Abstract
After being stable for nearly a century, the taxonomic history of the genus Xiphopenaeus has been marked by many changes in the last three decades. The taxonomic status of the Atlantic species has a low resolution, and many species are still undefined and grouped as cryptic species. Here we employed an integrative approach to define the species of Xiphopenaeus and the morphological characters needed to differentiate them. We combined the analyses of two molecular markers (COI and 16 S rDNA), scanning electron microscopy and light microscopy. Based on specimens from 17 localities from the Atlantic and Pacific oceans, we detected five divergent genetic groups, three in the Atlantic (A1, A2, A3) and two in the Pacific (P1, P2). Male secondary sexual characters were able to differentiate four out of the five genetic groups. Group A1 corresponds to X. kroyeri, and A2 and A3 correspond to new species. We redescribed the genus and two new species are described and illustrated: Xiphopenaeus dincao nov. sp. (A2) and Xiphopenaeus baueri nov. sp. (A3). Since the holotype of X. riveti was missing and the specimen analysed from group P2 was a female, the status of the species of Xiphopenaeus from the Pacific remains unresolved.
Similar content being viewed by others
Introduction
Cryptic species are two or more species considered as one due to their highly similar morphology1. The discovery of cryptic species has been increasing in the last decades due to the development of molecular tools, which indicates that they might be more common in the animal kingdom than previously thought2,3. An example of an unresolved taxonomic issue involving cryptic species occurs in penaeid shrimps of genus Xiphopenaeus Smith, 1869. This genus was described in 1869 based on the type-species Xiphopeneus hartii Smith, 1869, whose individuals came from the south of Bahia, Brazil. Later, X. hartii became a junior synonym of Penaeus kroyeri Heller, 1862 from Rio de Janeiro, and named Xiphopeneus kroyeri (Heller, 1862). For nearly 40 years X. kroyeri was the only known species of the genus. However, in 1907, a new species was described from the coast of Peru, Xiphopeneus riveti Bouvier, 19074. In 1969, the International Commission on Zoological Nomenclature (Opinion 864) changed the genus spelling to Xiphopenaeus5.
Xiphopenaeus kroyeri has an Atlantic distribution from North Carolina (USA) down to Rio Grande do Sul (Brazil). Xiphopenaeus riveti occurs in the Pacific from Sinaloa (Mexico) to Paita (Peru)4. Due to the high morphological similarity between X. kroyeri and X. riveti their taxonomy remained controversial: X. riveti was considered as a variety of X. kroyeri, or its sister species6,7. Perez-Farfante & Kensley4 revised the suborder Dendrobranchiata and considered X. riveti as a junior synonym of X. kroyeri. Thus, the genus was again considered monotypic and X. kroyeri its only valid species8. Gusmão et al.9 addressed the issue again, using molecular data from PCR/RFLP, isoenzyme polymorphisms and Cytochrome C Oxidase Subunit I sequences. They proposed the revalidation of X. riveti from the Pacific plus the existence of cryptic speciation in Xiphopenaeus kroyeri, which contained two entities they call: Xiphopenaeus sp. 1 and Xiphopenaeus sp. 2. These entities were not formally described, and neither were the morphological characters that could differentiate the species (synapomorphies). Eight years later, Piergiorge et al.10 came to the same conclusions, also using molecular techniques, but once again, no definitive morphological characters were given to differentiate these entities. Recently, Kerkhove et al.11, have detected Xiphopenaeus sp. 2 in north part of South America (Guiana and Caribbean Ecoregions), and pointed out differences in the colour of individuals between the two species.
Xiphopenaeus kroyeri sensu lato represents ~40% of the total shrimp fisheries in the Brazilian coast12 and often accounts for 90% of the shrimp biomass captured in shallow waters, up to 20 m of depth13,14,15. Moreover, the species is the second most important fishery resource of the southeast of Brazil, and the most targeted shrimp in the State of São Paulo, were the catch reach the maximum in early 1980s (8,905 tons) and then start to decrease until 2000 (629 tons), since then the biggest catch occurred in 2012 (3,258 tons)16,17,18. However, in 2018 X. kroyeri becomes the most exploited fishery resource in this state (2,246 tons)19.
Naturally, given the commercial importance of this resource, Xiphopenaeus kroyeri sensu lato has been constantly studied, despite the lack of a definitive taxonomic solution to define and/or distinguish the entities that are known to exist (c.f. Gusmão et al.9, Piergiorge et al.10). In the last 13 years, more than 50 articles have been published on diverse subjects — population biology, ecology, fishery biology, physiology, toxicology, sperm ultrastructure, bycatch — considering X. kroyeri as the only species of Xiphopenaeus in the Atlantic. Certainly, this was caused by the lack of knowledge on the morphological characters that could be used to differentiate the two species.
The correct taxonomic identification of important fishery resources is essential to enhance biodiversity knowledge and to develop adequate management and conservation strategies20,21,22. Recently, the combination of molecular tools and the detailed morphological analyses of the reproductive structures has proved to be very effective to solve taxonomic problems and to differentiate and describe cryptic species of decapod crustaceans23,24. Therefore, considering the controversial taxonomic history of Xiphopenaeus explained above and its high economic importance, here we employed an integrative analysis and combined molecular and morphological tools to characterize the species that constitute the genus Xiphopenaeus, based on specimens from 17 localities, 15 in the Atlantic and two in the Pacific cost of America. We provide a detailed redescription of the genus and the description of two new species.
Results
Molecular analysis
About 1,125 base pairs (bp), from our double-genes analyses, were used to construct the phylograms. A total of 91 sequences of the COI gene (barcoding region) were obtained. The final alignment had 596 base pairs. There were 111 variable sites: 11 in the 1st codon base, 2 in the 2nd, and 96 in the 3rd; and 93 variable sites were phylogenetically informative (Supplementary Fig. 1). The average nucleotide composition was: T = 33.7%, C = 20.8%, A = 27.4%, G = 18.1%. We obtained 15 sequences of the 16S gene. The final alignment had 529 base pairs. We detected 25 variable sites of which 16 were phylogenetically informative (Supplementary Fig. 2). An average nucleotide composition was: T = 31.0%, C = 21.6%, A = 34.7%, G = 12.8%. After adding the sequences of the four external group species, we obtained 179 variable sites, of which 81 were phylogenetically informative.
Phylogenetic analyses
Maximum likelihood phylogram based on the COI (barcoding region) gene indicated the existence of five groups, three from the Atlantic Ocean (A1, A2 and A3) and two from the Pacific (P1 and P2).
The phylogram of the concatenated COI and 16S sequences supported the same division into five groups (Figs. 1 and 2). Both trees show that P1 and P2 form a well-supported clade, which is a sister group of the clade formed by A2 and A3, while A1 forms an external clade regarding A2 and A3.
Maximum likelihood phylogram of 91 specimens of Xiphopenaeus, based on the COI gene (barcoding region). The numbers near the branches are bootstrap values (values lower than 50 are not shown).
Maximum likelihood phylogram of 16 specimens of Xiphopenaeus, based on the concatenated and partitioned sequences of the genes COI (barcoding region) and 16S. The numbers near the branches are bootstrap values (values lower than 50 are not shown).
The comparison of our specimens with those of Gusmão et al.9, based on the Palumbi region of the COI gene25, indicate that our clade A1 corresponds to Xiphopenaeus sp1, and clade A2 corresponds to Xiphopenaeus sp 2. Clade P2 corresponds to Xiphopenaeus riveti, and clades A3 and P1 are two genetic groups previously undetected (Fig. 3).
Maximum likelihood phylogram of specimens of Xiphopenaeus based on the COI gene (Palumbi region), including the specimens from our study assigned to the five genetic groups (underlined) and the sequences from Gusmão et al. (2006).
Genetic distances
The genetic distance within Xiphopenaeus regarding the COI gene varied from 0 to 13.5%, and the distance to the outgroups was 15.7−27.8%. There was a clear separation between groups, i.e., there was a low genetic distance within groups (0−1%) and a higher distance between groups. The lowest between-group distances were between A2 and A3, 2.7−3.3%, and the highest were 12.9−13.5%, between A1 and P2 (Fig. 4). Regarding the 16S gene, the genetic distance within Xiphopenaeus varied from 0.0 to 2.9%, and the distance to the outgroups varied from 7.3 to 38.1%. The results of the 16S corroborated the groups suggested by the COI, and the within-group distances were 0.0−0.4%. The lowest between-group distances occurred between A1 and P1 (1.0–1.2%), and the highest, between A3 and P2 (3.2–3.6%) (Fig. 5). Thus, based on COI and 16S genes, there is evidence of at least five genetic groups in Xiphopenaeus. Based on the combined analyses with morphological characters, two of these groups will be described below as new taxonomic entities.
Histogram of the pairwise genetic distances (Kimura-2-parameters) for the COI gene (barcoding region), within Xiphopenaeus, and between Xiphopenaeus and the outgroups. The lines above the bars indicate the range of values found in the pairwise comparisons between the groups revealed in the previous analyses. A1: Atlantic 1, A2: Atlantic 2, A3: Atlantic 3, P1: Pacific 1, P2: Pacific 2.
Histogram of the pairwise genetic distances (Kimura-2-parameters) for the 16S gene (barcoding region), within Xiphopenaeus, and between Xiphopenaeus and the outgroups. The lines above the bars indicate the range of values found in the pairwise comparisons between the groups revealed in the previous analyses. A1: Atlantic 1, A2: Atlantic 2, A3: Atlantic 3, P1: Pacific 1, P2: Pacific 2.
Morphological assessment
Gross Morphology
In the gross morphological analyses, we used 79 individuals from 16 localities which had at least one of the genes sequenced. The comparative analysis of the carapace (spine, grooves, and carinas), legs and mouthparts did not point to substantial variation capable to differentiate the genetic groups. The number of rostral teeth varied from four to six, but most individuals had five, irrespectively of the group. Individuals bearing four were seen only in groups P1 and A3, while six teeth were seen only in groups A1 and A2. There was individual variation regarding the teeth shape, rostrum length (in relation to the carapace), groove and carina depth, but they did not lead to a separation of the groups. The presence and size of the teeth of the dorsomedial carina in the fourth, fifth, and sixth abdominal segments also varied. Although in A1 they were smaller and less frequent, this character was also not enough to separate the groups.
The petasma and appendix masculina, however, were much more informative and separated the individuals according to the genetic groups. Thus, we decided to update the general description of Xiphopenaeus given by Perez-Farfante & Kensley4 adding a detailed redescription of these two male structures. The description of the appendix masculina is given for the first time on the literature on Xiphopenaeus.
Systematics
Suborder Dendrobranchiata Spence Bate, 1888
Superfamily Penaeoidea Rafinesque-Schmaltz, 1815
Family Penaeidae Rafinesque-Schmaltz, 1815
Xiphopenaeus Smith, 1869
Penaeus – Heller, 1862, Sber. Akad. Wiss. Wien, 45(1): 425.
Xiphopeneus Smith, 1869, Trans. Conn. Acad. Arts Sci., 2(1): 27. For details see Perez-Farfante & Kensley (1997), p. 149–152.
Redescription of the genus Xiphopenaeus
Integument glabrous. Rostrum long, considerably overreaching antennular peduncle, usually longer than carapace in adults, sinuous, styliform anteriorly; armed with dorsal teeth only, situated basally; epigastric tooth distinctly separated from first rostral. Carapace with orbital angle well marked, antennal, and hepatic spines present; pterygostomian angle produced but lacking spine; postocular sulcus well marked; clearly distinct orbito-antennal sulcus; short, almost indistinct cervical sulcus, clearly distinct orbito-antennal sulcus; hepatic sulcus and sharp hepatic carina reaching only base of pterygostomian region and posteriorly merging with long branchiocardiac sulcus and carina, respectively; longitudinal suture extending to about mid length of carapace, transverse suture lacking (in adults). Abdomen with sixth somite bearing interrupted cicatrix. Telson unarmed. Antennule lacking parapenaeid spine; antennular flagella long, dorsal (twice or more as long as carapace) longer than ventral. Palp of first maxilla entire, gradually tapering distally, produced into small, triangular, setose proximolateral lobule, broad, setose proximomesial and quite small, acute setose distomesial lobules, latter armed with slender spine; distolateral row of small spines present on ventral surface. Fourth and fifth pereopods long, much longer than third, subflagelliform, each with multiarticulate dactyl. Basial and ischial spines on first pereopod only.
Thelycum closed, with single plate of sternite XIV smooth, broad, not produced anteriorly into pair of flaps, its anterolateral hoods much reduced; anterior sternal invagination nearly as broad as sternite, forming spacious pocket extending as far as posterior thoracic ridge; median protuberance of sternite XIII also broad but quite short. Paired seminal receptacles (spermatheca) is bilobed, each consisting of large posterior lobe and small anterolateral one; sinuous slit-like opening lying on anterior end of posterior lobe, connecting with median pocket and extending laterally dorsal to posterolateral extremity of median protuberance.
General description of petasma and appendix masculina of the genus Xiphopenaeus
Petasma formed by the union of the endopods of the first pleopod pair, joining the two dorsolateral lobes by the cincinuli (Fig. 6B), and bearing a horn-like distolateral projection (DLP) (Fig. 6A). The distolateral projection has two regions. The proximal region extends from the endopod junction until 2/3 or 3/4 of the distolateral projection length (depending on the species). The distal region, which is oblique to the proximal, bears the opening; its posterior surface is covered by a row of teeth whose morphology varies in each species (Fig. 6A).
Scanning electron microphotographs showing the general morphology of the secondary sexual characters of Xiphopenaeus. A, Xiphopenaeus dincao nov. sp. (CCDB 6499): petasma (E - endopod; DLP - distolateral projection; P - proximal region of the DLP; D - distal region of the DLP); B, Xiphopenaeus dincao nov. sp. (CCDB 6499): junction between the endopods with cincinuli (seta); C, Xiphopenaeus kroyeri (CCDB 5019): appendix masculina in dorsal view (DS – dorsal surface; RP – rounded projection); D, Xiphopenaeus kroyeri (CCDB 5019): appendix masculina in ventral view (VS - ventral surface; RP - rounded projection; white arrow indicating the row of spines of the posterior margin).
The appendix masculina is subcircular (Fig. 6C) and has a rounded projection whose posterior margin that varies in length and is oriented towards the body midline. The dorsal surface is smooth (Fig. 6C); the central region of the ventral face is concave or convex and has rows of spines with varied distribution (Fig. 6D). Both characters vary depending on the species, and the species-specific descriptions are given below.
Xiphopenaeus kroyeri (Heller, 1862) (Figs. 7–9).
Xiphopenaeus kroyeri (Heller, 1862) (A) Lateral view (specimen ULLZ 15974); male; Ubatuba, São Paulo, Brazil. Photo: Darryl L. Felder; (B) Dorsal view of petasma (specimen CCDB 5019); (C) Detail of the right distolateral projection (specimen CCDB 5019).
Scanning electron microscopy. Brazil: São Paulo, Ubatuba. 4♂ (CCDB 5019). Male secondary sexual characters of Xiphopenaeus kroyeri. (A) petasma in dorsal view; the white arrow indicates the posterior margin of the distolateral projection; (B) distal region of the distolateral projection; white arrowheads indicate the teeth; black arrows indicate the petasma opening; (C) distolateral projection in ventral view; white arrowheads indicate the row of teeth of the distal region of the distolateral projection; the black arrow indicates the carina of the proximal region of the distolateral projection; (D) detailed ventral view of distolateral projection; white arrowheads indicate the row of teeth of the distal region of the distolateral projection; the black arrow indicates the carina of the proximal region of the distolateral projection; (E) Appendix masculina in dorsal view; (F) Appendix masculina in dorsal view; white arrowheads indicate the spines; (G) Appendix masculina in ventral view; the black arrow indicates the row of spines of the posterior margin, white arrows indicate the convex central region; (H) Appendix masculina in ventral view; the black arrow indicates the row of spines of the posterior margin, white arrows indicate the convex central region.
Holotype of Xiphopenaeus kroyeri (Heller, 1862): NHMW 342, Rio de Janeiro, Brazil collected by Kröyer, male. (A) lateral view; (B) Petasma in dorsal view; (C) detail of the right distolateral projection. Photos by Peter Dworschak.
Peneus Kroyeri Heller, 1862b: 425; Plate 2, fig. 51. [Rio Janeiro]
Xiphopeneus hartii Smith, 1869: 27, 40; Plate 1, Fig. 1. [Caravelas, Estado da Bahia, Brazil]
Material examined
Holotype: Rio de Janeiro, 1♂, col. Kröyer, NHMW 342 (Fig. 9).
Additional material
Brazil: Rio Grande do Norte, Baía Formosa, 06°21′23,3″S − 35°00′24,7″W, 25/IV/2014, col. M. Lopes & A. Carvalho-Batista, 6♂, 3♀ (CCDB 5337) – Alagoas, Maragogi, Praia de Maragogi, 09°00′48,59″S − 35°13′14,46″W, 05/X/2013, col. F.L. Mantelatto & F.B. Mantelatto, 1♂, 3♀ (CCDB 5338) - Sergipe, Aracajú, Praia do Atalaia, 26/VII/2013, col. G.L. Hirose, 1♀ (CCDB 5246) – Espírito Santo, Marataízes, 20°59′S − 40°47′W, 20/VI/2012, Col. F.L. Carvalho, D. Peiró & R. Robles, 3♂, 1♀ (CCDB 3985) – Rio de Janeiro, Macaé, 22°23,44′S − 41°44,57″W, 21/VII/2014, R.C. Costa et al., 3♂ (CCDB 5339) – São Paulo, Ubatuba, Praia do Cedro, 23°32′38,4″S − 45°09′54″W, 22/VII/2013, R.C. Costa et al., 4♂ (CCDB 5019) – Santos, 24°04′55,″S − 46°16′56,8″W, 24/X/2011, R.C. Costa et al., 2♂, 2♀ (CCDB 3663) – Santa Catarina, Penha, V/2014, R.C. Costa et al., 3♂, 1♀ (CCDB 5292).
Morphological characterization to be used in comparisons with other species
Petasma: In dorsal view, the posterior margin of the proximal region of the distolateral projection is straight (Figs. 7B, 8A). The distal region extends through 1/3 of the distolateral projection length and forms an obtuse angle towards the central-posterior part of the petasma (Figs. 7B,C, 8A,B). The opening is narrow and long and crevice-like and bears a row of upright teeth in the posterior margin, which is straight (Figs. 7C, 8B). In ventral view, the row of teeth of the distal region posterior margin forms a carina; the part of the carina next to the endopod is more evident (Fig. 8C,D).
Appendix masculina subcircular with a rounded projection towards the body median part and bearing two spines in the dorsal surface (Fig. 8E,F). The posterior margin of the ventral surface is covered by small sparse spines, with a few rows in the central convex region (Fig. 8G,H).
Type locality
Rio de Janeiro, State of Rio de Janeiro, Brazil
Distribution
Colombia, Venezuela, Guyana, Suriname, French Guyana, Brazil (Maranhão, Rio Grande do Norte, Alagoas, Sergipe, Bahia, Espírito Santo, Rio de Janeiro, São Paulo, Santa Catarina).
Remarks
The comparison with the holotype of Xiphopenaeus kroyeri, deposited in the Museum of Natural History of Vienna (Austria), indicated that this species corresponds to our clade A1 and also to Xiphopenaeus sp.1 detected by Gusmão et al.9 Based on the material examined here, this species seems to be the very abundant. It was the most abundant species in almost all localities of the northern, southern, and southeastern coasts of Brazil.
Xiphopenaeus dincao nov. sp
Xiphopenaeus dincao nov. sp. (A) Lateral view of the holotype (MZUSP 39350), male, Maragogi, Alagoas, Brazil. (B) Petasma in dorsal view; (C). Detail of the right distolateral projection. Photos by Julia Fernandes Perroca.
Scanning electron microscopy. Brazil: Alagoas, Maragogi, 3♂ (CCDB 6499), 1♂ (MZUSP 39350). Male secondary sexual characters of Xiphopenaeus dincao nov. sp. (A) petasma in dorsal view; the white arrow indicates the posterior margin of the distolateral projection; (B) distal region of the distolateral projection; white arrowheads indicate the teeth; black arrows indicate the petasma opening; (C) distolateral projection in ventral view; white arrowheads indicate the row of teeth of the distal region of the distolateral projection; the black arrow indicates that the carina of the proximal region of the distolateral projection is absent; (D). Detailed ventral view of distolateral projection; white arrowheads indicate the row of teeth of the distal region of the distolateral projection; the black arrow indicates the carina of the proximal region of the distolateral projection is absent; (E) – Appendix masculina in dorsal view; (F) Appendix masculina in dorsal view; white arrowheads indicate the spines; (G) Appendix masculina in ventral view; the black arrow indicates the row of spines of the posterior margin, white arrows indicate the central convex region; (H) – Appendix masculina in ventral view; the black arrow indicates the row of spines of the posterior margin, white arrows indicate the central convex region.
Xiphopenaeus sp. 2 — Gusmão et al. 2006: 491, 496–500, Figs 3–5; Kerkhove et al. 2019: 853–858, Figs 1–5.
Xiphopenaeus sp. II — Piergiorge et al. 2014: 349–353, Figs 2–3.
Holotype
Brazil: Alagoas, Maragogi, Praia de Maragogi, 09°00′48.59″S − 35°13′14.46″W, 05/X/2013, col. F.L. Mantelatto & F.B. Mantelatto, 1♂ (MZUSP 39350).
Paratypes
Brazil: Alagoas, Maragogi, Praia de Maragogi, 09°0′48.59″S − 35°13′14.46″W, 05/X/2013, col. F.L. Mantelatto & F.B. Mantelatto, 5♂, 2♀ (CCDB 6499) - São Paulo, Cananéia, X/2014, R.C. Costa, 2♂, 5♀ (CCLC 418).
Additional material examined
Brazil: Amapá, Oiapoque, Estuário do Rio Oiapoque, Parna Cabo Orange, 04°22′17.6″N–51°24′26.4″W, 22/VIII/2013, col. I.M. Vieira, A.G. Santiago & E.G. Oliveira, 1♂ (IEPA 1618) – Pará, Vigia, Ponta Seca, 0°51′45.00″S – 48°7′50.00″W, 19/XI/1994, col. M.P. Barros, 2♂ (MCP 2024).
Description
Petasma: In dorsal view, the proximal region occupies 3/4 of the distolateral projection length (Figs. 10B, 11A), with rounded posterior margin (Figs. 10A,B, 11A,B). The distal region is as long as wide and bears a convex row of teeth and the opening, which is wide and rounded (Figs. 10C, 11B). In ventral view the row of teeth of the posterior margin enters the proximal region but ends abruptly before its wider portion. In this species the carina of the ventral surface of the proximal region is absent (Fig. 11C,D). In dorsal view the appendix masculina is subcircular but less rounded than in X. kroyeri and its protruding tip has many spine rows (Fig. 11E,F). The posterior rounded projection is longer and narrower than in X. kroyeri. In ventral view the spines are more prominent in the margins and become smaller over the central convex region (Fig. 11G,H).
Etymology
The specific epithet “dincao” is given in the honour of the late Dr. Fernando D′Incao, in recognition of his contribution to the Brazilian Carcinology, in particular to the study of penaeoid shrimps from the Brazilian coast. It is to be treated as a noun in apposition.
Type locality
Maragogi, Alagoas, Brazil.
Distribution
Colombia11, Suriname11, French Guiana11, Brazil9,10 and presen study (Amapá, Pará, Rio Grande do Norte, Alagoas, Bahia, São Paulo).
Remarks
This species refers to the specimens of clade A2, previously known as Xiphopenaeus sp. 29,10,11. Besides the description, this is the first record of this taxon to Amapá, Pará and Alagoas. Despite the vast list of works in the literature that studied biology of X. kroyeri, it was not possible to identify in which of these studies were used specimens of the described new species and thus the synonymic list was short.
Xiphopenaeus baueri nov. sp
Xiphopenaeus baueri nov. sp.; (A) Lateral view of the holotype (MZUSP 39351), male, Tabasco, Mexico; (B) Petasma in dorsal view; (C) Detail of the right distolateral projection. Photo by Julia Fernandes Perroca.
Scanning electron microscopy. Mexico: Tabasco, 3♂ (CCDB 5461), 1♂ (MZUSP39351). Male secondary sexual characters of Xiphopenaeus baueri nov. sp. (A) petasma in dorsal view; the white arrow indicates the posterior margin of the distolateral projection; (B) distal region of the distolateral projection; white arrowheads indicate the teeth; black arrows indicate the petasma opening; (C) distolateral projection in ventral view; white arrowheads indicate the row of teeth of the distal region of the distolateral projection; the black arrow indicates that the carina of the proximal region of the distolateral projection is absent; (D) – Detailed ventral view of distolateral projection; white arrowheads indicate the row of teeth of the distal region of the distolateral projection; the black arrow indicates the carina of the proximal region of the distolateral projection is absent; (E) Appendix masculina in dorsal view; (F) Appendix masculina in dorsal view; white arrowheads indicate the spines; (G): Appendix masculina in ventral view; the black arrow indicates the row of spines of the posterior margin, the white arrow indicates the central convex region; (H) – Appendix masculina in ventral view; the black arrow indicates the row of spines of the posterior margin, the white arrow indicates the central convex region
Holotype
Mexico: Tabasco, 18°31′40.25″N – 93°19′43.95″W, 05/XI/2014, col. Ku, M.A.M., 1♂ (MZUSP 39351).
Paratypes
Mexico: Tabasco, 18°31′40.25″N – 93°19′43.95″W, 05/XI/2014, col. Ku, M.A.M., 5♂, 3♀ (CCDB 5461).
Additional material examined
USA: Isle Dernier, Louisiana, 16/XI/1992, col. Bauer R.T., 3♂ (CCDB 5394) – Puerto Rico: Mayagüez Bay, XII/1985, col. R.T. Bauer (CCLC 0417). Brazil: Amapá, Oiapoque, Estuário do Rio Oiapoque, Parna Cabo Orange, 04°22′17.6″N – 51°24′26.4″W, 22/VIII/2013, col. I.M. Vieira, A.G. Santiago & E.G. Oliveira, 1♀ (IEPA 1617) – Pará, Vigia, Ponta Seca, 0°51′45.00″S – 48°7′50.00″W, 19/XI/1994, col. M.P. Barros, 1♀ (MCP 2024).
Description
Petasma: In dorsal view, the proximal region occupies 3/4 of the distolateral projection length, posterior margins slightly rounded (Figs. 12B, 13A). The distal region extends for 1/4 of the distolateral projection length. The opening is wide and rounded, with a convex row of teeth (Figs. 12C, 13B). In ventral view, the row of teeth of the distal region of the posterior margin invades the proximal region and becomes sparser until it reaches its wider part (Fig. 13C,D). In this species the carina in the ventral surface of the proximal region is absent (Fig. 13C,D). The appendix masculina is subcircular but less rounded than in X. kroyeri (Fig. 13E,F) and has no prominent apex, but its posterior margin is covered with spines. The rounded projection is the widest of all species. In ventral view there are several rows of spines which cover the central convex region completely (Fig. 13G,H).
Etymology
The new species in named in the honour of our colleague Dr. Raymond Bauer, a recognized carcinologist who has devoted his career to the study of the biology of caridean shrimps, especially from Gulf of Mexico, the type locality of the new species herein described.
Type locality
Tabasco, Mexico.
Distribution
Mexico (Tabasco), USA (Louisiana, Texas); Puerto Rico, Brazil (Amapá, Pará).
Remarks
The individuals of our clade A3 correspond to a new species, undetected in previous studies. The shape of the petasma is very similar to that of Xiphopenaeus dincao nov. sp. The main character that differentiates these two species is the ventral surface of the appendix masculina covered with spines in Xiphopenaeus baueri nov. sp. The two species seem to occur in sympatry, at least in the north of Brazil, which may hamper their differentiation. In the Gulf of Mexico, however, Xiphopenaeus baueri nov. sp. is the only known species of Xiphopenaeus. Despite the vast list of works in the literature that studied biology of X. kroyeri, it was not possible to identify in which of these studies were used specimens of the described new species and thus the synonymic list was not provided.
Xiphopenaeus riveti - P1
Material examined
Costa Rica: Puntarenas, Sierpe, Terraba, GPS coordinates unknown, VI/2013, J.S. Vargas, 4♂, 1♀ (CCDB 5247).
Description
Petasma: in dorsal view the proximal region occupies 2/3 of the distolateral projection length and the posterior margin is strongly rounded (Fig. 14A). Opening narrow and long with a row of teeth slightly rounded (Fig. 14B). In ventral view, the row of teeth of the posterior margin reaches 3/4 of the proximal region of the distolateral projection and goes through the margins of a well-defined carina that occupies the entire proximal region of the distolateral projection (Fig. 14C,D). Appendix masculina subcircular (Fig. 14E,F); the rounded projection is more elongated than in X. kroyeri but less than in Xiphopenaeus baueri nov. sp.; the posterior distal margin has few spines. In ventral view, the posterior margin is densely covered by long spines; the concave central region of the ventral surface lacks spines (Fig. 14G,H).
Scanning electron microscopy. Mexico: Tehuantepec, 4♂ (CCDB 5247). Male secondary sexual characters of Xiphopenaeus riveti. (A) petasma in dorsal view; the white arrow indicates the posterior margin of the distolateral projection; (B) distal region of the distolateral projection; white arrowheads indicate the teeth; black arrows indicate the petasma opening; (C) distolateral projection in ventral view; white arrowheads indicate the row of teeth of the distal region of the distolateral projection; the black arrow indicates the carina of the proximal region of the distolateral projection; (D) –detailed ventral view of distolateral projection; white arrowheads indicate the row of teeth of the distal region of the distolateral projection; the black arrow indicates the carina of the proximal region of the distolateral projection; (E) Appendix masculina in dorsal view; (F) Appendix masculina in dorsal view; (G) Appendix masculina in ventral view; the black arrow indicates the row of spines of the posterior margin, the white arrow indicates the central convex region; (H) – Appendix masculina in ventral view; the black arrow indicates the row of spines of the posterior margin, the white arrow indicates the central convex region.
Discussion
Our results revealed that the genus Xiphopenaeus is composed of at least five species, distributed along the American continental coasts. A division of the genus in three species, including X. riveti and a new species from the Atlantic, was suggested previously9,10, without a formal taxonomic and nomenclatural record and a detailed description. However, these studies were restricted to the South American coast and one locality from the Pacific. Thus, besides supporting the revalidation of X. riveti and a species from the Atlantic (Xiphopenaeus dincao nov. sp.), our study also indicates the existence of a third species from the Atlantic (Xiphopenaeus baueri nov. sp.) and at least two entities from the Pacific. This last species (group P2) could not be described since only a female was available, and diagnostic morphological characters from the petasma are needed.
The use of molecular tools, in addition to the morphological ones, was extremely useful to strengthen and deepen our study, which confirms their usefulness in the taxonomic identification and to solve taxonomic and phylogenetic problems23,26,27,28,29,30. The between-group distances resulting from the phylogenetic analyses of COI and 16S were in the range of interspecific distances expected in decapods. Moreover, the genetic groups were supported by morphological differences in the male secondary sexual characters. Within the order Decapoda, the highest intraspecific distances known for the COI gene (barcoding region) are ~2%, while the interspecific distances between congeneric species are usually higher than 5%, reaching 10% in many cases, and even more than 30%31,32. For instance, in shrimps of the family Penaeidae from the coast of Egypt and in species of the genus Farfantepenaeus, the interspecific distances varied from 3 to 20%33,34. Thus, most interspecific distances detected here are above the threshold used to separate congeneric species based on the barcoding region.
The genetic distance between Xiphopenaeus dincao nov. sp. and Xiphopenaeus baueri nov. sp. for the COI gene are in between the intraspecific and interspecific thresholds of Decapoda. Even though intraspecific distances of up to 2.7% were reported for the penaeid shrimp Artemesia longinaris Spence Bate, 1888, it was less than 1% in other Atlantic Dendrobranchiata shrimps, such as Pleoticus muelleri (Spence Bate, 1888), Farfantepenaeus paulensis (Pérez-Farfante, 1967), Farfantepenaeus brasiliensis (Latreille, 1817), and Farfantepenaeus subtilis (Pérez-Farfante, 1967)22,35,36,37,38.
The intraspecific distances (0.0–0.2% in Xiphopenaeus dincao nov. sp.; 0.0–0.3% in Xiphopenaeus baueri nov. sp.) were much lower than the interspecific (2.7–3.3%), thus, there is a well-defined intraspecific gap. The DNA Barcoding technique uses this gap to identify the species39,40,41,42,43, and prove to be effective in the case of Xiphopenaeus.
The 16S gene is more conserved than the COI and has a low, or none intraspecific variation in decapod crustaceans. Moreover, in penaeid shrimps, the known interspecific distances between congeneric species are ~1%44,45. Nonetheless, our analysis of the 16S supported the genetic groups as distinct species, including the differentiation between Xiphopenaeus dincao nov. sp. and Xiphopenaeus baueri nov. sp.
The existence of a second species besides X. riveti in the Pacific (group P2) is an interesting and novel result since it has been undetected in previous studies. Unfortunately, we obtained DNA sequences only from a female from Tehuantepec, Mexico, warranting further descriptions. However, the genetic distances between P2 and the other Pacific specimens (P1), from Sierpe, Costa Rica, reinforce the idea that these two groups are indeed two distinct species. Further studies, with a more comprehensive sampling including more localities are needed to understand their geographic range in the Pacific. There is likely an overlap in the distribution range of these two species because the specimens from Panama, analysed by Gusmão et al.9, belong to our group P2, while the specimens from P1 came from Costa Rica, which is close to Panama. Since the holotype of X. riveti could not be located (it is probably lost), its comparison with specimens of these two groups was not possible.
An overlap between the geographical distribution of X. kroyeri and Xiphopenaeus dincao nov. sp. (as Xiphopenaeus sp. 1 and Xiphopenaeus sp. 2) along the Brazilian coast has been reported in Natal, Rio Grande do Norte and Ubatuba, São Paulo9, and later in Cananéia, São Paulo and in Caravelas, Bahia10. Here we show that they also overlap in Maragogi and Baía Formosa. Xiphopenaeus dincao nov. sp. and Xiphopenaeus baueri nov. sp. occurs in sympatry in Vigia and Oiapoque (Fig. 15). Considering that X. kroyeri has been collected in Caracas (Venezuela)9 and in São Luís, Maranhão (Brazil)46, the geographic distribution of these three species seem to overlap in the northern Atlantic coast of South America. In the present study, Xiphopenaeus dincao nov. sp. and Xiphopenaeus baueri nov. sp. were collected in the North of Brazil between Caracas and São Luís, Maranhão. Kerkhove et al.11 found X. kroyeri and Xiphopenaeus dincao nov. sp. (as Xiphopenaeus sp. 2) in Colombia and Guianan Marine Ecoregion. Therefore, based on our data, and on Gusmão et al.9,46, Piergiorge et al.10 and Kerkhove et al.11 the known geographical distribution of the species of the genus Xiphopenaeus is shown in Fig. 15.
Geographical occurrence of the Atlantic Xiphopenaeus species. Locality numbers: 1- Isle Derniere (29°03′23.5″N; 90°48′58.6″W); 2- Galveston (29°11′49.3″N; 94°53′60.0″W); 3- Tabasco (18°31′40.25″N; 93°19′43.95); 4- Carmen (18°39′51.1″N; 91°51′17.7″W); 5- Mayaguez Bay (18°12′01.0″N; 67°09′37.0″W); 6- Colombia (); 7- Caracas (10°41′51.2″N; 66°56′41.2″W); 8- Trinidad and Tobago (10°24′28.8″N; 61°29′34.8″W); 9- Guyana (6°58′55.27″N; 57°54′31.07″W); 10- Suriname (5°56′35″N; 55°9′46″W); 11- French Guyana (4°54′44.698″N; 52°15′29.376″W); 12- Oiapoque (04°22′17.6″N; 51°24′26.4″W); 13- Vigia (00°51′45.00″S; 48°7′50.00″W); 14- São Luís (01° 59′ 56.7816″ S; 44° 19′ 7.8528″ W); 15- Natal (05°52′S; 35°10′W); 16- Baía Formosa (06°21′23.3″S; 35°00′24.7″W); 17- Maragogi (09°0′48.59″S; 35°13′14.46″W); 18- Aracaju (10°54′34″ S; 37°04′29″W); 19- Poças (11°46′S; 37°32 W); 20- Ilhéus (14°46′S; 39°01′W); 21- Caravelas (17°44′S; 39°15′W); 22- Nova Almeida (20°03′S; 40°11′W); 23- Marataízes (20°59′S; 40°47′W) 24- Atafona (21°37′33.3″S; 41°00′47.2″W); 25- Macaé (22°23.44′S; 41°44.57″W); 26- Arraial do Cabo (22°58′S; 42°01′W); 27- Ubatuba (23°26′S; 45°04′W); 28- Santos (23°58′S; 46°19′W); 29- Cananéia (25°02′S; 47°55′W); 30- Guaratuba (25°52′44.3778″ S; 48°31′35.7996″ W); 31- Barra Velha (26°37′S; 48°40′); 32- Balneário Camboriú (26°59′07″S; 48°35′58″W); 33- Tehuantepec (16°08′56.6″N; 95°09′12.1″W); 34- Sierpe (8°58′26.2″N; 83°37′58.9″W); 35- Panama City (8°53′N; 79°35′W).
It is likely that the successive openings and closures of the Panama Isthmus allowed the diversification of the genus Xiphopenaeus until its definitive closure circa 2.8 million years ago47. The low genetic distances seen between Xiphopenaeus dincao nov. sp. and Xiphopenaeus baueri nov. sp. suggest that these species diverged more recently. Xiphopenaeus baueri nov. sp. was the only species found in the Gulf of Mexico and probably originated there. The Quaternary sea level changes created or strengthened the isolation between this region and the Caribbean, warranting the exchange of migrants48,49,50,51. This isolation pattern has also been observed in other crustaceans such as the hermit crabs Clibanarius vittatus (Bosc, 1802) and C. simetricus (Randall, 1840), the first restricted to southeastern coast of the United States and Gulf of Mexico, and the second distributed along the Caribbean and South America52. Furthermore, in Atya scabra (Leach, 1816), individuals from the Gulf of Mexico are isolated from those from the Caribbean and Brazil, which share haplotypes among them although genetic divergences remain within the intraspecific level53.
The external genitalia of Dendrobranchiata display important characters for the taxonomy of the group and is useful to separate morphologically highly similar congeneric species4,24,54. Here, morphological differences supporting the separation of the groups identified in the molecular analyses were found in the male secondary sexual characters — petasma and appendix masculina. Previously, the petasma of Xiphopenaeus has been described without many details on the distolateral projections4,55,56. Fransozo et al.57, who studied the petasma development of X. kroyeri in Ubatuba, did not report morphological differences among the individuals. The photo provided by the authors corresponds to the shape described here to Xiphopenaeus dincao nov. sp. Burkenroad6 described a difference between individuals from Bahia (Brazil) and Louisiana (USA), concerning the “small tooth” of the distolateral projection, probably referring to the distal region of the distolateral projection. Considering the known geographical distribution of Xiphopenaeus (see Fig. 15), the species analysed by Burkenroad6 were probably Xiphopenaeus kroyeri stricto sensu and Xiphopenaeus baueri nov. sp.
We did not find any differences in the female external genitalia that could be used to separate the species of Xiphopenaeus. We expected that the same pattern revealed by the petasma would be seen in the thelycum, since the morphological differentiation of the reproductive structures contributes to the reproductive isolation and favours the formation of cryptic species24. Therefore, it seems that the hypothesis that the male and female genitalia evolve in a “key and lock” model as a mechanism of reproductive isolation58, does not apply to all Dendrobranchiata, as also reported in Sicyonia H. Milne Edwards, 183059. Future studies on the ultrastructure of the internal part of the thelycum, including a larger number of specimens, are needed to solve the taxonomic issue based on females.
Previous description of the appendix masculina of Xiphopenaeus have been little informative. Smith56 described it as ovoid and flattened while Pérez-Farfante & Kensley4 described it as subcircular. Overall, the appendix masculina of Xiphopenaeus is similar to that of Rimapenaeus fuscina60, and may reflect the phylogenetic closeness between these genera61,62.
Microanatomic details may reveal crucial information to differentiate cryptic species63, and indeed, the use of SEM to analyse the petasma and appendix masculina revealed unknown details and ornamentations. Nonetheless, the gross anatomy of the petasma also allowed the identification of a few characters that were important to differentiate the species, without the need of such equipment (SEM). Thus, this information could facilitate and pave the way for further studies on the population biology and ecology of these cryptic species. According to Dall et al.7 the morphology of these structures are unique in each species. Using the stereomicroscope, it is possible to see the interspecific differences in the spines of the ventral face of the appendix masculina, which can also be enhanced using dyes like methyl blue.
To conclude, we demonstrate that the genus Xiphopenaeus is composed of at least five species, by combining morphological and molecular tools. Four out of five species can be differentiated based on the morphology, and two of them are described herein (Xiphopenaeus dincao nov. sp. and Xiphopenaeus baueri nov. sp.). Further studies addressing the status of the species from the Pacific and investigating the existence of more cryptic species are strongly encouraged.
Methods
Molecular analysis
We obtained specimens of the genus Xiphopenaeus from 17 localities: 15 from the Atlantic Ocean and two from the Pacific (Supplementary table S1 and S2). Most specimens came from the Crustacean Collection of the Department of Biology, FFCLRP, University of São Paulo, Brazil (CCDB). Others were collected during the development of research projects by members of the Laboratory of Marine and Freshwater Shrimps (LABCAM) and Laboratory of Bioecology ad Systematics of Crustaceans (LBSC). These specimens were stored in 80% ethanol and deposited in the collection mentioned above (CCDB) and Coleção de Crustáceos do Laboratório de Biologia de Camarões Marinhos e de Água Doce, Faculdade de Ciências, Universidade Estadual Paulista, Bauru, Brazil (CCLC). Additionally, we included specimens borrowed from the following scientific collections: Museu da Pontíficia Universidade Católica do Rio Grande do Sul (MCP); Instituto de Pesquisas Científicas e Tecnológicas do Estado do Amapá (IEPA), Colección Nacional de Crustáceos, Universidad Autónoma de Mexico (CNCR). We also received donations of specimens and tissues from the following scientific institutions: Zoological Collection of the University of Louisiana, Lafayette, USA (ULLZ) and Museo de Zoologia da Universidad de Costa Rica (MZ-UCR).
To extract DNA, muscle tissues were dissected from the abdomen and two common techniques were employed: the salting-out method64 with some modifications proposed by Mantelatto et al.26, and the Chelating Ion Exchange Resin (Chelex 100)65. Two molecular markers from mitochondrial genes, cytochrome c oxidase subunit I (COI) barcoding region66,67,68 (N = 91) and 16 S rDNA67 (N = 15) were used. Additionally, the Palumbi region of COI25 (N = 9) was used to allow the comparison of our specimens to those used by Gusmão et al.9 The amplification reactions contained bovine albumin 1% (Sigma), 10X Taq Buffer (Thermo Scientific), MgCl2 (25 mM), betaine (5 M), dNTPs (1.25 mM each), primers (10 or 20 µM) (Supplementary table S3), Thermus aquaticus polymerase (5 U µl−1) (Thermo Scientific), 1.0–5.5 µl of extracted DNA (50−100 ng ml−1), and distilled and deionized water to complete 25 µl.
The thermal cycler settings used for the amplification for COI were: 4 min at 94 °C for initial denaturation; 35 cycles of 30 s at 94 °C, 30 s at 40–46 °C, 60 s at 72 °C; and final extension for 10 min at 72 °C. For the 16 S they were: 4 min at 94 °C for initial denaturation; 40 cycles of 30 S at 48 °C; and final extension for 10 min at 72 °C. The results were checked in a 1.5% agarose gel stained with GelRed. Amplicons were purified with the SureClean Plus kit (Bioline USA Inc.) and sequenced using the BigDye Terminator Mix in an ABI 3730 XL DNA Analyzer (Applied Biosystems), following the manufacturer’s instructions.
Forward and reverse sequences were aligned to obtain the consensus sequence using BioEdit v.7.0.569. Consensus sequences were aligned separately for each gene with the software MUSCLE (Multiple Sequence Comparison by Log-Expectation)70 on the online platform EMBL-EBI (European Molecular Biology Laboratory — The European Bioinformatics Institute)71 with the default parameters. The presence of stop codons in the COI sequences, which could indicate the occurrence of pseudogenes, was ruled out using the online translation tool EMBOSS Sixpack available in the EMBL-EBI Portal72,73.
Phylogenetic analyses
The substitution saturation of all sequences was previously tested with the saturation test of Xia et al.74 using the software DAMBE. Highly variable regions were removed from the aligned sequences using Gblocks75,76 available online through the Castresana Lab, Animal Biodiversity and Evolution Program (http://molevol.cmima.csic.es/castresana/index.html).
The phylograms based on the Maximum Likelihood criterion were constructed in the program RAxML-HPC2 on X-SEDE77 available in the Cyber Infrastructure for Phylogenetic Research (CIPRES) website78. The default parameters of RAxML were used to perform the analysis for the GTR model. To measure the consistency of the topology we selected the option to automatically determine the number of bootstraps to be used in the RAxML79. Consequently, 1000 bootstrap pseudo-replicates were run, and only the values > 50% were reported.
Genetic distances
Genetic distances were calculated with the Kimura 2-Parameter model80 based on COI (barcoding region) and 16S rDNA sequences separately, using MEGA 6.0681. We also included five other sequences of Dendrobranchiata species in our alignments to serve as external groups to rout the distance and phylogenetics analysis (Supplementary Table S4).
Morphological assessment
The adult specimens used in the molecular analyses, and those from the biological collections CCDB and CCLC available for morphological analyses were carefully examined under a stereomicroscope. We searched for details in the characters and for morphological differences between the genetic groups indicated by the molecular analysis.
For the scanning electron microscopy (SEM), the petasma and appendix masculina were dissected from 15 voucher specimens preserved in 80% alcohol. These structures were dehydrated in a graded ethanol series of, 80%, 90%, and then placed 3x in 100% ethanol for 30 min. Afterwards, they were dried in a critical point dryer with liquid CO2 in an EMS 850 (Electron Microscopy Sciences) sputtering, properly placed on stubs with carbon adhesive tape and sputter-coated with gold (50 nm) in a Denton Vacuum Desk II sputtering. Micrographs were obtained in a Jeol JSM 5410 scanning electron microscope. Voucher specimens were deposited in CCDB (Catalog numbers — 5019, 5247) and in collection of Museu de Zoologia da Universidade de São Paulo (Catalog numbers — MZUSP 39350, MZUSP 39351). Ten samples containing two cryptic species were mixed and then checked using the morphological differences obtained from both stereomicroscopy and SEM. All samples were submitted again to the molecular protocol to validate the morphological characters.
Change history
22 January 2020
An amendment to this paper has been published and can be accessed via a link at the top of the paper.
References
Bickford, D. et al. Cryptic species as a window on diversity and conservation. Trends Ecol. Evol. 22, 148–155 (2007).
Pfenninger, M. & Schwenk, K. Cryptic species are homogeneously distributed among taxa and biogeographical regions. BMC Evol. Biol. 7, 121, ISI:000248497600001 (2007).
Trontelj, P. & Fiser, C. Cryptic species should not be trivialized. Syst. Biodiv. 7, 1–23 (2009).
Pérez-Farfante, I. & Kensley, B. Penaeoid and sergestoid shrimps and prawns of the world. Keys and diagnoses for the families and genera. Bull. Mus. Nat. d’Hist. Natur. 175, 1–233 (1997).
International Commission on Zoological Nomenclature - Opinion 864. Penaeid generic names (Crustacea, Decapoda): Addition of twenty-eight to the Official List. Bull. Zool. Nomencl. 25(4/5), 138–147 (1969).
Burkenroad, M. D. The Penaeidea of Louisiana with a discussion of their world relationships. Bull. Amer. Mus. Nat. Hist. 68, 61–143 (1934).
Dall, W., Hill, B. J., Rothlisberg, P. C. & Sharples, D. J. The biology of the Penaeidae.in Advances in Marine Biology (eds Blaxter, J. H. S. & Southward, A. J.) 1–489 (San Diego: Academic Press 1990).
De Grave, S. & Fransen, C. H. J. M. Carideorum catalogus: the recent species of the dendrobranchiate, stenopodidean, procarididean and caridean shrimps. Zool. Med. 85, 196–585 (2011).
Gusmão, J., Lazoski, C., Monteiro, F. A. & Solé-Cava, A. M. Cryptic species and population structuring of the Atlantic and Pacific seabob shrimp species, Xiphopenaeus kroyeri and Xiphopenaeus rivetii. Mar. Biol. 149, 491–502 (2006).
Pierjorge, R. M., Pontes, M. N., Duarte, A. V. B. & Gusmão, J. Haplotype-specific singlelocus multiplex PCR assay for molecular identification of sea-bob shrimp, Xiphopenaeus kroyeri (Heller, 1862), cryptic species from the Southwest Atlantic using a DNA pooling strategy for simultaneous identification of multiple samples. Bioch. Syst. Ecol. 54, 348–353 (2014).
Kerkhove, T. R. H. et al. Multilocus data reveal cryptic species in the Atlantic seabob shrimp Xiphopenaeus kroyeri (Crustacea: Decapoda). Biol. J. Linnean Soc. 127, 847–862 (2019).
Instituto Brasileiro do Meio Ambiente e dos Recursos Naturais Renováveis (IBAMA). Estatística da Pesca 2007 (Brasil) – Grandes Regiões e Unidades da Federação Brasileira: Ministério do Meio Ambiente. Available at https://www.ibama.gov.br/sophia/cnia/livros/estatisticadepescadigital.pdf. (2007).
Fransozo, A., Costa, R. C., Mantelatto, F. L., Pinheiro M. A. A. & Santos, S. Composition and abundance of shrimp species (Penaeidea and Caridea) in Fortaleza Bay, Ubatuba, São Paulo, Brazil in Modern Approaches to the Study of Crustacea (eds. Briones, E.E. & Alvarez, F.) 117–125 (Kluwer Academic, 2002).
Costa, R. C. et al. Carcinofauna acompanhante da pesca do camarão sete-barbas Xiphopenaeus kroyeri em Macaé, Rio de Janeiro, sudeste brasileiro. Bolm. Inst. Pesca. 42, 611–624 (2016).
Pantaleão, J. A. F., Carvalho-Batista, A., Fransozo, A. & Costa, R. C. The influence of upwelling on the diversity and distribution of marine shrimp (Penaeoidea and Caridea) in two tropical coastal areas of southeastern Brazil. Hydrobiologia. 763, 381–395 (2016).
D′Incao, F., Valentini, H. & Rodrigues, L. F. Avaliação da pesca de camarões nas regiões sudeste e sul do Brasil. 1965–1999. Atlântica. 24, 103–116 (2002).
Castro, R. H., Costa, R. C., Fransozo, A. & Mantelatto, F. L. Population structure of the seabob shrimp Xiphopenaeus kroyeri (Heller, 1862) (Crustacea: Penaeoidea) in the littoral of São Paulo, Brazil. Sci. Mar. 69, 105–112 (2005).
Instituto de Pesca de São Paulo. Programa de Monitoramento da Atividade Pesqueira Marinha e Estuarina do Instituto de Pesca (PMAP). Available at http://www.propesq.pesca.sp.gov.br/relatorio/30. Accessed on 30 July 2019.
Ávila-da-Silva, A. O. et al. Produção pesqueira marinha e estuarina do estado de São Paulo dezembro 2018. Informe Pesqueiro de São Paulo. 104, 1–4 (2019).
Pérez-Farfante, I. Illustrated key to Penaeoid shrimps of commerce in the Americas. NOAA Tech. Rep. NMFS. 64, 1–32 (1988).
Bortolus, A. Error cascades in the biological sciences: the unwanted consequences of using bad taxonomy in ecology. AMBIO: J. Human Environ. 37, 114–118 (2008).
França, N. F. C. et al. Farfantepenaeus subtilis (Pérez-Farfante, 1967) and F. brasiliensis (Latreille, 1817) (Decapoda, Penaeidae): Ontogenetic comparison using the combined analysis of secondary sexual characters and molecular markers. Fish. Res. 216, 89–95 (2019).
Magalhães, T., Robles, R., Felder, D. L. & Mantelatto, F. L. Integrative taxonomic study of the purse crab genus Persephona Leach, 1817 (Brachyura: Leucosiidae): combining morphology and molecular data. PLoS One. 11, e0152627 (2016).
Tavares, C. & Gusmão, J. Description of a new Penaeidae (Decapoda: Dendrobranchiata) species, Farfantepenaeus isabelae sp. nov. Zootaxa. 4171(3), 505–516 (2016).
Palumbi, S. R. & Benzie, J. Large mitochondrial DNA differences between morphologically similar penaeid shrimp. Mol. Mar. Biol. Biotechnol. 1(1), 27–34 (1991).
Mantelatto, F. L., Robles, R. & Felder, D. L. Molecular phylogeny of the western Atlantic species of the genus Portunus (Crustacea: Brachyura, Portunidae). Zool. J. Linn. Soc. 150(1), 211–220 (2007).
Mantelatto, F. L. et al. DNA sequence database as a tool to identify decapod crustaceans on the São Paulo coastline. Mitoch. DNA Part A. 29(5), 805–815 (2018).
Bracken-Grissom, H. D., Felder, D. L., Vollmer, N. L., Martin, J. W. & Crandall, K. A. Phylogenetics links monster larva to deep-sea shrimp. Ecol. Evol. 2(10), 2367–2373 (2012).
Negri, M., Pileggi, L. G. & Mantelatto, F. L. Molecular barcode and morphological analyses reveal the taxonomic and biogeographical status of the stripedlegged hermit crab species Clibanarius sclopetarius (Herbst, 1796) and Clibanarius vittatus (Bosc, 1802) (Decapoda: Diogenidae). Invertebr. Syst. 26(5/6), 561–571 (2012).
Pileggi, L. G. & Mantelatto, F. L. Taxonomic revision of doubtful Brasilian freshwater shrimp species of genus Macrobrachium (Decapoda, Palaemonidae). Iheringia, Sér. Zool. 102(4), 426–437 (2012).
Costa, F. O. et al. Biological identifications through DNA barcodes: the case of the Crustacea. Can. J. Fish. Aquat. Sci. 64(2), 272–295 (2007).
Martzen da Silva, J. et al. Systematic and evolutionary insights derived from mtDNA COI barcode diversity in the Decapoda. Plos One. 6(5), e19449 (2011).
Cheng, J., Sha, Z. & Liu, R. DNA barcoding of genus Metapenaeopsis (Decapoda: Penaeidae) and molecular phylogeny inferred from mitochondrial and nuclear sequences. Bioch. Syst. Ecol. 61, 376–384 (2015).
Timm, L. et al. Tree money grows on: the first inclusive molecular phylogeny of the economically important pink shrimp (Decapoda: Farfantepenaeus) reveals cryptic diversity. Invertebr. Syst. 33, 488–500 (2019).
Carvalho-Batista, A. et al. Inferring population connectivity across the range of distribution of the stiletto shrimp Artemesia longinaris Spence Bate, 1888 (Decapoda, Penaeidae) from DNA barcoding: implications for fishery management. Zookeys. 457, 271–288 (2014).
Carvalho-Batista, A. et al. Genetic comparison of the red shrimp Pleoticus muelleri (Decapoda: Solenoceridae) using the barcode gene reveals the absence of cryptic speciation along its distribution. Reg. Stud. Mar. Sci. 24, 392–399.
Teodoro, S. A., Terossi, M., Costa, R. C. & Mantelatto, F. L. Genetic homogeneity in the comercial pink shrimp Farfantepenaeus paulensis revealed by COI barcoding gene. Estuar. Coast. Shelf Sci. 166, 124–130 (2015).
Teodoro, S. A., Terossi, M., Mantelatto, F. L. & Costa, R. C. Discordance in the Identification of Juvenile Pink Shrimp (Farfantepenaeus brasiliensis and F. paulensis): an integrative approach using morphology, morphometry and barcoding. Fish. Res. 183, 244–253 (2016).
Hebert, P. D. N., Penton, E. H., Burns, J. M., Janzen, D. H. & Hallwachs, W. Ten species in one: DNA barcoding reveals cryptic species in the neotropical skipper butterfly Astraptes fulgerator. PNAS. 101(41), 14812–14817 (2004).
Hebert, P. D. N., Stoeckle, M. Y., Zemlak, T. S. & Francis, C. M. Identification of birds through DNA barcodes. PLoS Biol. 2(10), e312 (2004).
Waugh, J. DNA barcoding in animal species: progress, potential and pitfalls. BioEssays. 29(2), 188–197 (2007).
Frézal, L. E. & Leblois, R. Four years of DNA barcoding: current advances and prospects. Infect. Gen. Evol. 8, 727–736 (2008).
Ward, R. D. DNA barcode divergence among species and genera of birds and fishes. Mol. Ecol. Res. 9, 1077–1085 (2009).
Quan, J., Zhuang, Z., Deng, J., Dai, J. & Zhang, Y. Phylogenetic relationships of 12 Penaeoidea shrimp species deduced from mitochondrial DNA sequences. Bioch. Gen. 42(9-10), 331–345 (2004).
Francisco, A. K. & Galetti Junior, P. M. Genetic distance between broodstocks of the marine shrimp Litopenaeus vannamei (Decapoda, Penaeidae) by mtDNA analyses. Gen. Mol. Biol. 28(2), 258–261 (2005).
Gusmão, J., Pierjorge, R. M. & Tavares, C. The contribution of genetics in the study of the sea-bob shrimp populations from the Brazilian coast. Bolm. Inst. Pesca. 39(3), 323–338 (2013).
O′Dea, A. et al. Formation of the Isthmus of Panama. Sci. Adv. 2, e1600883 (2016).
Avise, J. C. Phylogeography: retrospect and prospect. J. Biogeogr. 36(1), 3–15 (2009).
Hewitt, G. The genetic legacy of the Quaternary ice ages. Nature. 405, 907–913 (2000).
Hewitt, G. M. Genetic consequences of climatic oscillations in the Quaternary. Phil. Trans. R. Soc. Lond., B. Biol. Sci. 359, 183–195 (2004).
Ludt, W. B. & Rocha, L. A. Shifting seas: the impacts of Pleistocene sea-level fluctuations on the evolution of tropical marine taxa. J. Biogeog. 42, 25–38 (2015).
Negri, M., Lamaitre, R. & Mantelatto, F. L. Molecular and morphological resurrection of Clibanarius symmetricus (Randall, 1840), a cryptic species hiding under the name for the thinstripe hermit crab C. vittatus (Bosc, 1802) (Decapoda: Anomura: Diogenidae). J. Crustacean Biol. 34, 848–861 (2014).
Oliveira, C. M. C. A., Terossi, M. & Mantelatto, F. L. Phylogeographic structuring of the amphidromous shrimp Atya scabra (Crustacea, Decapoda, Atyidae) unveiled by range-wide mitochondrial DNA sampling. Mar. Freshwater Res. 70(8), 1078–1093 (2019).
Pérez-Farfante, I. A new species and two new subspecies of shrimp of the genus Penaeus from the Western Atlantic. Proc. Biol. Soc. Wash. 80, 83–100 (1967).
Heller, C. Beiträge zur näheren Kenntnis der Macrouren. Sitzungsber. Kaiserl. Akad. Wiss. 45, 389–426 (1862).
Smith, S. I. Notice of the Crustacea collected by Prof. C.F. Hart on the coast of Brazil in 1867. Trans. Connect. Acad. Arts Sci. 2, 1–41 (1869).
Fransozo, V., Santos, D. C., López-Greco, L. S. & Bolla, E. A. Jr. Development of secondary sexual characters in the seabob shrimp Xiphopenaeus kroyeri (Heller 1862) (Crustacea, Decapoda, Penaeidae): a scanning electron microscope study. Invertebr. Reprod. Dev. 55(1), 6–15 (2011).
Eberhard, W. G. Sexual Selection and Animal Genitalia. 244pp. (Harvard University Press, 1985).
Bauer, R. T. Role of the petasma and appendices masculinae during copulation and insemination in the penaeoid shrimp, Sicyonia dorsalis (Crustacea: Decapoda: Dendrobranchiata). Invertebr. Reprod. Dev. 29(3), 173–184 (1996).
Pérez-Farfante, I. A key to the American Pacific shrimps of the genus Trachypenaeus (Decapoda, Penaeidae), with the description of a new species. Fish. Bull. 69(3), 635–646 (1971).
Tavares, C., Serejo, C. & Martin, J. W. A preliminary phylogenetic analysis of the Dendobranchiata based on morphological characters in Crustacean Issues 18: Decapod Crustacean Phylogenetics (eds. Martin, J. W., Crandall, K. A. & Felder, D. F.) 261–279 (CRC Press, 2009).
Camargo, T. R. et al. Sperm ultrastructure of shrimp from family Penaeidae (Crustacea: Dendrobranchiata) in a phylogenetic context. Arthropod Struct. Dev. 46, 588–600 (2017).
Jörger, K. M. & Schrödl, M. How to describe a cryptic species? Practical challenges of molecular taxonomy. Front. Zool. 10, 59 (2013).
Miller, S. A., Dykes, D. D. & Polesky, H. F. A simple salting out procedure for extracting DNA from human nucleated cells. Nucleic Acids Res. 16, 1215 (1988).
Estoup, A., Lagiarder, C. R., Perrot, E. & Chourrout, D. Rapid one-tube DNA extraction for reliable PCR detection of fish polypmorphic markers and transgenes. Mol. Mar. Biol. Biotech. 5, 295–298 (1996).
Folmer, O., Black, M., Hoeh, W., Lutz, R. & Vrijenhoek, R. DNA primers for amplification of mitochondrial Cytochrome C Oxidase subunit I from diverse metazoan invertebrates. Mol. Mar. Biol. Technol. 3(5), 294–299 (1994).
Schubart, C. D. & Huber, M. G. J. Genetic comparisons of german populations of the stone crayfsh, Austropotamobius torrentium (Crustacea: Astacidae). Bull. Fr. Peche Piscic. 380, 1019–1028 (2006).
Mantelatto, F. L. et al. New primers for amplification of cytochrome c oxidase subunit I barcode region designed for species of Decapoda (Crustacea). Nauplius. 24, e2016030 (2016).
Hall, T. A. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp. Ser. 41, 95–98 (1999).
Edgar, R. C. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 32, 1792–1797 (2004).
McWilliam, H. et al. Analysis tool web services from the EMBL-EBI. Nucleic Acids Res. 41, 597–600 (2013).
Rice, P., Longden, I. & Bleasby, A. EMBOSS: the European molecular biology open software suite. Trends Genet. 16, 276–277 (2000).
Li, W. et al. The EMBL-EBI bioinformatics web and programmatic tools framework. Nucleic Acids Res. 43, 580 (2015).
Xia, X., Xie, Z., Salemi, M., Chen, L. & Wang, Y. An index of substitution saturation and its application. Mol. Phylogenet. Evol. 26(1), 1–7 (2003).
Castresana, J. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol. Biol. Evol. 17(4), 540–552 (2000).
Talavera, G. & Castresana, J. Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments. Syst. Biol. 56, 564–577 (2007).
Stamatakis, A. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics. 22(21), 2688–2690 (2006).
Miller, M. A., Pfeiffer, W. & Schwartz, T. “Creating the CIPRES Science Gateway for inference of large phylogenetic trees” in Proceedings of the Gateway Computing Environments Workshop (GCE) 1–8 (New Orleans, LA, 2010).
Stamatakis, A., Hoover, P. & Rougemont, J. A rapid bootstrap algorithm for the RAxML web servers. Syst. Biol. 57(1), 758–771 (2008).
Kimura, M. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J. Mol. Evol. 16(2), 111–120 (1980).
Tamura, K., Stecher, G., Peterson, D., Filipski, A. & Kumar, S. MEGA6: Molecular Evolutionary Genetics Analysis version 6.0. Mol. Biol. Evol. 30(12), 2725–2729 (2013).
Acknowledgements
The present study is part of the PhD thesis of ACB supported by a scholarship from the Conselho Nacional de Desenvolvimento Científico e Tecnológico – CNPq. The major support came from the multidisciplinary research project by the São Paulo Research Foundation – FAPESP, Brazil (Temático Biota 2010/50188–8, Coleções Científicas 2009/54931–0, PROTAX 2016/50376-5) and the Coordenação de Aperfeiçoamento de Nível Superior, Brazil – CAPES - Código de Financiamento 001 (Ciências do Mar II #2007/2014–23038.004310/2014–85, #2005/2014–23038.004308/2014–14 and #1989/2014–23038.004309/2014–51) granted to RCC, FLM and FJZ and CNPq (302748/2010–5, 471011/2011–8, 490314/2011–2, PROTAX 440417/2015–5, 406006/2012–1) to FLM. FJZ, FLM and RCC would like to thank CNPq for ongoing Research Scholarship (PQ 305919/2014–8, PQ 304968/2014–5, and 303314/2017–6, respectively). MT is grateful to FAPESP (PD 2011/11901–3). The authors would like to thank Dra. Claudia Fiorillo and to the FCAV Electron Microscopy and Invertebrate Morphology laboratories (UNESP – Jaboticabal) for technical support, and Isabel Soares for the map with the distribution of Xiphopenaeus species. Finally, the authors are grateful to many colleagues and friends (Darryl Felder, Fernando Alvarez, Ingo Wehrtmann, Jose L. Villalobos, Marcos Tavares, Peter Dworschak, Raymond Bauer, Wanderley Costa) for donating specimens, lending material from collections, allowing and helping with collection visits and fieldwork, for transporting some loans from and to the collections, and nomenclatural discussion.
Author information
Authors and Affiliations
Contributions
A.C.B., R.C.C., and F.L.M. idealized and executed the project; R.C.C., F.L.M. and F.J.Z. provided all institution and laboratory facilities and coordinated the main grants that supported the project; A.C.B., M.T. and F.L.M. visited collections; A.C.B., M.T., F.J.Z. carried out the laboratory work and performed the analyses. All authors read, corrected, and approved the final version of the text.
Corresponding author
Ethics declarations
Competing interests
The authors declare no competing interests.
Additional information
Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
Supplementary information
Rights and permissions
Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.
About this article
Cite this article
Carvalho-Batista, A., Terossi, M., Zara, F.J. et al. A multigene and morphological analysis expands the diversity of the seabod shrimp Xiphopenaeus Smith, 1869 (Decapoda: Penaeidae), with descriptions of two new species. Sci Rep 9, 15281 (2019). https://doi.org/10.1038/s41598-019-51484-3
Received:
Accepted:
Published:
DOI: https://doi.org/10.1038/s41598-019-51484-3
This article is cited by
-
Distinguishing fanged frogs (Limnonectes) species (Amphibia: Anura: Dicroglossidae), from Thailand using high resolution melting analysis
Scientific Reports (2023)
-
DNA barcode reveals high cryptic diversity in the commercially important Penaeini shrimps (Decapoda, Penaeidae)
Organisms Diversity & Evolution (2023)
-
Environmental factors modulated the fatty acid profile of the shrimp Xiphopenaeus spp. in Cananéia and Ubatuba southeast Brazilian coast
Environmental Science and Pollution Research (2023)
Comments
By submitting a comment you agree to abide by our Terms and Community Guidelines. If you find something abusive or that does not comply with our terms or guidelines please flag it as inappropriate.
