Building a Teleost Fish Traceability Program Based on Genetic Data from Pacific Panama Fish Markets.

Fish tissue samples from 203 adult individuals were collected in the main ports and markets of the Pacific coast of Panama. Molecular identification based on a cytochrome oxidase I gene segment of all species was verified by GENBANK reference sequences. A total of 34 species from 14 families (Ariidae, Caranjidae, Centropomidae, Gerreidae, Haemulidae, Lobotidae, Lutjanidae, Malacanthidae, Mugilidae, Scianidae, Scombridae, Serranidae, Sphyraenidae, Stromateidae) were identified at the species level from 164 sequences. Additionally, three Caribbean species were molecularly identified among the analyzed samples (Mycteroperca xenarcha, Paralonchurus brasilensis and Lobotes surinamensis). Species diversity was slightly higher in the Gulf of Panama than in the Gulf of Chiriquí. For species with five or more individual sequences, genetic diversity and genetic connectivity parameters such as total number of haplotypes (H), haplotype diversity (Hd), and nucleotide diversity (π) were calculated. Overall, pelagic-migratory species showed higher values of genetic diversity than coastal and estuarine species with some exceptions. Connectivity between Gulf areas was compared using values of genetic distances and genetic differentiation (Fst). The high level of connectivity observed between the Gulf of Chiriqui and the Gulf of Montijo indicates the existence of a single stock in that area for the following species: Scomberomorus sierra, Caranx caninus and Lutjanus guttatus. The demographic history of the most common species was examined using Tajima's D values, suggesting population expansion for two snapper species, L. peru and L. argentiventris, having significant and higher values. Another important contribution from this research was the production of primers and dual-labeled probes for environmental DNA detection using qPCR for the five most abundant species (spotted rose snapper, yellow snapper, green jack, Pacific crevalle jack and the Pacific sierra fish). These markers represent a new set of tools for environmental DNA (eDNA) detection and molecular traceability of three commercially important fish species along the supply chain including landing sites and markets of the main fishery areas.

Assessment of the dolphinfish Coryphaena hippurus (Perciformes: Coryphaenidae) fishery in Pacific Panama.

The dolphinfish (Coryphaena hippunis) is a highly migratory pelagic species commercially exploited by industrial, artisanal and recreational fisheries in tropical and subtropical areas of the world's oceans. Herein, we evaluated the dolphinfish industrial fishery in Pacific Panama for the first time generating a growth model and examining fluctuations in annual total catch and in catch per unit effort (CPUE) over a four-year period (2006-2009). Annual and monthly catch values and biological parameters of 14913 individuals were obtained onboard industrial vessels, landing sites and records from processing plants. Size frequency for industrial vessels showed a normal distribution between 353 and 1,715 mm (average, 1010.85 mm; n = 10,459). Fish weight averaged 4.94 kg (SD). Sex ratio was slightly biased toward females. More than 90% of the analyzed fish were sexually mature. The length-weight relationship was positive and significant, reflecting allometric growth. Growth parameters using the von Bertalanffy equation revealed a growth efficiency of θ = 4.61, which is within the reported range for Coryphaena hippurus (3.95-4.70). The largest fish were between age classes 2 and 3 (700 - 1400 mm). Total catch per year and catch per unit effort (CPUE) per year fluctuated, with the highest values recorded between 2008 and 2009. Catch values reported herein are preliminary and appear to be below those recorded elsewhere in the region and cautiously may represent an indicator of sustainable use of this marine resource even considering the absence of management actions in Panama.

History, applications, methodological issues and perspectives for the use environmental DNA (eDNA) in marine and freshwater environments / Historia, aplicaciones, aspectos metodológicos y perspectivas para el uso del ADN ambiental (ADNa) en ecosistemas marinos y de agua dulce

Genetic material (short DNA fragments) left behind by species in nonliving components of the environment (e.g. soil, sediment, or water) is defined as environmental DNA (eDNA). This DNA has been previously described as particulate DNA and has been used to detect and describe microbial communities in marine sediments since the mid-1980’s and phytoplankton communities in the water column since the early-1990’s. More recently, eDNA has been used to monitor invasive or endangered vertebrate and invertebrate species. While there is a steady increase in the applicability of eDNA as a monitoring tool, a variety of eDNA applications are emerging in fields such as forensics, population and community ecology, and taxonomy. This review provides scientist an understanding of the methods underlying eDNA detection as well as applications, key methodological considerations, and emerging areas of interest for its use in ecology and conservation of freshwater and marine environments. Rev. Biol. Trop. 62 (4): 1273-1284. Epub 2014 December 01.

El material genético que liberan los organismos en los componentes no vivos del ecosistema (aire, suelo, agua y sedimentos) recibe el nombre de ADN ambiental (ADNa) (eDNA, por su nombre en inglés). Este ADN previamente definido como ADN particulado ha sido utilizado desde mediados de la década de los ochenta y principios de los noventas para describir la composición de las comunidades microbianas en sedimentos marinos y de comunidades microbianas y fitoplanctónicas en la columna de agua. Recientemente el ADNa es utilizado principalmente para la detección y monitoreo de especies invasoras y en peligro. No obstante, existen múltiples áreas en las que este método puede ser utilizado como por ejemplo en ciencias forenses, ecología de poblaciones y comunidades, y taxonomía. Esta revisión proporciona información sobre esta nueva herramienta molecular, sus actuales y futuras aplicaciones, historia, principales consideraciones metodológicas y áreas emergentes para su uso en ecología y conservación de ambientes marinos y de agua dulce.

Assessing environmental DNA detection in controlled lentic systems.

Little consideration has been given to environmental DNA (eDNA) sampling strategies for rare species. The certainty of species detection relies on understanding false positive and false negative error rates. We used artificial ponds together with logistic regression models to assess the detection of African jewelfish eDNA at varying fish densities (0, 0.32, 1.75, and 5.25 fish/m3). Our objectives were to determine the most effective water stratum for eDNA detection, estimate true and false positive eDNA detection rates, and assess the number of water samples necessary to minimize the risk of false negatives. There were 28 eDNA detections in 324, 1-L, water samples collected from four experimental ponds. The best-approximating model indicated that the per-L-sample probability of eDNA detection was 4.86 times more likely for every 2.53 fish/m3 (1 SD) increase in fish density and 1.67 times less likely for every 1.02 C (1 SD) increase in water temperature. The best section of the water column to detect eDNA was the surface and to a lesser extent the bottom. Although no false positives were detected, the estimated likely number of false positives in samples from ponds that contained fish averaged 3.62. At high densities of African jewelfish, 3-5 L of water provided a >95% probability for the presence/absence of its eDNA. Conversely, at moderate and low densities, the number of water samples necessary to achieve a >95% probability of eDNA detection approximated 42-73 and >100 L, respectively. Potential biases associated with incomplete detection of eDNA could be alleviated via formal estimation of eDNA detection probabilities under an occupancy modeling framework; alternatively, the filtration of hundreds of liters of water may be required to achieve a high (e.g., 95%) level of certainty that African jewelfish eDNA will be detected at low densities (i.e., <0.32 fish/m3 or 1.75 g/m3).

History, applications, methodological issues and perspectives for the use of environmental DNA (eDNA) in marine and freshwater environments.

Genetic material (short DNA fragments) left behind by species in nonliving components of the environment (e.g. soil, sediment, or water) is defined as environmental DNA (eDNA). This DNA has been previously described as particulate DNA and has been used to detect and describe microbial communities in marine sediments since the mid-1980's and phytoplankton communities in the water column since the early-1990's. More recently, eDNA has been used to monitor invasive or endangered vertebrate and invertebrate species. While there is a steady increase in the applicability of eDNA as a monitoring tool, a variety of eDNA applications are emerging in fields such as forensics, population and community ecology, and taxonomy. This review provides scientist with an understanding of the methods underlying eDNA detection as well as applications, key methodological considerations, and emerging areas of interest for its use in ecology and conservation of freshwater and marine environments.

Population genetics of a trochid gastropod broadens picture of Caribbean Sea connectivity.

BACKGROUND: Regional genetic connectivity models are critical for successful conservation and management of marine species. Even though rocky shore invertebrates have been used as model systems to understand genetic structure in some marine environments, our understanding of connectivity in Caribbean communities is based overwhelmingly on studies of tropical fishes and corals. In this study, we investigate population connectivity and diversity of Cittarium pica, an abundant rocky shore trochid gastropod that is commercially harvested across its natural range, from the Bahamas to Venezuela. METHODOLOGY/PRINCIPAL FINDINGS: We tested for genetic structure using DNA sequence variation at the mitochondrial COI and 16S loci, AMOVA and distance-based methods. We found substantial differentiation among Caribbean sites. Yet, genetic differentiation was associated only with larger geographic scales within the Caribbean, and the pattern of differentiation only partially matched previous assessments of Caribbean connectivity, including those based on larval dispersal from hydrodynamic models. For instance, the Bahamas, considered an independent region by previous hydrodynamic studies, showed strong association with Eastern Caribbean sites in our study. Further, Bonaire (located in the east and close to the meridional division of the Caribbean basin) seems to be isolated from other Eastern sites. CONCLUSIONS/SIGNIFICANCE: The significant genetic structure and observed in C. pica has some commonalities in pattern with more commonly sampled taxa, but presents features, such as the differentiation of Bonaire, that appear unique. Further, the level of differentiation, together with regional patterns of diversity, has important implications for the application of conservation and management strategies in this commercially harvested species.

Observaciones sobre la larva del cangrejo marino tropical (Decapoda: Porcellanidae) Petrolisthes armatus en el Golfo de Nicoya, Costa Rica

Observations on the larvae of the tropical marine crab Petrolisthes armatus in the Gulf of Nicoya, Costa Rica. During October and November 1998 (rainy season), and December, February and March 1999 (dry season), larvae distribution of Petrolisthes armatus and associated decapods were sampled in three different sites at the Punta Morales peninsula, Gulf of Nicoya, Costa Rica. A total of 6014 decapod larvae were collected, and 73 belonged to the genus Petrolisthes spp. No significant total larval density differences were found between seasons (p>0.05); but there was a greater density of P. armatus and other decapod larvae (p>0.05) during the dry season. In addition, no significant variations on temperature and oxygen concentration were observed. P. armatus larval abundance was higher during low tide, in contrast with other decapod larvae. Significant differences among sites were found for other decapod larvae, but not for P. armatus. The only parameter that varied significantly between seasons was salinity and results demonstrate that this factor regulates temporal concentration of larvae. Moreover, flow-tide oscillations were the most important spatial factor in larval dynamics. We propose this mechanism: P. armatus liberates larvae during high tide; these larvae leave the coastal area during low tide and return to the rocky intertidal ecosystem during high tide, when they are ready to settle as megalopa (pre-juvenile stage). Parallel laboratory observations showed higher survival rates at lower salinities (15 ups against 35 ups) and that the duration of the period from zoea I to megalopa was, in average, 19 days. Rev. Biol. Trop. 56 (3): 1209-1223. Epub 2008 September 30.

Durante octubre y noviembre de 1998 (estación lluviosa) y diciembre, febrero y marzo de 1999 (estación seca) se muestreó la distribución de la larva de Petrolisthes spp, así como la densidad del total de las larvas de decápodos en superficie y a 3 metros de profundidad. Los muestreos se realizaron en tres sitios de la zona de Punta Morales, Golfo de Nicoya, Costa Rica, por medio de arrastres con una red de plancton de 280 µm. Se recolectaron un total de 6014 larvas de decápodos de las cuales 73 (1.21%) pertenecían al género Petrolisthes spp. No se encontraron diferencias significativas entre estaciones (p > 0.05), sin embargo fue posible observar una mayor densidad tanto de P. armatus como de larvas de decápodos en estación seca. Temporalmente el único parámetro físico-químico que varió significativamente fue la salinidad. En cuanto a la variación espacial no se encontraron diferencias significativas por profundidad, ni para Petrolisthes spp. ni para larvas de decápodos asociados (p > 0.05), a pesar de que la variación de algunos parámetros como la temperatura y el oxígeno si lo fue. Entre mareas se encontraron diferencias significativas para las larvas de Petrolisthes spp., no así para larvas de decápodos. Para la especie estudiada se observó un mayor número de larvas en marea baja. Entre los sitios hubo diferencias significativas para las larvas de decápodos, pero no para Petrolisthes spp.; físico-químicamente estos sitios son muy parecidos y solo difieren en penetración de luz, lo que parece no afectar a la larva de Petrolisthes. spp. Los resultados demuestran que el principal factor que regula la concentración temporal de las larvas es la salinidad, mientras que espacialmente las oscilaciones en el flujo mareal son de mayor importancia. Debido a las diferencias observadas marealmente para la concentración de larvas se propone el siguiente mecanismo: P. armatus libera sus larvas en el máximo de marea, éstas salen hacia fuera de la costa con la marea baja y se reincorporan con la marea alta, cuando están cerca de la fase previa al asentamiento (la megalopa). Adicional a los resultados en el medio natural para esta especie también se estudió en el laboratorio la duración del periodo larval y la supervivencia de las larvas a salinidades extremas utilizándose los valores máximos y mínimos registrados en el medio natural (15 ups y 35 ups). Este ensayo demostró que las larvas presentan un mayor porcentaje de supervivencia en salinidades menores (15 ups) y que la duración del período de desarrollo es de 19 dias.

[Observations on the larvae of the tropical marine crab Petrolisthes armatus in the Gulf of Nicoya, Costa Rica]. / Observaciones sobre la larva del cangrejo marino tropical (Decapoda: Porcellanidae) Petrolisthes armatus en el Golfo de Nicoya, Costa Rica.

During October and November 1998 (rainy season), and December, February and March 1999 (dry season), larvae distribution of Petrolisthes armatus and associated decapods were sampled in three different sites at the Punta Morales peninsula, Gulf of Nicoya, Costa Rica. A total of 6014 decapod larvae were collected, and 73 belonged to the genus Petrolisthes spp. No significant total larval density differences were found between seasons (p > 0.05); but there was a greater density of P. armatus and other decapod larvae (p > 0.05) during the dry season. In addition, no significant variations on temperature and oxygen concentration were observed. P. armatus larval abundance was higher during low tide, in contrast with other decapod larvae. Significant differences among sites were found for other decapod larvae, but not for P. armatus. The only parameter that varied significantly between seasons was salinity and results demonstrate that this factor regulates temporal concentration of larvae. Moreover, flow-tide oscillations were the most important spatial factor in larval dynamics. We propose this mechanism: P. armatus liberates larvae during high tide; these larvae leave the coastal area during low tide and return to the rocky intertidal ecosystem during high tide, when they are ready to settle as megalopa (pre-juvenile stage). Parallel laboratory observations showed higher survival rates at lower salinities (15 ups against 35 ups) and that the duration of the period from zoea I to megalopa was, in average, 19 days.

Composition of the zooplankton community, with emphasis in copepods, in Punta Morales, Golfo de Nicoya, Costa Rica

The composition of the mesozooplanktonic community was studied in the Punta Morales estuary, Gulf of Nicoya,Pacific coast of Costa Rica,during 1997.Oblique plankton hauls were performed during high and low tide using a 280 µm mesh screen net equipped with a flowmeter.The community was characterized by holoplanktonic and meroplanktonic organisms.For the holoplanktonic community,the main groups were copepods (80%)and chaetognaths (16%).The most abundant species were the copepods Acartia lilljeborgii and Paracalanus parvus.A.lilljeborgii is a typical estuarine species that maintains high populations in estuarine systems.Meroplankton was represented mainly by crustacean larvae (66%),and icthyoplankton (18%).The dominance of crustacean larvae and icthyoplankton is an evidence of the ecological importance of the Punta Morales zone

Se estudió la composición de la comunidad mezoplanctónica en Punta Morales,Golfo de Nicoya, Pacífico de Costa Rica,en 1997,arrastrando oblicuamente una red de plancton (280 µm,con flujómetro)durante marea alta y baja.La comunidad estuvo caracterizada por la presencia de organismos holo y meroplanctónicos.Los principales grupos holoplanctónicos fueron copépodos (80%)y quetognatos (16%).Las especies más abundantes fueron los copépodos Acartia lilljeborgii y Paracalanus parvus;A. lilljeborgii es una especie estuarina típica que mantiene altas poblaciones en sistemas estuarinos.El meroplancton estuvo representado principalmente por larvas de crustáceos (66%),e ictioplancton (18%).La dominancia de larvas de crustáceos e ictioplancton evidencian la importancia ecológica de la zona de Punta Morales

Composition of the zooplankton community, with emphasis in copepods, in Punta Morales, Golfo De Nicoya, Costa Rica.

The composition of the mesozooplanktonic community was studied in the Punta Morales estuary, Gulf of Nicoya, Pacific coast of Costa Rica, during 1997. Oblique plankton hauls were performed during high and low tide using a 280 microm mesh screen net equipped with a flowmeter. The community was characterized by holoplanktonic and meroplanktonic organisms. For the holoplanktonic community, the main groups were copepods (80%) and chaetognaths (16%). The most abundant species were the copepods Acartia lilljeborgii and Paracalanus parvus. A. lilljeborgii is a typical estuarine species that maintains high populations in estuarine systems. Meroplankton was represented mainly by crustacean larvae (66%), and icthyoplankton (18%). The dominance of crustacean larvae and icthyoplankton is an evidence of the ecological importance of the Punta Morales zone.

Abundance of Petrolisthes armatus (Crustacea: Porcellanidae) on a tropical estuarine intertidal rocky beach, Gulf of Nicoya estuary, Costa Rica

Population of the porcellanid crab Petrolisthes armatus was studied on a rocky intertidal beach located at the Punta Morales peninsula in the mid upper Gulf of Nicoya estuary, Pacific coast of Costa Rica, from December 1997 to November 1998 (14 dates). Horizontal plankton tows (280 micron mesh net) were also made to verify the presence of P. armatus larvae. Crabs were collected every 3 m along three 18 m long transects, at two sites on the beach, by placing a bottomless bucket fringed with canvas to prevent the organisms from escaping under the rim. A total of 15,382 P. armatus were collected. Only 146 (0.95%) crabs had a carapace length longer than 10 mm, and 8995 (58.5%) were in the size range of 2 to 4.5 mm. The remaining crabs 6241 (40.5%) were in the size range of 4.6 to 10 mm. Male and female P. armatus were represented by 2777 and 3518 individuals respectively, with a sex ratio of 1:1.26. Ovigerous females were found at all dates and included 2937 individuals (83% of females). Plankton tows yielded only 73 larvae of P. armatus (Zoea 1), with a density of 1.2 larvae/m3. No statistically significant seasonal trends in the population of this species were detected. P. armatus appears to reproduce continuously the year around in Punta Morales, and some peaks of abundance were present during the dry and rainy seasons. These trends are similar to trends reported for other crustacean species in the Gulf of Nicoya.