Research Article |
Corresponding author: Fernando Mantelatto ( flmantel@usp.br ) Academic editor: Ingo S. Wehrtmann
© 2014 Abner Carvalho-Batista, Mariana Negri, Leonardo Pileggi, Antonio Castilho, Rogério Costa, Fernando 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:
Carvalho-Batista A, Negri M, Pileggi LG, Castilho AL, Costa RC, Mantelatto FL (2014) 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. In: Wehrtmann IS, Bauer RT (Eds) Proceedings of the Summer Meeting of the Crustacean Society and the Latin American Association of Carcinology, Costa Rica, July 2013. ZooKeys 457: 271-288. https://doi.org/10.3897/zookeys.457.6569
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Artemesia longinaris is a marine shrimp endemic to the southwestern Atlantic and distributed from Atafona, Rio de Janeiro (Brazil) to Rawson, Chubut (Argentina). In recent years, this species has become an important target of the commercial fishery as a consequence of the decline in the fishery of more traditional and profitable marine shrimps. In addition, phenotypic variations have been documented in populations along its distribution. Therefore, investigations on the genetics of the fishing stocks are necessary for the development of sustainable management strategies and for understanding the possible sources of these variations. The mitochondrial gene Cytochrome Oxidase I (COI) was used to search for evidence of genetic structure among the populations of A. longinaris and to analyze the phylogenetic relationships among them. A total of 60 specimens were collected from seven different localities, covering its geographical range. The final alignment showed 53 haplotypes (48 individuals and 5 shared), with no biogeographical pattern. The low genetic divergence found, with a non-significant FST value, also suggests the absence of population structure for this gene. These findings indicate a continuous gene flow among the populations analyzed, suggesting that the phenotypic variation is a consequence of different environmental conditions among the localities.
Cytochrome Oxidase I, gene flow, Penaeoidea , phenotypic plasticity
Artemesia longinaris Spence Bate, popularly known as Argentine stiletto shrimp, plays an important role in the marine trophic chain of the southwestern Atlantic, as food for different species of fish and cephalopods (
In the last decades, catches in the states of south and southeast Brazil have reached thousands of tons (
Artemesia longinaris has a distribution restricted to the southwestern Atlantic, from Atafona (Rio de Janeiro, Brazil, 21°37'S) to Rawson (Chubut, Argentina, 43°18'S) (
Consequently, environmental conditions differ considerably throughout the range of A. longinaris. For example, in the Ubatuba region (São Paulo, Brazil) the temperature (16–30 °C) and salinity (28–38) vary widely because of the intrusion of different water masses (
In addition, phenotypic variations among A. longinaris populations have been noted. The body size and the mean size at sexual maturity (CL50%) increase with the latitude, from Ubatuba (São Paulo, Brazil) to Mar del Plata (Buenos Aires, Argentina), but decrease with latitude from the Farol de São Tome (Rio de Janeiro, Brazil) to Ubatuba (
In view of these environmental variations,
Knowledge of the genetic structure of populations is important for the development and success of strategies for sustainable long-term management of fishery resources (
This study had the following aims: to evaluate the hypothesis of genetic structure among the populations of A. longinaris; investigate their phylogenetic relationships; and detect, if possible, evidences of speciation. To achieve these purposes, we used a partial sequence of the mitochondrial COI gene as the molecular marker. The population concept adopted was proposed by
The specimens were obtained, at scientific cruises, from seven localities in the southwestern Atlantic (Table
Southwest Atlantic collection sites. Map showing the localities of the specimens of Artemesia longinaris analyzed: 1 Macaé, Brazil 2 Ubatuba, Brazil 3 Santos, Brazil 4 Cananéia, Brazil 5 São Francisco do Sul, Brazil 6 Rio Grande, Brazil 7 Mar del Plata, Argentina. The gray band indicates the complete geographical distribution of Artemesia longinaris.
List of specimens used for molecular analysis with respective site of collection, catalogue numbers, and GenBank accession numbers of Artemesia longinaris. The letters CCDB preceding the catalogue numbers represent the Crustacean Collection of the Department of Biology, Faculty of Philosophy, Sciences and Letters at Ribeirão Preto, University of São Paulo.
Locality | Catalogue numbers | GenBank Accession Numbers |
---|---|---|
Macaé-Rio de Janeiro, Brazil (22°23'44"S; 41°44'57"W) |
CCDB 3782 | KF572060–KF572069 |
Ubatuba-São Paulo, Brazil (23°27'24"S; 45°01'20"W) |
CCDB 3806, 3429 | KF572070–KF572082 |
Santos-São Paulo, Brazil (24°03'59"S; 46°16'57"W) |
CCDB 4008 | KF572083–KF572084 |
Cananéia-São Paulo, Brazil (25°08'15"S; 47°50'40"W) |
CCDB 3655 | KF572085–KF572089 |
São Francisco do Sul-Santa Catarina, Brazil (26°05'52"S; 48°33'82"W) |
CCDB 3851 | KF572090–KF572098 |
Rio Grande-Rio Grande do Sul, Brazil (32°10'23"S; 52°06'10"W) | CCDB 3928 | KF572099–KF572108 |
Mar del Plata-Buenos Aires, Argentina (37°58'57"S; 57°32'15"W) | CCDB 869, 4150 | KF572109–KF572119 |
The protocols for DNA extraction, amplification and sequencing followed
An ~700-bp region of a partial sequence of the mitochondrial COI gene was amplified by the polymerase chain reaction (PCR) using the pair of primers: HCO1 (5’-TAAACTTCAGGGTGACCAAAAAATCA-3’) and LCO1 (5’-GGTCAACAAATCATAAAGATATTGG-3’) (
The editing and construction of a consensus sequence for the two strands were conducted using the computational program BIOEDIT 7.3.1.0 (
For both the genetic distance and phylogenetic analyses, sequences of three other penaeid species were included in the alignment as an outgroup: F. brasiliensis, F. paulensis (GenBank accession numbers KF783861–KF783862) and Rimapenaeus constrictus (Stimpson) (GenBank accession number KF783863). We also attempted to use a sequence of the same portion of the COI gene of A. longinaris available in GenBank (accession number EU400383.1) (
The haplotype number was calculated in the program DNASP 4.10.9 (
A total of 60 sequences of the COI gene from individuals sampled in the seven localities was obtained. The final multiple sequence alignment included 645 base pairs. The number of variable sites was 66 (10.23%), 8 (12.12%) in the first codon position and 58 (87.88%) in the third position, and 30 of the variable sites were phylogenetically informative. Adding three species as the outgroup, the number of variable sites was 143 (28.49%), 72 of which were phylogenetically informative. The average nucleotide composition for A. longinaris was 28.41% (A), 30.99% (T), 19.47% (G), and 21.12% (C).
The intraspecific genetic distance of A. longinaris ranged from 0 to 2.7%, and the average distance was 1.1 ± 0.2%. The interspecific genetic distance, including the outgroup, ranged from 21.3 to 27.1%. Average distance among individuals in each population ranged from 0.81 ± 0.25% at Cananéia to 1.42 ± 0.24% at Macaé (Table
Average distance (%) among Artemesia longinaris individuals ± standard deviation in each locality.
Locality | Average distance (%) | Standard deviation (±) |
---|---|---|
Macaé | 1.42 | 0.24 |
Ubatuba | 1.07 | 0.19 |
Santos | 1.25 | 0.43 |
Cananéia | 0.81 | 0.25 |
São Francisco do Sul | 1.37 | 0.26 |
Rio Grande | 1.08 | 0.19 |
Mar del Plata | 0.88 | 0.21 |
Artemesia longinarisAverage distance (%) among localities (numbers on bottom) ± standard deviation (values on top).
Locality | 1 | 2 | 3 | 4 | 5 | 6 | 7 |
---|---|---|---|---|---|---|---|
1 Macaé | 0.19 | 0.25 | 0.21 | 0.22 | 0.19 | 0.19 | |
2 Ubatuba | 1.21 | 0.23 | 0.18 | 0.19 | 0.18 | 0.17 | |
3 Santos | 1.30 | 1.08 | 0.23 | 0.23 | 0.23 | 0.23 | |
4 Cananéia | 1.17 | 0.95 | 0.78 | 0.20 | 0.18 | 0.19 | |
5 São Francisco do Sul | 1.37 | 1.21 | 1.13 | 1.02 | 0.19 | 0.20 | |
6 Rio Grande | 1.20 | 1.04 | 1.13 | 0.96 | 1.20 | 0.17 | |
7 Mar del Plata | 1.16 | 0.96 | 0.97 | 0.83 | 1.11 | 0.95 |
Both the Neighbor-Joining and Maximum Likelihood analysis indicated no structure by localities (Figs
Based on the 60 sequences, 53 haplotypes were identified. Of these, 48 represented single individuals. The locality of Santos was not included in the analysis of haplotype, nucleotide diversity and molecular variance (Tables
Haplotype network of Artemesia longinarisaccording to Median-Joining analysis. Each circle represent one haplotype found in the localities (53 haplotypes in 60 specimens). The size of the circle of each haplotype is proportional to its frequency in the sample. Each small dash represents a mutational step.
Number of Artemesia longinaris individuals sampled, number of haplotypes, D.H. = haplotype diversity, and D.N. ± D.P. = nucleotide diversity ± standard deviation for each locality.
Locality | Number of samples | Number of haplotypes | D. H. | D. N. ± D. P. |
---|---|---|---|---|
Macaé | 10 | 10 | 0.10 | 1.38×10-3 ± 0.79×10-3 |
Ubatuba | 13 | 13 | 0.08 | 1.05×10-3 ± 0.4×10-3 |
Santos | 2 | 2 | ||
Cananéia | 5 | 5 | 0.20 | 0.80×10-3 ± 0.5×10-3 |
São Francisco do Sul | 9 | 9 | 0.11 | 1.34×10-3 ± 0.8×10-3 |
Rio Grande | 10 | 9 | 0.12 | 1.05×10-3 ± 0.6×10-3 |
Mar del Plata | 11 | 11 | 0.91 | 0.87×10-3 ± 0.5×10-3 |
The analysis of molecular variance (AMOVA) did not detect structure among the localities, and the observed variation occurred predominantly within the localities. The FST indices were not significant (p > 0.05) (Table
The intraspecific genetic distance for A. longinaris (0–2.7%) is much lower than the interspecific distance between A. longinaris and the out-group species (21.3–27.1%). This result not only confirms A. longinaris as a single taxon throughout its distribution, but also supports the utilization of this methodology in the identification of penaeid shrimps from the Brazilian coast. The difference between the intra and interspecific genetic variation of the barcode region of the COI gene is termed the “barcode gap” (
Our analyses showed genetic homogeneity among the populations of A. longinaris along its entire geographical distribution. The FST value obtained reflects this absence of geographical genetic structure. In species with high genetic variation and few shared haplotypes, negative FST values are probably associated with the imprecision of the algorithms used in this type of analysis, and can be interpreted as zero (
Despite the absence of significant genetic variability at the intraspecific level described here, phenotypic variability was previously observed among the populations of A. longinaris (see introduction). The determination of an individual phenotype is a consequence of the interaction between genotype and environment (
Recent studies with other decapods, with sampling at several points of the South American coast, found similar results on genetic homogeneity (
We can conjecture that similar larval dispersal occurs with A. longinaris, in which its larval development lasts 24 to 32 days, according to the temperature (
It is thought that the dynamics of water masses in the region provides ideal conditions for larval drift of A. longinaris through the southwestern Atlantic. Coastal Water (CW), for instance, is a water mass that cover the geographical range of this study (
According to
Our results, encompassing samples from its entire distribution, support the hypothesis that A. longinaris migrates over long distances, and is able to establish populations in different areas when conditions are appropriate. It is therefore possible to consider A. longinaris as a metapopulation, which fits the model of source and sink proposed by
Thus, these localities, where the populations are considered sources, would be strategic for the implementation of management measures such as the creation of protected areas or offseason periods, in order to maintain the fisheries in these areas and also in all range of its distribution. The role of marine protected areas in enhance fisheries in adjacent regions depend if they act as sources or as sinks (
Studies investigating the larval dispersal and the migration of juveniles and adults of this species must be conducted in order to verify whether the model described by
Our results confirm that the DNA barcoding technique is an efficient tool for the identification of penaeid shrimps from the Brazilian coast. In addition to the validation of A. longinaris as a single taxon, with no genetic differentiation among the populations through its entire geographical distribution, we showed the importance of the effect of the environmental conditions specific to each locality in the expression of the phenotypic characteristics of the individuals in a population.
The genetic homogeneity is maintained by the larval dispersal and high migratory capacity, which assure gene flow among populations. These characteristics make it possible for individuals to be transported by water masses and currents of the southwestern Atlantic.
In addition, this study also indicate the importance of populations of south Brazil and Macaé as sources, to provide individuals to other areas. Thus these populations should be considered essential in developing management strategies for the species.
This paper is part of the multidisciplinary research project Temático BIOTA – FAPESP (Fundação de Amparo à Pesquisa do Estado de São Paulo), which aims to produce a fine-scale assessment of the marine decapod biodiversity of the State of São Paulo. Financial support for this project was provided by research grants from FAPESP (Temático Biota 2010/50188-8; Coleções Científicas 2009/54931-0) and CNPq (Proc. 301359/2007-5; 473050/2007-2; 504322/2012-5) to FLM. ACB thanks CNPq for a MSc scholarship (#130655/2011-2), MN thanks FAPESP for an ongoing PhD scholarship (2012/06300-3), LGP thanks CAPES for an ongoing Postdoctoral scholarship (02630/2009-5), and FLM and RCC acknowledge CNPq for research grants (PQ 302748/2010-5 and 304784/2011-7, respectively). We are extremely grateful to several colleagues and friends (Emiliano O´Campo, Laura Lopez-Greco, Mariana Terossi and Rafael Robles) for their help in collections, for making available some essential fresh specimens, for lending material from collections used in our research, for critical discussions during the preparation of this manuscript, and for help in the sequencing step. Special thanks to all members of LBSC for their assistance during the development of this study and to Instituto Oceanográfico (IO/USP) for logistical support during field work. We also thank to Dr. Janet W. Reid (JWR Associates) for providing the English review service and anonymous reviewers for all comments and suggestions. The collections of species conducted in this study complied with current applicable state and federal laws of Brazil (DIFAP/IBAMA/126/05; permanent license to FLM for collection of Zoological Material No. 11777-1 MMA/IBAMA/SISBIO).