía de los Yariguíes, vereda La Belleza, municipality of El Carmen de Chucurí, Santander Department, Colombia (06°34'N, 73°34'W, 731–789 m a.s.l.; Fig. 1), from 17 February to 1 May 2018, during the dry season. Specimens were found in two separate humid spots near the Río Cascajales, which drains Tropical moist broadleaf forests, within the ecoregion of the Magdalena valley montane forests, in the foothills of the Cordillera Oriental, Colombia (Dinerstein et al. 1995; Olson and Dinerstein 2002).

Previous fieldwork conducted between 1998–1999 by John Lynch in collaboration with the first author, successfully allowed the detection of microhabitats and several specimens of Microcaecilia nicefori (Lynch 1999); subsequently, between 2000 to date, fieldwork with caecilians such as Oscaecilia polyzona (Lynch and Acosta 2004), Caecilia sp., C. thompsoni, and C. isthmica (unpublished data) allowed successful detection of microhabitats and multiple specimens.

The collecting technique, which was used to obtain specimens of the new species, consists of first asking local people about the locations where they have spotted caecilians using the common names of “blind snakes”, or “captain worms” (“lombrices capitanas”), or “motolas” (this common name is specific for the Department of Santander). Subsequently, the reported sites are visited and inspected to select sites under the shade of vegetation, and where the soil is not compact and very humid (usually associated with water springs that form a mosaic of marshy and dry areas). Collecting efforts are focused in the selected damp microhabitats, digging with a hoe to a depth of approximately 20 cm (approximate sampling effort of 2-person-hour to collect five specimens). Coordinates and elevations were obtained with a Garmin GPSMAP 64SC (map datum WGS 84). Collected specimens were euthanized using 20% benzocaine (Chen and Combs 1999), fixed in 10% formalin, and preserved in 70% ethanol. Tissue samples from two individuals were obtained immediately after euthanasia and preserved in 96% ethanol. Specimens were deposited at the Biological Collections of the Instituto de Investigación de Recursos Biológicos Alexander von Humboldt, Villa de Leyva, Boyacá, Colombia (IAvH-Am and IAvH-CT) and the Amphibian Collection of the Universidad Industrial de Santander, Bucaramanga, Santander, Colombia (UIS-MHN-A).

Phylogenetic analysis

To test the generic assignment of the new species and to explore the relationships of other endemic caecilians from Colombia, available mitochondrial DNA sequences of the genes 16S and CO1 from members of all Neotropical caecilian families (Caeciliidae, Typhlonectidae, Siphonopidae, Dermophiidae, and Rhinatrematidae) were analyzed (Table 1). The analysis included a fragment of COI (ca. 651 bp) and a fragment of 16S (ca. 510 bp). Sequences for most terminals were obtained from GenBank (Table 1). We added new sequences for eight Colombian terminals representing the new species, Caecilia thompsoni, C. isthmica, Typhlonectes natans, Epicrionops aff. parkeri, and Microcaecilia nicefori (Appendix 1). The cryptobranchid Cryptobranchus alleganiensis was used to root the tree. Laboratory protocols and primers are those of Palumbi (1996), Ivanova et al. (2006), and Carr et al.(2011). Bidirectional PCR products were used for Sanger sequencing at the Instituto de Genética of the Universidad Nacional de Colombia. Resulting sequences were visualized, assembled, checked for stop codons (COI), and edited in Geneious Pro v 10.2.3 (Kearse et al. 2012). All sequences were deposited in the Barcode of Life Data System (BOLD; Ratnasingham and Hebert 2007) and GenBank (Table 1). Sequences of each gene were aligned independently using the MAFFT plugin v 7.388 within Geneious, considering the secondary structure of RNA in 16S and implementing the G-INS-I algorithm. Subsequently, sequences of both genes were concatenated in a single dataset using Geneious, which was used to construct a Maximum Likelihood phylogeny using IQ-TREE (Nguyen et al. 2015), performing a partitioned analysis based on four partitions (16S, COI first codon position, COI second codon position, COI third codon position) using the partition finder algorithm (-m option TESTMERGE; Lanfear et al. 2012) in IQ-TREE and best fitting models for each partition selected by the same program (Chernomor et al. 2016; Kalyaanamoorthy et al. 2017). Each partition was allowed to have its own set of branch lengths (-sp option). Branch support analysis was performed with 1000 ultrafast bootstrap replicates (Hoang and Chernomor 2017).

Table 1.

List of species examined and GenBank or Barcode of life Data Systems (BOLD) accession numbers for each gene analyzed in this study. See Appendix 1 for locality details.

Species Family Tissue code 16S GenBank; BOLD number CO1 GenBank; BOLD number Source
Caecilia gracilis Caeciliidae KX757086 NC_023508 Maciel et al. 2017, San Mauro et al. 2014
Caecilia isthmica Caeciliidae IAvH-CT-22982 MN555719; SABIO393-19 MN555727; SABIO393-19 This study
Caecilia pulchraserrana sp. nov Caeciliidae IAvH-CT-227334 MN555715; SABIO005-18 MN555723; SABIO005-18 This study
Caeciliidae IAvH-CT-22733 MN555718; SABIO002-18 MN555726; SABIO002-18 This study
Caecilia tentaculata Caeciliidae NC_023507 NC_023507 San Mauro et al. 2014
Caecilia thompsoni Caeciliidae IAvH-CT-22986 MN555717; SABIO392-19 MN555725; SABIO392-19 This study
Caecilia volcani Caeciliidae FJ784371 NC_020137 Crawford et al. 2010, Zhang and Wake 2009
Oscaecilia ochrocephala Caeciliidae GQ244474 GQ244474 Zhang and Wake 2009
Dermophis mexicanus Dermophiidae NC_020138 Zhang and Wake 2009
Epicrionops cf. marmoratus Rhinatrematidae KF540151 KF540151 San Mauro et al. 2014
Rhinatrema nigrum Rhinatrematidae GQ244468 GQ244468 Zhang and Wake 2009
Epicrionops aff. parkeri Rhinatrematidae IAvH-CT-21477 MN555716; CBIHA031-17 MN555724; CBIHA031-17 This study
Microcaecilia dermatophaga Siphonopidae NC_023514 NC_023514 San Mauro et al. 2014
Microcaecilia sp. Siphonopidae GQ244473 GQ244473 Zhang and Wake 2009
Microcaecilia unicolor Siphonopidae NC_023515 NC_023515 San Mauro et al. 2014
Microcaecilia nicefori Siphonopidae IAvH-CT-22985 MN555722; CAECI002-19 MN555729; CAECI002-19 This study
Siphonops annulatus Siphonopidae KU495581 KU495581 Lyra et al. 2017
Siphonops hardyii Siphonopidae KU495582 KU494789 Lyra et al. 2017
Siphonops insulanus Siphonopidae KU495583 KU494790 Lyra et al. 2017
Siphonops paulensis Siphonopidae KU495584 KU494791 Lyra et al. 2017
Potomotyphlus kaupii Typhlonectidae NC_023516 NC_023516 San Mauro et al. 2014
Typhlonectes compressicauda Typhlonectidae KU495605 KU494812 Lyra et al. 2017.
Typhlonectes natans Typhlonectidae AF154051 AF154051 Zardoya and Meyer 2000.
Typhlonectidae IAvH-CT-22983 MN555720; SABIO394-19 MN555728; SABIO394-19 This study
Typhlonectidae IAvH-CT-22984 MN555721; CAECI001-19 This study

Morphology

Criteria and terminology for morphological descriptions, diagnostic characters, and data for other species of Caecilia follow Lynch (1999), Gower and Wilkinson (2002), Maciel et al. (2009), Maciel and Hoogmoed (2011), Kamei et al. (2009), Wilkinson and Kok (2010), Donnelly and Wake (2013), and Wilkinson et al. (2009, 2013, 2015). For comparative purposes, specimens of C. guntheri, C. isthmica, C. thompsoni, and C. subdermalis were examined (Appendix 1). Morphological observations were made using a stereoscope Nikon optical device SMZ-1B, with High Intensity Illuminator NI-150 Nikon and App Scope 3xSRA41. Measurements were taken using a Mitutoyo precision digital caliper to ± 0.1 mm; and using the following abbreviations for anatomical features and ratios of measurements:

ADD anal disc diameter;

AM anteromedial limit of the mouth on the upper jaw;

BH body height at midbody;

C1 first collar length;

C2 second collar length;

CM corner of the mouth;

CMB circumference at midbody;

D diameter at midbody;

ED eye diameter;

END distance between eye and naris;

HH head height at level with CM;

HL head length;

HW head width at CM;

HWNG1 head width at NG1;

IND distance between nares;

IOD interorbital distance;

TL total length;

TL/D TL divided by diameter at midbody (ratio of length/diameter);

LPOD distance between eye and lip;

ND naris diameter;

NG1 first nuchal groove;

NG2 second nuchal groove;

NG3 third nuchal groove;

PA primary annulus;

PAG primary annular groove;

PM premaxillary-maxillary tooth;

ST snout tip;

STD distance between snout tip and anterior margin of mouth;

STND distance between ST and naris;

STLPD distance between ST and lip;

STOD distance between ST and eye;

TA tentacular aperture;

INTA distance between TAs;

TAOD distance between TA and eye;

TALPD distance between TA and lip;

TANRD distance between TA and naris;

TASTD distance between TA and ST;

VP vomeropalatine tooth;

WC2 width at second collar;

WCH width of choanae;

WBV width of body at vent level;

WMB width at midbody;

TL/HL TL divided by HL;

TL/WMB TL divided by WMB;

TL/HW TL divided by HW;

HL/HW HL divided by HW.

Dermal scale pockets and subdermal scales were searched using the criteria proposed by Wilkinson et al. (2013) and sex and maturity were determined by examination of gonads. Live specimens were photographed with a digital camera model Canon EOS 70D and preserved specimens with a digital camera Canon EOS 5D Mark II.

Results

Phylogenetic analysis

The final concatenated molecular dataset consisted of a matrix of 1273 bp, 567 sites were parsimony-informative, 111 were singletons, and 595 were constant sites. The best fitting substitution model for both CO1 and 16S was TIM2+F+I+G4 after testing the large selection of models in IQ-TREE. The ML tree is shown in Fig. 2 (LnL: –15725.921). Our phylogenetic analysis recovered the new species nested within a moderately well-supported (84%) monophyletic Caecilia, in a maximally supported monophyletic Caeciliidae. The new species appears most closely related, of the sampled species, to C. volcani but support for this relationship is not strong (58%). Rhinatrema nigrum and R. bivittatum were recovered as monophyletic with the sister group Epicrionops. Siphonops was inferred to be paraphyletic with respect to Luetkenotyphlus (Siphonopidae), and Microcaecilia nicefori was recovered as the sister group of Dermophidae + Siphonophidae, the latter including the remaining Microcaecilia (with Brasilotyphlus guarantanus nested within it) and the paraphyletic Siphonops.

Figure 2. 

Maximum Likelihood tree inferred from the analysis of a concatenated dataset comprising partial sequences of two mitochondrial genes. Numbers above branches indicate bootstrap support values (percent) (* = 100% bootstrap). Scale bar indicates nucleotide substitutions per site. The phylogenetic position of Caecilia pulchraserrana sp. nov. is shown in bold.

Description of new species

Generic assignment. The new species is assignable to the genus Caecilia because its eyes are not covered by bone and it has tentacles below the nostrils (Type D sensu Lynch, 1999, Fig. 3 D–E). In addition, the new species is nested within the Caecilia clade (Fig. 2) in our Maximum Likelihood phylogenetic analysis.

Figure 3. 

Holotype of Caecilia pulchraserrana sp. nov. Adult female, IAvH-Am-1548. A, B Lateral views of body C dorsal D ventral E lateral views of head F Frontal view of cephalic region, the arrow indicates the narial plug G dorsal and H lateral views of caudal region I ventral view of vent.

Caecilia pulchraserrana sp. nov.

Figs 3, 4, 5; Tables 2, 3, 4

Holotype

IAvH-Am-15487 (field number ARA 7872; Figs 3, 4C), an adult female collected 25 February 2018 by A. R. Acosta-Galvis, Miguel Torres, and Daniela García.

Type Locality

(Fig. 1) Colombia, Santander Department, El Carmen de Chucurí Municipality, vereda La Belleza, Cascajales River, 06°34'8.9"N, 73°34'20.2"W, 789 m a.s.l.

Paratypes

Four specimens (Fig. 4), IAvH-Am-15488 (field number ARA 7871) and UIS-MHN-A-6575 (field number ARA 7689), adult females, collected with holotype, and IAvH-Am-15489–90 (field numbers ARA 7690–1, respectively), adult males (exhibiting phallus, Fig. 5 A–C), 06°34'41.1"N, 73°34'28.9"W, 731 m a.s.l., collected 19 February 2018 by A. R. Acosta-Galvis and Miguel Torres.

Figure 4. 

Caecilia pulchraserrana sp. nov. in life. A Adult female, paratype, IAvH-Am-15488, TL= 232 mm B adult female, paratype, IAvH-Am-15488, TL= 232 mm C adult female, holotype, IAvH-Am-15487, TL= 206 mm D–E adult female. paratype, UIS-MHN-A-6575, TL= 195 mm.

Figure 5. 

Phallus (everted cloaca) of adult males Caecilia pulchraserrana sp. nov. A Ventro-lateral view (IAvH-Am-15489) B Ventro-lateral view of vent and C dorsal surface of the phallus (IAvH-Am-15490).

Referred specimens

UIS-MHN-A-6576–7 (field numbers ARA 7692–3, respectively), juveniles, 06°34'41.1"N, 73°34'28.9"W, 731 m a.s.l., collected 19 February 2018 by A. R. Acosta-Galvis and Miguel Torres. Tissues for molecular analysis (IAvH-CT-22733–4) were extracted from these specimens.

Diagnosis

Caecilia pulchraserrana sp. nov. differs from its congeners by the combination of having 100–104 dorsally incomplete primary annular grooves, a small size (195–232 mm), lips and ventral margin of upper jaw with a pink-orange (salmon) color (Fig. 4), and lacking secondary annular grooves and dermal scale pockets.

Species comparisons

Regarding the species of the genus Caecilia, the absence of secondary annular grooves distinguishes C. pulchraserrana sp. nov. from C. abitaguae Dunn, 1942, C. albiventris Daudin, 1803, C. armata Dunn, 1942, C. antioquiaensis Taylor, 1968, C. bokermanni Taylor, 1968, C. dunni Hershkovitz, 1938, C. flavopunctata Roze & Solano, 1963, C. gracilis Shaw, 1802, C. guntheri Dunn, 1942, C. isthmica Cope, 1878, C. leucocephala Taylor, 1968, C. marcusi Wake, 1985, C. mertensi Taylor, 1973, C. museugoeldi Maciel & Hoogmoed, 2018, C. nigricans Boulenger, 1902, C. occidentalis Taylor, 1968, C. pressula Taylor, 1968, C. perdita Taylor, 1968, C. subnigricans Dunn, 1942, C. subterminalis Taylor, 1968, C. tentaculata Linnaeus, 1758, C. tenuissima (Taylor, 1973), C. thompsoni Boulenger, 1902, and C. volcani Taylor, 1969.

Caecilia pulchraserrana sp. nov. shares with C. attenuata Taylor, 1968, C. caribea Dunn, 1942, C. corpulenta Taylor, 1968, C. crassisquama Taylor, 1968, C. degenerata Dunn, 1942, C. inca Taylor, 1973, C. orientalis Taylor, 1968, C. pachynema Günther, 1859, and C. subdermalis Taylor, 1968 the absence of secondary annular grooves and the presence of incomplete primary annular grooves. However, the new species can be distinguished from these nine species by having a lower number of primary annular grooves (100–104 vs. 114–199). Caecilia pulchraserrana sp. nov. most closely resembles C. degenerata, which also lacks subdermal scales, but differs from it in having fewer primary annuli.

Description of holotype

An adult female (Fig. 3). Head dorsoventrally flattened and slightly narrower than body; head width at CM 63% of width at midbody, head width at CM 72% of head length; head length 3.5% of total length; interorbital distance 40% of head width. Snout projects 1.6 mm beyond mouth; tip of snout rounded in dorsal and lateral view (Fig. 3); area between the eye and naris flattened. Eyes visible but small, eye diameter 4% of head length and 13.5% of eye-nostril distance; nares small, margins slightly protuberant, directed posterodorsally, visible from above. Tentacular openings circular and small, slightly raised above skin, laterally positioned near margin of mouth (Type D sensu Lynch 1999, Fig. 3D, E), slightly closer to corner of mouth than to nostrils. Tongue anteriorly attached, surface smooth with some longitudinally oriented grooves. Teeth pointed, recurved, with size decreasing posteriorly; premaxillary-maxillary and dentary teeth monocuspid and visible externally. Premaxillary-maxillary teeth 13, posterior maxillary teeth smaller. Premaxillary-maxillary series extending behind level of choanae. Vomeropalatine teeth 10, monocuspid, relatively uniform, moderately recurved, not visible externally, similar in size. Dentary teeth 12, moderately recurved, faintly larger than premaxillary-maxillary teeth. Choanae subovoid; narial plugs visible (Fig. 3F). Nuchal grooves indistinct dorsally and ventrally, incompletely encircling body with transverse grooves on the collars, in ventral surfaces. First collar shorter than second. Body subcylindrical, slightly deeper than wide (Fig. 3A, B); body width at midbody 4% of total length. Width along body varies slightly, narrower at terminal region. Primary annuli 104 incomplete dorsally and ventrally. Primary annular grooves completely encircling the body. Secondary grooves absent (Fig. 3G–I). Dermal scale pockets absent. Vent circular; disc around vent conspicuous enlarged (Fig. 3I) with seven denticulations anterior, seven nearly equal posterior denticulatios (Fig. 3I); anal papillae absent, and unsegmented terminal shield of 4.9 mm length.

Color in life

(Fig. 4): Jaw margins, area between the eye and naris, and tentacular regions pink-orange (salmon); eyeballs completely violet blue (Fig. 4b); periorbital region salmon; body dark brownish with thin salmon-colored chromatophores; ventral surface of body slightly paler than dorsum; annular grooves on sides of body slightly darker than general body color.

Color in preservative

(ethanol 70%; Fig. 3): Body dark slate gray dorsally with diffuse khaki chromatophores; jaw margins, rostral and periocular regions yellowish; ventral and lateral surfaces slightly paler than dorsum; vent disk jaw margins and area between the eye and naris yellowish.

Variation of type series

(Tables 3, 4). There is little variation among type specimens. Head flattened and slightly narrower than body, head width at CM 58–97% of width at midbody; head width at CM 72–92% of head length; head length 2–4% of total length; interorbital distance 36–50% of head width. Eye diameter 4–8% of the head length and 10–19% of eye-nostril distance. Nares small, slightly protuberant, directed posterodorsally, and visible from above. Premaxillary-maxillary teeth 11–13. Vomeropalatine teeth 9–12. Dentary teeth 10–13. First collar 66–96% of second collar. Body width at midbody 2–4% of total length. Primary annuli incomplete dorsally and ventrally. Secondary grooves and dermal scales absent. Vent circular; disc around with 12–15 anal denticulations. Denticulations usually seven-eight anteriorly, and seven posteriorly, nearly equal in size (Fig. 3I).

Table 2.

Morphological data of the Colombian species of Caecilia that lack secondary annular grooves and possess incomplete primary annular grooves. Abbreviations are given in Material and methods.

Species PAG TL (mm) TL/D Dermal scale pockets Sample size Source
C. caribea 142–152 390–585 53–55 Absent 4 Dunn 1942, Lynch 1999
C. corpulenta 129–132 152–441 19–35 Absent 6 Taylor 1968, Lynch 1999
C. degenerata 123–137 390–1050 38–58 Absent 9 Lynch 1999
C. orientalis 114–124 231–673 29–55 Present 8 Lynch 1999
C. subdermalis 116–138 131–680 28–54 Present 32 Lynch 1999
C. pulchraserrana sp. nov. 100–104 195–232 9–12 Absent 7 This study
Table 3.

Morphometric (in mm) and meristic data of the type series of Caecilia pulchraserrana sp. nov. Abbreviations are given in Materials and methods.

IAvH-Am-15487 Holotype IAvH-Am-15490 Paratype IAvH-Am-15489 Paratype IAvH-Am-15488 Paratype UIS-MHN-A-6575 Paratype
Sex F M M F F
PAG 104 100 101 103 100
TL 206 214 200 232 195
HW 5.4 5.3 5.0 4.8 4.3
HWNG1 5.2 4.2 4.4 4.9 4.3
WC2 5.8 4.6 4.0 5.2 4.8
WMB 8.5 6.2 5.5 8.1 6.2
CMB 22 18 17 23 18
WBV 5.2 3.7 4.0 4.4 3.5
HL 7.4 5.8 6.4 6.0 5.1
HH 5.1 4.8 4.0 4.4 3.8
IND 1.7 1.6 1.5 2.0 1.2
IOD 2.9 2.6 2.3 2.8 2.5
ED 0.3 0.4 0.4 0.2 0.4
ND 0.18 0.18 0.16 0.16 0.15
END 2.3 2.3 1.6 2.5 2.1
STD 6.9 5.6 5.7 6.0 5.2
STND 0.8 0.6 0.4 0.7 0.7
STLPD 2.2 2.1 2.1 2.0 1.8
STOD 3.3 2.7 2.5 3.4 2.9
TA 0.27 0.19 0.30 0.26 0.33
INTA 2.3 2.2 1.8 2.3 1.9
TAOD 2.5 2.1 1.9 2.6 2.1
TALPD 1.0 1.3 0.6 1.4 0.99
TANRD 0.99 0.67 0.69 0.75 0.7
TASTD 0.6 0.7 0.7 0.2 0.7
LPOD 1.0 1.2 0.9 1.0 0.7
WCH 0.16 0.11 0.09 0.11 0.14
C1 1.6 1.2 1.6 1.1 0.9
C2 1.7 1.5 2.4 1.5 1.1
BH 7.0 4.4 4.1 6.5 5.1
ADD 2.9 2.6 2.9 2.7 2.6
VP 11 9 10 9 11
Premaxillary-maxillary teeth 13 11 14 14 12
Dentary teeth 12 13 10 11 12
Table 4.

Ratios and percentages of measurements of the type series of Caecilia pulchraserrana sp. nov. Abbreviations are given in Materials and methods.

IAvH-Am-15490 Paratype IAvH-Am-15489 Paratype IAvH-Am-15488 Paratype IAvH-Am-15487 Holotype UIS-MHN-A-6575 Paratype
Sex M M F F F
C1/C2 75.9 66.1 70.5 96.4 82.7
TL/D 11.8 11.7 10.0 9.3 10.8
TL/HL 39.9 40.0 48.2 38.1 44.5
TL/ WMB 34.1 35.9 28.3 24.1 31.5
L/HW 36.7 30.8 38.2 27.7 37.8
HL/HW 92.0 77.0 79.2 72.9 85.0

Distribution and natural history

Caecilia pulchraserrana sp. nov. is currently known from two adjacent, relictual tropical wet forest localities on the western slope of the Cordillera Oriental of Colombia (Serranía de los Yariquíes; Fig. 1) at elevations between 731–789 m a.s.l. The Serrania of the Yariguies corresponds to an isolated mountain range that is part of the western slope of the Cordillera Oriental of Colombia (Fig. 1). Caecilia pulchraserrana sp. nov. is a fossorial species associated with marshy areas surrounded by secondary vegetation at the forest edge (Fig. 6). The specimens were collected during the dry season in very wet soils lacking rocks (i.e., bogs; Fig. 6), in a slightly inclined area (nearly 5°of slope) covered with vegetation of the family Heliconiaceae (Heliconia spp., Fig. 6).

Figure 6. 

Habitat of Caecilia pulchraserrana sp. nov. in the Serranía de los Yariguíes in Santander Department, El Carmen de Chucurí Municipality, vereda La Belleza, Cascajales River, 06°34'8.9"N, 73°34'20.2"W, 789 m a.s.l.. A View showing standing water in marshy area B Transitional change of wetter (right) to drier (left) microhabitat.

Caecilia pulchraserrana sp. nov. was obtained during the initial 10 minutes of removal with a hoe.We extracted the first specimen in intermediate substrates between marshy and dry areas; after 40 minutes of excavation in these selected areas, we obtained four additional specimens. Using these same criteria, when moving two kilometers above the original point, an area with similar characteristics was located and within 20 minutes we collected two additional specimens. Caecilia pulchraserrana sp. nov. was collected on black sandy soils with high organic matter content. These caecilians move quickly under the substrate, so once the first specimen is detected it is important to quickly create channels to surround and block them from escaping.

Etymology

The specific epithet is formed from the Latin pulchra (nominative feminine singular of pulcher), meaning beauty, and the Spanish adjective serrana (feminine singular of serrano), from the sierra or serranía. This specific name refers to the type locality of the species: vereda La Belleza (beauty in English) in the western foothills of the Serranía de Los Yariguíes. The specific name was chosen using a citizen science approach. First, scientists and inhabitants of the El Carmen de Chucurí municipality gathered a list of possible names for the new species. Then, the list of potential names and their meanings was shared with the local people, who voted to choose their preferred name.

Discussion

Phylogenetic relationships

Our description of Caecilia pulchraserrana sp. nov. brings the number of known species of Caecilia to 35 (Frost 2018). Molecular data are currently available for only six of these species (including the three newly sequenced species analyzed here), which precludes a thorough analysis of the relationships within the genus. Consequently, our phylogenetic analysis (Fig. 2) was designed mainly to test the generic placement of C. pulchraserrana sp. nov. in addition to exploring the relationships of C. isthmica and C. thompsoni (two other species that are endemic to Colombia). Our results recovered C. pulchraserrana sp. nov., C. isthmica, and C. thompsoni within Caecilia (Fig. 2), corroborating the generic placement of the new species and the monophyly of the genus, as previously hypothesized by Wilkinson et al. (2011). Our analysis recovered Oscaecilia as the sister group of Caecilia, which agrees with the results of San Mauro et al. (2014) but disagrees with those of Pyron and Wiens (2011), who instead recovered Caecilia as paraphyletic with respect to Oscaecilia.

Our phylogenetic analysis only included two mitochondrial loci and a small number of species and should not be considered as a robust resolution of caecilian relationships. Nevertheless, our results highlight several potential cases of non-monophyletic taxa and suggest that a taxonomic revision, including a major generic rearrangement, is warranted. Our study includes, for the first time, the Colombian endemics Epicrionops aff. parkeri (Rhinatrematidae) and Microcaecilia nicefori in molecular phylogenetic analyses. On one hand, recent contributions (Maciel et al. 2018) have allowed taxonomic rearrangements within Rhinatrematidae, with Rhinatrema nigrum and R. bivittatum being recovered as monophyletic, supporting previous claims (Wilkinson and Gower 2010; Wilkinson et al. 2011; Pyron and Wiens 2011; San Mauro et al. 2014) that Epicrionops could be transferred to Rhinatrema. Our analysis recovers Epicrionops aff. parkeri nested within a monophyletic Epicrionops (E. marmoratus+ E. aff. parkeri with 89%), which was sister to Rhinatrema (Fig. 2), corroborating the results obtained by Maciel et al. (2018).

On the other hand, Microcaecilia nicefori was recovered as the sister taxon to a clade formed by the dermophiids Gymnophis multiplicata + Dermophis mexicanus and the remaining siphonopids, including Microcaecilia, Brasilotyphlus guarantanus, Siphonops, and Luetkenotyphlus. In addition, Microcaecilia and Siphonops were recovered as paraphyletic with respect to Brasilotyphlus guarantanus and Luetkenotyphlus brasiliensis, respectively (Fig. 2). Recently, Correia et al. (2018) also presented evidence that Microcaecilia is paraphyletic with respect to Brasilotyphlus. The placement of Luetkenotyphlus brasiliensis within Siphonops contrasts with results of Pyron and Wiens’ (2011) and Maciel et al.'s (2019) analyses that found Luetkenotyphlus and Siphonops to be sister taxa. Although analyses by San Mauro et al. (2006), San Mauro et al. (2014) and Correia et al. (2018) also recovered Luetkenotyphlus and Siphonops as sister groups, these studies only included one species of Siphonops (S. annulatus). Therefore, additional molecular data are needed to clarify the delimitation of these clades.

Consistent with previous findings (i.e., Correia et al. 2018), our phylogenetic analysis recovers Microcaecilia as non-monophyletic. Previously, based on evidence from dentition (relationship between VPs and rows of PM) and orbit (open versus closed orbit), Wilkinson et al. (2013) suggested that some Microcaecilia, including the type species of the genus (Dermophis albiceps Boulenger, 1882; not included herein), are more closely related to M. nicefori (Gymnophis nicefori Barbour, 1925, the type species of Parvicaecilia, currently in the synonymy of Microcaecilia; analyzed here for the first time) than to other species of Microcaecilia. That is, the position of trans-Andean Microcaecilia nicefori compared to other cis-Andean members of the genus suggests the revalidation of the genus Parvicaecilia. However, our analysis does not represent solid evidence due to several aspects, such as the low number of genes used, the low support values (a bootstrap value of only 45%), and the absence of key terminals, such as the type species of the Amazonian Microcaecilia (M. albiceps (Boulenger, 1882). Thus, inclusion of relevant taxa, such as M. albiceps, in future phylogenetic analyses is key to guiding taxonomic changes. At the interfamilial level, our results provide evidence for the first time that Shiphonopidae is paraphyletic with respect to Dermophiidae due to the placement of M. nicefori (Fig. 2). Additional, large scale phylogenetic studies are required to rigorously test this finding.

Status of the trans-Andean populations of Caecilia degenerata

Lynch (1999) suggested that Caecilia degenerata is restricted to the Cordillera Oriental of Colombia (Departments of Boyacá, Cundinamarca and Santander). However, morphological and biogeographical evidence suggests that the cis- and trans-Andean populations are not conspecific. The type series was collected at two cis-Andean localities: Garagoa (Boyacá Department), the type locality, and Choachí (Cundinamarca Department), ca. 90 km southwest of the type locality (Dunn, 1942). Later, Ruiz-Carranza et al. (1996) and Lynch (1999) examined a series of trans-Andean specimens collected at Muzo (Boyacá Department), Tena and Sasaima (Cundinamarca Department), and Charalá (Santander Department), and referred them to C. degenerata, based on morphological similarity and (presumably) relative geographical proximity. Although the absence of secondary annular grooves, the number of primary annular grooves (127–138 in the cis-Andean populations vs. 123–137 in the trans-Andean populations), and the ratio of length/diameter (32–60 in the cis-Andean populations vs 48–58 in the trans-Andean populations; Ruiz-Carranza et al. 1996, Lynch 1999) are consistent with the hypothesis of conspecific populations. The cis- and trans-Andean populations are isolated by biogeographic barriers that includes high and steep mountains, xerophytic areas, and rainy environments, factors that usually play a fundamental role in the speciation of Andean amphibians (Lynch et al. 1997). To test the conspecificity of the populations of C. degenerata, a more extensive sampling of specimens, populations, and additional molecular data are required. Finally, although Taylor (1968) recorded specimens of C. degenerata in Tomaque (probably in Colombia or Peru) and Río Pache (probably in Peru), we agree with Lynch (1999) that C. degenerata is restricted to the (eastern) Cordillera Oriental of Colombia.

Conclusions

Caecilia pulchraserrana sp. nov. is described as an endemic species from the Serranía de los Yariguies. The species is similar to C. degenerata, from which it can be distinguished using morphological characters. According to their morphology, we hypothesize there is a group of closely related species that comprises C. caribea, C. corpulenta, C. degenerata, C. orientalis, and C. subdermalis. The trans-Andean Microcaecilia nicefori is an endemic and poorly known species from Colombia. We provide here the first analysis of molecular data that tests its phylogenetic position. Our results address the need to evaluate with more evidence the status of the genus Parvicaecilia Taylor, 1968 (currently under the synonymy of Microcaecilia), and the potential non-monophyly of the family Siphonopidae. Further analyses sampling additional taxa and molecular markers are required to establish a more robust classification for Gymnophiona.

Acknowledgments

This research was supported by Santander Bio, a project funded by the Sistema General de Regalías, administered by the Departamento Nacional de Planeación (BPIN 2017000100046), executed by the Gobernación de Santander, and operated by the Instituto de Investigación de Recursos Biológicos Alexander von Humboldt and the Universidad Industrial de Santander (Inter-administrative Agreement 2243, Gobernación de Santander). Specimens were collected under a permit issued by the Instituto de Investigación de Recursos Biológicos Alexander von Humboldt (Decree 1376 of 2013). We thank Javier Barriga for providing invaluable support during fieldwork. We specially thank Marjorie Pinzón Arias for interchanging knowledge with local people from El Carmen de Chucurí to come up with the name of the new species. Special thanks to the inhabitants of the Vereda La Belleza, El Carmen de Chucurí municipality, for participating in and allowing us to carry out the biodiversity inventories. We are also grateful to Miguel Torres and Daniela García for collaborating actively on discovering and collecting several specimens of the new species. In addition, we thank the collaboration of Yeison Tolosa in the process of obtaining material of Microcaecilia nicefori. Mark Wilkinson, David Gower, and Santiago J. Sánchez-Pacheco provided comments, suggestions and corrections that greatly improved the manuscript. Special thanks to Eduardo Tovar-Luque for his expert technical assistance with the molecular work.

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Appendix 1

Additional specimens examined in this study. Number of specimens examined of each species in parenthesis.

Caecilia guntheri (2): COLOMBIA: NARIÑO: La Planada Natural Reserve, 7 km South of Chucunes, 1780 m above sea level; IAvH-Am-1396; RISARALDA: Pueblo Rico Municipality, Vereda Montebello, Montezuma Reserve, 4°33'40.5"N, 74°21'4.9"W, 1650 m above sea level, IAvH-Am-8872.

Caecilia isthmica (1): COLOMBIA: SUCRE: San Benito Abad Municipality, Vereda La Caimanera, site La Caimanera, 9°2'33.7"N, 74°54'17.6"W, 26 m above sea level, IAvH-Am-8246 (tissue IAvH-CT-22982).

Caecilia subdermalis (10): COLOMBIA: CALDAS: Norcasia Municipality, Hidromiel camp, 5°34'16.4"N, 74°53'24.8"W, 850 m above sea level. IAvH-Am-9663; HUILA, Acevedo Municipality, Cueva de los Guácharos National Natural Park, 1820 m above sea level. IAvH-Am-0687, IAvH-Am-3541, IAvH-Am-3549, IAvH-Am-4316-7, IAvH-Am-4322-23, IAvH-Am-4708, IAvH-Am-5388.

Caecilia thompsoni (1): COLOMBIA: CUNDINAMARCA: La Mesa Municipality, site Payacal, La Gran Via, Tacarcuna Farm, 04°39'6,77"N, 74°25'1.0"W; 1100 m above sea level, MUJ 3713 (tissue IAvH-CT-22986).

Epicrionops aff. parkeri (2): COLOMBIA: ANTIOQUIA: municipality of El Carmen de Viboral, vereda El Porvenir, creek afferent to the Melcocho River, 5°54'7.9"N, 75°10'25.6"W, 898 m above sea level, IAvH-Am-14608, IAvH-Am-14609 (tissue IAvH-CT-21477).

Microcaecilia nicefori (1): COLOMBIA: TOLIMA: municipality of Coello, El Neme farm (outside of town), 4°7'12.50"N, 74°55'21.10"W, 327 m above sea level, IAvH-Am-14879 (tissue IAvH-CT-22985).

Typhlonectes natans (2): COLOMBIA: SUCRE: San Benito Abad Municipality, Vereda La Caimanera, site La Caimanera, 9°27'1"N, 74°54'26.7"W, 25 m above sea level, IAvH-Am-8275 (tissue IAvH-CT-22983). NORTE DE SANTANDER: San José de Cúcuta Municipality, Aguasal Creek, Footbridge about 1.2 km northeast of the community of Aguasal, 08°13'05"N, 072°32'31.2"W, 62 m above sea level, IAvH-Am-14559 (tissue IAvH-CT-22984).