Research Article |
Corresponding author: Fernando Luis Mantelatto ( flmantel@usp.br ) Academic editor: Martin Schwentner
© 2024 Nielson Felix Caetano França, Célio Magalhães, Fernando Luis Mantelatto.
This is an open access article distributed under the terms of the Creative Commons Attribution License (CC BY 4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Citation:
Felix Caetano França N, Magalhães C, Mantelatto FL (2024) Integrative approach revealing a species complex in the Neotropical freshwater crab Dilocarcinus septemdentatus (Herbst, 1783) (Decapoda: Trichodactylidae) with a description of a new species. Arthropod Systematics & Phylogeny 82: 385-405. https://doi.org/10.3897/asp.82.e115268
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The taxonomic status of the freshwater crab Dilocarcinus septemdentatus (Herbst, 1783) is still not well established. Currently, the main issue involves synonymization with D. spinifer H. Milne Edwards, 1853, based on a variation of the angulation of the gonopod apex. These species are distributed along rivers and lakes in northern South America, with disjunct occurrences in central-west Brazil and Argentina. Due to these inconsistencies, an integrative approach was performed to elucidate these questions, with morphological (including NanoCT-Scan) and molecular analysis (Maximum Likelihood Trees, Bayesian Inference, Genetics Distance Matrix, and Haplotype Network), based on mitochondrial markers COI and 16S rRNA. Both analysis revealed and supported the existence of a species complex under the name of D. septemdentatus. Based on the results obtained, we propose the revalidation of D. spinifer, the description of a new species, and the redescription of D. septemdentatus s. str., with a neotype designation for this species. The hypothesis that this species complex originated in the Pebas System, an extensive mega wetland system that existed along the lowlands of Western Amazonia from late Oligocene to late Miocene (c. 23–11 mya) is discussed.
CT-scan, DNA barcode, Haplotype diversity, Molecular systematics, Taxonomy
The primary freshwater crab genus Dilocarcinus H. Milne Edwards, 1853 has a somewhat complex taxonomic history. In the first comprehensive revision of the group,
In their specific treatment of the genus,
Such a wide area of occurrence, with the existence of isolated spots (central-west region of Brazil, state of Goiás, and Argentina, near Santa Fé), raises the hypothesis that this species corresponds, in fact, to more than one cryptic species under the same nomination. The occurrence of complexes of two or more cryptic species has been increasingly reported for freshwater crabs using molecular tools (
All specimens used in the present study were evaluated through visits to, or loans from, the crustacean collections of the following institutions: Coleção de Crustáceos do Departamento de Biologia (CCDB), Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil; Forschungsinsitut und Naturmuseum Senckenberg (
Other abbreviations used: cl = carapace length; cw = carapace width; G1, G2 = male first and second gonopods; P2–5 = second to fifth pereiopods. Measurements are in millimeters and are given in parentheses (cw, cl) after specimen counts when available; ‘?’ is used when the measurement could not be obtained. Tissue samples were also obtained, under appropriate permits, from the specimens available in the referred collections, except for the
Morphological analysis was performed on specimens of D. septemdentatus from different geographic distribution as listed in the material examined section. When indicating the number and sex (♂ = male; ♀ = female) of the specimens examined, one symbol corresponds to a single individual of the respective sex, while two symbols correspond to two or more individuals of the respective sex.
The morphological examination was conducted by assessing somatic (shape and number of carapace anterolateral teeth; the number of fused abdominal somites) and gonopods (shape and angulation of the apex) characters. In addition to this preliminary assessment, a search for other potentially taxonomically informative characters was also performed, but none was found relevant. The terminology for gonopod structures was adapted from
Both molecular analyzes were performed based on mitochondrial genes: Cytochrome Oxidase subunit I (COI) and 16S Ribosomal RNA (16S). These markers have proven their effectiveness in studies with decapod crustaceans, both phylogenetic and variability in different taxon levels, including primary crabs (
The steps of DNA extraction, amplification, purification, and sequencing followed the protocols of
Approximately 600 base pairs (bp) corresponding to the COI gene and 500 corresponding to 16S were amplified using the primers listed in Table
List of used primers, their respective genes, and studies where they were developed.
Gene | primer | Sequences | References |
COI | Pty1 | 5’ CGCCTGTTTATCAAAAACAT 3’ | Souza-Carvalho et al. (pers. communication) |
Pty2 | 5’ CCGGTCTGAACTCAGATCACGT 3’ | ||
16S | 16SL2 | 5’ TGCCTGTTTATCAAAAACAT 3’ | Schubart et al. (2002) |
1472 | 5’ AGATAGAAACCAACCTGG 3’ |
|
|
16SL15 | 5’ GACGATAAGACCCTATAAAGCTT 3’ | Schubart et al. (2001) |
The PCR products were evaluated using agarose gel electrophoresis (1.5%), visualized on an L-PIX EX® photodocumenter, purified using the SureClean® Plus kit (according to the supplier’s protocol), and sequenced using the ABI Big Dye® Terminator Mix in an ABI Prism 3100 Genetic Analyzer®, from the FCAV Technology Department of UNESP in Jaboticabal, São Paulo, Brazil.
The strands obtained (forward and reverse) were evaluated, edited, and used to create consensus sequences, using GENEIOUS PRIME® (2021.2.2 Biomatters Ltd). Sequence identification was confirmed using the GenBank BLAST tool (http://blast.ncbi.nlm.nih.gov/Blast.cgi). Information regarding the sequences used are listed in Table
Information on specimens of Dilocarcinus species used in molecular analyses. CCDB: Coleção de Crustáceos do Departamento de Biologia da FFCLRP/USP;
Specimen | Voucher | Locality | GenBank Access | |
COI | 16S | |||
Dilocarcinus spinifer 027 | CCDB 5034 | Altamira/PA | OP252629 | — |
Dilocarcinus spinifer 028 | CCDB 5034 | Altamira/PA | OP252630 | — |
Dilocarcinus spinifer 029 | CCDB 5034 | Altamira/PA | OP252631 | — |
Dilocarcinus septemdentatus 033 |
|
Carauari/AM | OP252632 | OP263690 |
Dilocarcinus septemdentatus 034 |
|
Carauari/AM | OP252633 | — |
Dilocarcinus septemdentatus 045 |
|
Res. Mamirauá/AM | OP252634 | OP263691 |
Dilocarcinus montinavis sp. n. 050 |
|
Serra do Navio/AP | OP252635 | OP263692 |
Dilocarcinus montinavis sp. n. 159 |
|
Flona do Amapá/AP | OP252636 | OP263693 |
Dilocarcinus montinavis sp. n. 160 |
|
Flona do Amapá/AP | — | OP263694 |
Dilocarcinus pagei 021 | CCDB 6338 | Castilho/SP | OP236481 | OP245228 |
Goyazana castelnaui | CCDB 4651 | Palmas/TO | MG344686 | MG344657 |
Fourteen sequences were used and obtained from individuals previously identified as D. septemdentatus (8 from COI and 6 from 16S), and four sequences from D. pagei and Goyazana castelnaui (H. Milne Edwards, 1853) (one from each gene). The G. castelnaui sequences were chosen as an outgroup for the phylogenetic analyses due to the close relationship between this species and those of the genus Dilocarcinus (see
All alignments were performed on the MAFFT v.7 online servers (
Concatenated alignments were used, with sequences from both genes of D. septemdentatus, from D. pagei (sister group), and from G. castelnaui (outgroup), for the reconstruction of phylograms, one by the Maximum Likelihood (ML) method and another by Bayesian Inference (IB). ML analysis was performed on the IQ-TREE (http://www.iqtree.org) (
After comparing the results of both approaches, only the phylogram of the tree by IB was presented, with the bootstrap value (right) and posterior probability (left) (> 95%), considering that all clades were recovered by both analyzes.
Finally, a divergence time estimation analysis with concatenated partitions, referring to COI and 16S, was also included in BEAST v.2.6.7. For this purpose, all configurations of the phylogenetic analysis by IB were considered, with the addition of information for the calibration of the molecular clock (Relaxed Log model), obtained from the fossil record of trichodactylid crabs from the Middle Eocene (dated to approximately 38–47.8 mya) (see
The morphological analysis included specimens identified a priori as D. septemdentatus sensu
The main variation observed in D. septemdentatus sensu
Computerized nano-tomography of the distal portion of the male right first gonopod of Dilocarcinus septemdentatus,
It was also interesting to note a correlation found between the shape of the apex of G1 and the shape of the carapace front among the specimens examined. Specimens with bent distal portion of the G1 (forms a and c) usually show a sinuous frontal margin of the carapace, with a distinct median concavity (Fig.
The results evidenced that the specimens considered under the name D. septemdentatus sensu
Phylogram generated by the Bayesian Inference method, based on concatenated alignments of the COI and 16S genes of specimens belonging to the Dilocarcinus septemdentatus sensu
Intra- and interlineage genetic distances of Dilocarcinus septemdentatus, D. spinifer, and Dilocarcinus montinavis sp. n. for COI and 16S genes. Values in percentage (%).
COI | ||
Lineage 1 (D. septemdentatus) | Lineage 3 (D. montinavis sp. n.) | |
Lineage 1 (D. septemdentatus) | 0–0.68 | |
Lineage 2 (D. spinifer) | 5.29–5.90 | |
Lineage 3 (D. montinavis sp. n.) | 4.09–5.31 | 0–0.51 |
16S | ||
Lineage 1 (D. septemdentatus) | ||
Lineage 1 (D. septemdentatus) | 0–1.70 | |
Lineage 3 (D. montinavis sp. n.) | 4.29–6.73 |
The analysis of estimated divergence time pointed to an interval between 19 and 13 mya, in which it is estimated that the process of separation of L1 from L2 and L3 occurred. In turn, it is estimated that the separation between D. spinifer (L2) and Dilocarcinus montinavis n. sp. (L3) occurred in the interval from 14 to 8 Ma. Fig.
Phylogram with estimated divergence time generated by the Bayesian Inference method, based on concatenated alignments of the COI and 16S genes of specimens belonging to the Dilocarcinus septemdentatus sensu
The haplotype network generated with D. septemdentatus sensu
Parsimony haplotype network of COI (A) and 16S (B) gene fragments from populations of the Dilocarcinus septemdentatus sensu
Based on the obtained results, it is proposed herein the resurrection of Dilocarcinus spinifer as a valid species, besides proposing the description of a new species for the genus based on morphological and molecular data, as well as adjustments in the diagnosis and description of the studied species.
Order Decapoda Latreille, 1803
Infraorder Brachyura Latreille, 1803
Family Trichodactylidae H. Milne Edwards, 1853
Dilocarcinus spinifer H. Milne Edwards, 1853 [subsequent designation by
Cancer n. 957 —
Cancer
Orbicularis
—
Cancer
Orbicularis
—
Cancer septemdentatus Herbst, 1783: 155.
Arica septemdentata
—
Dilocarcinus septemdentatus
—
Orthostoma septemdentatum
—
Dilocarcinus (Dilocarcinus) septemdentatus — Bott 1969: 44, pl. 8, fig. 14a, b, pl. 20, fig. 45.
G1 with distal portion strongly curved laterally; subdistal lobe moderately to well developed; apex directed laterally, approximately as long as the subdistal lobe.
Carapace (Fig.
Dilocarcinus septemdentatus, neotype male (cw 47.9, cl 37.6),
Neotype (designated herein): Male (cw 47.9, cl 37.6),
Brazil, state of Pará, municipality of Peixe-Boi, Peixe-Boi River.
SURINAME — • 1 ♂, NHM 1959.3.20.6, 1838, I.T. Sandersen. — Paramaribo District: • 2 ♂ (cw 48.2, cl 37.8; cw 48.7, cl 39.9),
Dilocarcinus pagei Stimpson, 1861: • 7 ♀♀ (cw 36.5, cl 30.7 – 45.7:38.9),
Dilocarcinus spinifer
H. Milne Edwards, 1853: 215 — H.
Dilocarcinus castelnaui
— H.
Orthostoma spiniferum Ortmann, 1897: 326 (in key), 327.
Trichodactylus (Dilocarcinus) spinifer
—
Dilocarcinus (Dilocarcinus) spinifer — Bott 1969: 45, pl. 8, figs 15a, b; pl. 20, fig. 46.
Dilocarcinus septemdentatus
—
G1 (Fig.
Carapace (Fig.
Lectotype (designated herein): 1 ♂ (cw 38.8, cl 31.8), dry,
Cayenne, French Guiana.
SURINAME: • 1 ♂,
BRAZIL, Maranhão: municipality of Paulino Neves, riacho São José, 02°49′26.2″S 42°32′38.3″W (
Northern and southern South America, occurring in coastal river basins from Suriname, French Guiana, and Brazil (states of Pará and Maranhão), the Amazon River basin in Brazil and Peru, the Araguaia-Tocantins Rivers basin, and the middle Paraná River basin in northern Argentina (Fig.
Both male syntypes of D. spinifer are dried specimens that are glued by the abdomen to the base of the box in which they are preserved. The left G1 of the larger specimen (
The three species studied here exhibit a sympatric and sometimes even syntopic geographic distribution (Fig.
The specimen figured by
Dilocarcinus septemdentatus
—
G1 with distal portion distinctly sinuous, strongly curved laterally; subdistal lobe (“sl” in Figs
Carapace (Fig.
Dilocarcinus montinavis sp. n., holotype male (cw 39.5, cl 32.7),
Third maxilliped (Fig.
Chelipeds (Fig.
Median line of sternum as deep sulcus extending from somites V–VIII, interrupted by transversal link at somites VI/VII; furrow corresponding to endosternite IV/V reaching midline, following ones ending about halfway between beginning of sternopleonal cavity and midline.
Pleon (Fig.
G1 (Figs
G2 (Fig.
Holotype: 1 ♂ (cw 39.5, cl 32.7),
1 ♂ 1 ♀,
Serra do Navio region, rio Amapari, Cupixi, state of Amapá, Brazil.
The specific epithet refers to the region where the type locality of the species is situated, Serra do Navio (Serra = mountain range; Navio = ship). It is composed by the root (mont) of the Latin word montes (nominative plural, meaning “mountains”), the connecting vowel i, and the word navis (genitive singular, meaning “of the ship”).
The currently known distribution is limited to the state of Amapá, rio Araguari basin, Brazil (Fig.
The type series of the present species was listed by
Although Dilocarcinus montinavis sp. n. (Lineage 3) was retrieved as a sister species of D. spinifer (Lineage 2) in the concatenated tree using ML and IB analyzes (Fig.
The very short apex of the G1 of Dilocarcinus montinavis sp. n. is also found in the G1 of Dilocarcinus truncatus Rodríguez, 1992. Both species can be morphologically distinguished from each other by the orientation of the G1 distal portion, which is sinuous and distinctly curved laterally in the former (Fig.
The existence of cryptic species under the name of D. septemdentatus sensu
Each lineage recovered in the present phylogenetic analyzes can be related to a particular morphology of the G1 (Fig.
The variation in the curvature of the G1 distal portion (Figs
Although several studies in the last two decades have refined paleoclimatic and paleoenvironmental reconstructions of Cenozoic South America (
However, considering the wide geographic distribution of the genus Dilocarcinus along the lowland areas of the Amazon, Paraguay-Paraná and northern South America coastal river basins (
Taking these constraints into account, as well as possible non-intentional errors in the molecular clock calibration process (
The radiation of the D. septemdentatus complex towards the eastern Amazonia and coastal river basins of northern South America must have occurred from the late Miocene onwards coevally with the gradual evolution of the Western Amazonia from a megawetland to a fluviodeltaic system following the combined effect of late Miocene global sea-level lowstand and ongoing Andean orogeny coupled with surface processes (sedimentation and erosion) on the Western Amazonia that culminated in the overcoming of the Purus arch and the reorganization of the drainage system into the present-day eastward-flowing Amazon River during the late Miocene and early Pliocene (c. 10.5–4.5 mya) (
A possible hypothesis to explain the current occurrence of D. spinifer in the middle Paraná River basin (
Confirmation of these hypotheses, or another more consistent one to better explain the origin and distribution of this species complex, however, can only be achieved when the aforementioned constraints, in particular the inclusion of other species of the genus in the analysis, can be overcome.
The morphology-based studies on the systematics of the trichodactylid genus Dilocarcinus included either eight (
Author contributions. Conceptualization, C.M. and F.L.M.; methodology, N.F.C.F., C.M. and F.L.M.; perform the molecular analysis, N.F.C.F.; investigation, morphological and molecular analysis, N.F.C.F., C.M. and F.L.M.; data curation, N.F.C.F., C.M. and F.L.M.; preparing, writing, review and editing, N.F.C.F., C.M. and F.L.M.; supervision, C.M. and F.L.M.; project administration, F.L.M.; resources and funding acquisition, F.L.M. All authors have read and agreed to the published version of the manuscript.
Competing interests. The authors declare no competing interests.
This study is part of LBSC’s research efforts to investigate the diversity of decapod crustaceans along the Brazilian drainages and is a product of the NFCF’s Doctorate thesis. This project was supported by Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) (Projetos Temáticos Biota 2010/50188-8 and INTERCRUSTA 2018/13685-5; Coleções Científicas 2009/54931-0; PROTAX 2016/50376-5 and 2021/08075-6) for FLM. Additional support was also provided by Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq), for the Research grant (PQ 302253/2019-0) for FLM. NFCF thanks Coordenação de Aperfeiçoamento Pessoal de Nível Superior (CAPES) for PROEX DS scholarship (Proc. 88887.369727/2019-00 – Financing code 001). Brazilian specimens were obtained under collection permits (permanent license to FLM for collection of Zoological Material No. 11777-2 MMA/IBAMA/SISBIO and SISGEN AE942E3, CEA7CD5, AEF142F). Thanks are due to the following colleagues for their support on loaning specimens and/or assistance during visits of the authors to their respective institutions: Daniel Cavalari, Flavio Bockmann (FFCLRP/USP); Jéssica Colavite, Sérgio L. S. Bueno (IB/USP); Inácia M. Vieira (IEPA); Marcio L. Oliveira, Thiago Mahlmann (