The Atlantic goliath grouper is a critically endangered species that inhabits estuarine and reef environments and is threatened primarily by fishing activities and habitat destruction. Despite the urgent need for protection, its genetic conservation status remains unknown. The aim of the present study was to evaluate the gene flow among the populations of the species along the coast of Brazil based on the control region of the mitochondrial DNA. The results indicate low haplotype diversity (0.40-0.86) and very low nucleotide diversity (0.1-0.5%). They also show that the genetic diversity of the species varies considerably along the coast and that this finding may be especially important for the identification of priority areas for its conservation. The population analyses indicate a low but significant degree of genetic structuring (ΦST =0.111), probably due to the occurrence of rare haplotypes at some locations, although the genetic differentiation between sites was not correlated with geographic distance (r=0.0501; p=0.7719), and the shared haplotypes indicate that gene flow occurs among all locations along the Brazilian coast. The results of the pairwise FST indicate a high degree of genetic differentiation between locations. The incipient population structuring detected in the present study is not related systematically to the geological or physical features of the Brazilian coast. The complex interaction of fluctuations in sea level, marine currents, and the reproductive characteristics of the species hampers the identification of the specific role of each of these processes in the gene flow dynamics of the population units of the Atlantic goliath grouper. The low overall levels of genetic diversity, the pairwise FST values and the significant population structuring among groups (ΦCT) identified in the present study all reinforce the critically endangered status of the species and are inconsistent with the presence of a single, panmictic population of groupers on the Brazilian coast. The results of this study suggest that, though it may be incipient, the observed genetic structuring must be taken into account in order to prevent potential problems, such as outbreeding depression, in the management of wild stocks.
El mero guasa del Atlántico está críticamente en peligro, habita en ambientes estuarinos y arrecifes, los cuáles están amenazados principalmente por las actividades de pesca y la destrucción de su hábitat. A pesar de la necesidad urgente de protección, su estado de conservación genética aún es desconocido. El objetivo del presente estudio fue evaluar el flujo génico entre las poblaciones de esta especie a lo largo de la costa de Brasil analizando la variabilidad genética de la región control del ADN mitocondrial. Los resultados indican baja diversidad haplotípica (0.40-0.86), y una muy baja diversidad nucleotídica (0.1-0.5%). Además se observa que la diversidad genética de la especie varía considerablemente a lo largo de la costa y este resultado puede ser especialmente relevante para la identificación de áreas prioritarias de conservación. Los análisis poblacionales indican un bajo, pero significativo grado de estructuración genética (ΦST =0.111), lo cual es probablemente debido a la ocurrencia de haplótipos raros en algunas localidades, aunque la diferenciación genética entre sitios no está correlacionada con la distancia geográfica (r=0.0501; p=0.7719), y los haplotipos compartidos indican que el flujo génico ocurre entre todas las localidades a lo largo de la costa brasileña. Los resultados de la distancia dos a dos indican un FST de alto grado de diferenciación genética entre las localidades. La incipiente estructuración poblacional detectada en este estudio no está relacionada sistemáticamente con las características biogeográficas de la costa brasileña. La compleja interacción de las fluctuaciones en el nivel del mar, las corrientes marinas, y las características reproductivas de la especie dificultan la identificación del rol específico de cada uno de estos procesos en la dinámica del flujo genético de las diferentes unidades poblacionales del mero guasa del Atlántico. Los bajos niveles generales de la diversidad genética, los valores de FST dos a dos, y la significante estructuración poblacional entre los grupos (ΦCT) identificada en el presente estudio, todo refuerza el estado de peligro crítico de la especie y son inconsistentes con la existencia de una simple, población panmíctica de meros guasa de la costa brasileña. Los resultados de este estudio sugieren que, a pesar de que puede ser incipiente, la estructuración genética observada debe ser tenida en cuenta con el fin de evitar problemas potenciales, tales como la depresión exogámica, cuando se maneja poblaciones silvestres.
The Atlantic goliath grouper
Slow growth, longevity and behavioural traits such as the tendency to form breeding groups make
The dispersal of pelagic larvae is correlated with connectivity among different environments and likely depends on local oceanographic patterns, the biological attributes of the larvae, and specific aspects of the reproductive behaviour of the adults, which facilitate local recruitment (
The first molecular data on
The 218 samples of
Additional sequences of Atlantic goliath grouper were obtained in GenBank under numbers FJ176303 to FJ176329. These sequences refer to specimens collected in Bragança + Ajuruteua (Pará: PA) (N=92), called in this study by ‘Bragança’, Parnaíba (Piauí: PI) (N=12), Fortaleza (Ceará: CE) (N=2) and Natal (Rio Grande do Norte: RN) (N=9) (
Population Unit | Municipality (State) | N | Coordinates | Source |
---|---|---|---|---|
1 | Bragança (PA): BRA | 102 | 01o03’S 46º46’W | |
2 | Parnaíba (PI): PAR | 12 | 02o54’S 41º46’W | |
3 | Fortaleza (CE): FOR | 02 | 03o43’S 38º32’W | |
4 | Natal (RN): NAT | 09 | 05o45’S 35º12’W | |
5 | Tamandaré (PE): TAM | 25 | 08º41’S 35º06’W | This study |
6 | Vaza Barris (SE): VBS | 14 | 11º08’S 37º10’W | This study |
7 | Caravelas (BA): CAR | 50 | 17º43’S 39º16’W | This study |
8 | Conceição da Barra (ES): CBR | 111 | 18º36’S 39º44’W | This study |
9 | Babitonga (SC): BAB | 5 | 26º16’S 48º42’W | This study |
The DNA was extracted using the saline protocol described by
The sequencing reaction (
The sequences were analysed and edited using the Geneious program v.4.8.5 (
Nucleotide composition and intra-species genetic distances were estimated using the two-parameter Kimura model with 10000 bootstrap pseudoreplicates with the aid of the Mega program v.5.2 (
Nine a priori sampling units were defined according to geographical criteria: Bragança, Parnaíba, Fortaleza, Natal, Tamandaré, Vaza Barris, Caravelas, Conceição da Barra and Babitonga. For the analyses, the samples were grouped for each unit using the DnaSP v.5 program (
The relationship among haplotypes was established through the Haploviewer program (
The “isolation by distance” model was analysed using the Mantel test (BioEstat v.5.3;
The control region was sequenced in 330 individuals (338 bp). A total of 319 bps were conserved sites, 19 were variable and 12 were informative for the parsimony analyses. Nucleotide frequencies were T=0.331, C=0.145, A=0.316 and G=0.208. The overall haplotype diversity of the control region was moderate, with the lowest values being found in the Babitonga, Caravelas and Parnaíba populations and the highest ones in the Tamandaré, Conceição da Barra, Bragança, Vaza Barris and Natal populations (range across all populations: 0.400 to 0.861). Total haplotype diversity was 0.757. However, nucleotide diversity was low in all population units, ranging from 0.001 to 0.005 (
Population unit | Haplotypes | Haplotype diversity (h) | Nucleotide diversity (p) | Tajima’s D | Fu’s Fs | |
---|---|---|---|---|---|---|
N | Uniques | |||||
1. Bragança | 23 | 12 | 0.806±0.034 | 0.001±0.001 | -1.278 | -12.504* |
2. Parnaíba | 2 | - | 0.530±0.076 | 0.001±0.001 | 1.381 | 1.152 |
3. Fortaleza | 1 | - | 0.000±0.000 | 0.000±0.000 | 0.000 | 0.000 |
4. Natal | 5 | 2 | 0.861±0.087 | 0.002±0.002 | -0.551 | -1.593 |
5. Tamandaré | 8 | 5 | 0.710±0.087 | 0.004±0.003 | -0.979 | -2.284 |
6. Vaza Barris | 6 | 2 | 0.846±0.061 | 0.005±0.003 | 0.191 | -0.238 |
7. Caravelas | 6 | 2 | 0.516±0.077 | 0.002±0.002 | -0.980 | -1.786 |
8. Conceição da Barra | 12 | 3 | 0.798±0.025 | 0.005±0.003 | -0.241 | -1.970 |
9. Babitonga | 2 | 1 | 0.400±0.237 | 0.001±0.001 | -0.816 | 0.090 |
The results indicate moderate levels of haplotype diversity in Bragança (0.806), Natal (0.861), Vaza Barris (0.846), Conceição da Barra (0.798) and Tamandaré (0.710), and the lowest levels in Parnaíba (0.530), Caravelas (0.516) and Babitonga (0.400). While nucleotide diversity was extremely low (0.001 to 0.005) for all populations, the highest values were recorded for TAM, VBS and CBR, and much lower ones for Bragança, Parnaíba and Babitonga (
The pairwise FST values for comparisons between populations varied considerably, between 0.005 and 0.833. However, Caravelas (Bahia) was significantly different from six populations: Bragança, Parnaíba, Fortaleza, Natal, Vaza Barris, and Conceição da Barra (
Population unit | 1.BRA | 2.PAR | 3.FOR | 4.NAT | 5.TAM | 6.VBS | 7.CAR | 8.CBR | 9.BAB |
---|---|---|---|---|---|---|---|---|---|
1. BRA | 1072* | 1482* | 1981 | 2351* | 2721 | 3588* | 3709* | 5161 | |
2. PAR | 0.322* | 410* | 909* | 1279* | 1649* | 2516* | 2637* | 4089* | |
3. FOR | 0.561* | 0.832* | 499* | 869* | 1239* | 2106* | 2227 | 3679* | |
4. NAT | 0.121 | 0.264* | 0.617* | 370 | 740 | 1607* | 1728 | 3180 | |
5. TAM | 0.044* | 0.185* | 0.571* | 0.029 | 370 | 1237 | 1358 | 2810 | |
6. VBS | 0.009 | 0.267* | 0.522* | 0.021 | 0.010 | 867* | 988 | 2440 | |
7. CAR | 0.195* | 0.259* | 0.707* | 0.010* | 0.043 | 0.151* | 121* | 1573 | |
8. CBR | 0.032* | 0.229* | 0.522 | 0.056 | 0.013 | 0.005 | 0.082* | 1452 | |
9. BAB | 0.251 | 0.406* | 0.833* | 0.153 | 0.090 | 0.206 | -0.048 | 0.130 |
The SAMOVA indicated incipient genetic structuring among the Brazilian populations (ΦST=0.083 to 0.121; p<0.001), with three to five distinct populations (k) being observed (
No of groups (k) | Comparisons | Source of Variations | F statistic | Percentage of variation | p-value |
---|---|---|---|---|---|
3 | (PAR) × (CAR) × (BRA, NAT, TAM, VBS, CBR) | Among groups | ΦCT=0.090 | 9.00 | 0.047 |
Among population within groups | ΦSC=0.034 | 3.17 | 0.010 | ||
Within populations | ΦST=0.121 | 87.83 | 0.000 | ||
4 | (PAR) × (NAT) × (CAR) × (BRA, TAM, VBS, CBR) | Among groups | ΦCT=0.087 | 8.78 | 0.030 |
Among population within groups | ΦSC=0.030 | 2.80 | 0.019 | ||
Within populations | ΦST=0.115 | 88.42 | 0.000 | ||
5 | (BRA) × (PAR) × (NAT) × (CAR) × (BRA, TAM, VBS, CBR) | Among groups | ΦCT=0.083 | 8.28 | 0.029 |
Among population within groups | ΦSC=0.000 | 0.06 | 0.431 | ||
Within populations | ΦST=0.083 | 91.66 | 0.000 |
A total of 30 haplotypes were identified, none of which was present in all locations. However, haplotypes 19 and 23 were widely distributed and common in all population units, except those for which the samples were small, i.e. Fortaleza and Babitonga (
The Bragança, Conceição da Barra, and Tamandaré units showed the greatest number of haplotypes (76.7%, 40.0% and 26.7% of the total, respectively). Overall, 19 (63%) of the haplotypes were identified in a single unit, of which 12 were rare. The Bragança (12 haplotypes) and Tamandaré (5 haplotypes) units had the greatest number of exclusive haplotypes (56%) in comparison with other populations (
Haplotypes | N | BRA | PAR | FOR | NAT | TAM | VBS | CAR | CBR | BAB | Accession numbers |
---|---|---|---|---|---|---|---|---|---|---|---|
Hap_1 | 6 | 3 | 2 | 1 | KP331716 | ||||||
Hap_2 | 9 | 9 | KP331717 | ||||||||
Hap_3 | 39 | 14 | 3 | 1 | 1 | 20 | KP331718 | ||||
Hap_4 | 4 | 4 | KP331719 | ||||||||
Hap_5 | 1 | 1 | KP331720 | ||||||||
Hap_6 | 1 | 1 | KP331721 | ||||||||
Hap_7 | 1 | 1 | KP331722 | ||||||||
Hap_8 | 6 | 1 | 1 | 4 | KP331723 | ||||||
Hap_9 | 1 | 1 | KP331724 | ||||||||
Hap_10 | 2 | 2 | KP331725 | ||||||||
Hap_11 | 1 | 1 | KP331726 | ||||||||
Hap_12 | 1 | 1 | KP331727 | ||||||||
Hap_13 | 3 | 2 | 1 | KP331728 | |||||||
Hap_14 | 2 | 2 | KP331729 | ||||||||
Hap_15 | 1 | 1 | KP331730 | ||||||||
Hap_16 | 1 | 1 | KP331731 | ||||||||
Hap_17 | 6 | 2 | 1 | 3 | KP331732 | ||||||
Hap_18 | 1 | 1 | KP331733 | ||||||||
Hap_19 | 144 | 41 | 5 | 2 | 13 | 4 | 34 | 41 | 4 | KP331734 | |
Hap_20 | 1 | 1 | KP331735 | ||||||||
Hap_21 | 1 | 1 | KP331736 | ||||||||
Hap_22 | 2 | 2 | KP331737 | ||||||||
Hap_23 | 44 | 9 | 7 | 1 | 4 | 2 | 5 | 16 | KP331738 | ||
Hap_24 | 11 | 2 | 2 | 7 | KP331739 | ||||||
Hap_25 | 7 | 1 | 4 | 1 | 1 | KP331740 | |||||
Hap_26 | 5 | 1 | 2 | 2 | KP331741 | ||||||
Hap_27 | 22 | 1 | 1 | 7 | 12 | 1 | KP331742 | ||||
Hap_28 | 3 | 3 | KP331743 | ||||||||
Hap_29 | 1 | 1 | KP331744 | ||||||||
Hap_30 | 3 | 3 | KP331745 |
Tajima’s D values were negative for the majority of
The analysis of the mitochondrial control region revealed moderate to low genetic diversity (
The neutrality tests (Tajima’s D and Fu’s Fs) in the present study lend support to the hypothesis of a low degree of genetic variation. Based on Tajima’s D and Fu’s Fs, there is no evidence that any of the Atlantic goliath grouper populations along the coast of Brazil are in a process of demographic or spatial expansion. Tajima’s D for the pooled data of all units also does not suggest population expansion (D=–1.269; p>0.10). However, Fu’s Fs was significant (Fs=–12.505; p<0.02) for the Bragança (Pará) population, indicating population expansion. Mangroves are important nursery areas for
The amplitude of the pairwise genetic differentiation (FST) and the comparison of three population groups (1. Parnaíba 2. Caravelas 3. Bragança, Natal, Tamandaré, Vaza Barris and Conceição da Barra) indicate the existence of significant structuring (ΦCT=0.09, p<0.05) in the
The greater genetic differentiation between the Caravelas sample and both distant (Bragança and Parnaíba) and adjacent (Vaza Barris and Conceição da Barra) populations may be accounted for by the transgression and regression events that occurred on the Brazilian coast during the Quaternary (
In addition to the fluctuations in sea level, the Parnaíba region is affected by the Intertropical Convergence zone (ITCZ). Between 40-8 thousand years ago (kya), the ITCZ shifted towards the northern coast of Brazil, affecting the surface temperature of the sea and wind intensity, creating semi-arid conditions in northeastern Brazil. These conditions were interrupted by short cycles of higher precipitation, and one long cycle between 15-11 kya, when the ITCZ migrated between the equator and northeastern Brazil (
The results of this study showed that haplotypes were widely shared, although the SAMOVA identified significant ΦST values, which indicate a certain amount of population differentiation (
The significant differences in FST and the complex haplotype network found for the Bragança, Parnaíba, Caravelas and Conceição da Barra population units indicate that these locations are not isolated. However, the dispersal of larvae or adults may be occasional, with a lower degree of genetic exchange than that required to completely homogenize the population, possibly due to the existence of a barrier to gene flow, which may influence the degree of genetic differentiation among localities (
The circulation patterns of the Brazil Current and North Brazil Current in the South Atlantic (
The population structure found in the present study indicates limited gene flow, and although the small sample size may also have been important here, the size of the samples analysed in the present study was similar to that used in the studies of
This reduced mitochondrial diversity may be related to the faster genetic drift in these haploid genes, inherited maternally, in comparison with the diploid, biparental nuclear genes (
The data on the haplotypes shared among the population units of the Atlantic goliath grouper along the coast of Brazil emphasize the importance of regional haplotype richness for the genetic diversity of the species. Local impacts can have negative effects on the genetic conservation due to this sharing of haplotypes, which may extend throughout the geographic distribution of
The moderate haplotype diversity and extremely low degree of nucleotide diversity suggest the random fixation of variation and possible genetic drift in the study region, as a consequence of population depression resulting from founder effects or bottleneck events. However, the ample genetic diversity found among population units (0.400-0.861) in the present study indicate that the effects of these events have varied considerably among the different regions, in turn reinforcing the need for the application of conservation measures in priority areas with the main focus on financial limitations.
The results of this study indicate low levels of genetic diversity, primarily in the populations from Parnaíba (Piauí) and Caravelas (southern Bahia). Ceará (Fortaleza) and Babitonga (Santa Catarina) also showed low values, although the sample size was prohibitively low in these cases. The ΦST and FST values also indicate the genetic differentiation of these populations in relation to the others located along the Brazilian coast. It is important to note, however, that few genetic data are available for the populations from the coast of southern Brazil between Conceição da Barra (Espírito Santo) and Babitonga (Santa Catarina). These populations may be problematic, given the unique geological and oceanographic characteristics of this region, which may cause different patterns of genetic diversity and gene flow in this region. Nevertheless, it does not appear reasonable to assume that the Atlantic goliath grouper of the Brazilian coast is in a state of panmixia, considering the levels of pairwise genetic differentiation found in the present study (FST) and the significant differences found among population groups (ΦCT).
Based on the findings of the present study, and the critically endangered status of the species, the current ban on the harvesting of the Atlantic goliath grouper should be maintained, considering 1) the variation found in the genetic diversity of the subpopulations located along the Brazilian coast, indicating that they have suffered differing degrees of impact and threat; 2) the very low level of nucleotide diversity, which suggests a greatly reduced effective population size and indicates that overfishing and habitat destruction in recent decades may have had negative genetic effects for future generations; 3) the distinct findings for the mitochondrial and nuclear markers, which reinforce the need for analysis of additional molecular markers (i.e. Msats and MHC genes); and 4) the lack of data from some regions of the Brazilian coast, which may be important for understanding the dynamics of the population as a whole. The conservation of the Atlantic goliath grouper will depend on political efforts for the creation of coastal protection areas, especially in mangroves and breeding grounds, and the participation of local communities in the decision-making process.
The authors are grateful to the Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES), the Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP), the Fundação de Amparo à Pesquisa do Espírito Santo (FAPES), the Projeto Meros do Brasil, which is supported by Petrobrás S.A. (through the Programa Petrobrás Ambiental), and Transpetro Transportes S.A. for financial support. R.A. Torres is especially grateful to CNPq for the research fellowship provided (Grant Numbers 306099/2011-0 and 301208/2012-3).