Research Article

Taxonomic Diversity of the Fish Community Associated with Soft Bottoms in A Coastal Lagoon of the West Coast of Baja California Sur, Mexico  

Jose Pérez-Castilloz , Emelio Barjau-González , Juan Manuel López-Vivas , José Ángel Armenta-Quintana
1 Departamento Académico de Ciencias Marinas y Costeras, Universidad Autónoma de Baja California Sur, CP 23080, La Paz, B.C.S., México
2 Departamento Académico de Ciencia Animal y Conservación del Hábitat, Universidad Autónoma de Baja California Sur, CP 23080, La Paz, B.C.S., México
Author    Correspondence author
International Journal of Marine Science, 2019, Vol. 9, No. 2   doi: 10.5376/ijms.2019.09.0002
Received: 03 Nov., 2018    Accepted: 01 Dec., 2018    Published: 21 Dec., 2018
© 2019 BioPublisher Publishing Platform
This is an open access article published under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
Preferred citation for this article:

Pérez-Castillo J., Barjau-González E., López-Vivas J.M., and Armenta-Quintana J.Á., 2018, Taxonomic diversity of the fish community associated with soft bottoms in a coastal lagoon of the west coast of Baja California Sur, México, International Journal of Marine Science, 9(2): 20-29 (doi: 10.5376/ijms.2019.09.0002)



The San Ignacio lagoon is located inside the “Biosphere reserve El Vizcaíno”. It is an important area in terms of ecology, biology, fisheries and tourism and is used by many species as feeding and breeding grounds. Therefore, the study of the fish community of this lagoon will bring a better understanding of the role these organisms play in the ecosystem. The aim of this study was to describe the taxonomic diversity of the icthyiofauna associated to soft bottoms. Six bimonthly samplings were carried out from April 2013 to April 2014 in 11 sites, obtaining a total of 66 replicates. An experimental trawl net was used to catch the fish. Physicochemical variables such as water temperature and salinity were recorded at each site. A total of 2,887 organisms were collected, belonging to six families, 38 genera and 46 species. There was a positive correlation between temperature and salinity and a high fish diversity. Families Haemullidae and Serranidae had the higher number of species, five species each, followed by Sciaenidae with four species, and Paralichthydae and Clupeidae, with three species each. Species considered as residents were Pleuronichthys guttulatus, Calamus brchysomus, Chaetodisterus zonatus and Sphoeroides annulatus. Regarding Fisher’s alpha diversity and taxonomic distinctness, both showed differences related to temperature and salinity between months. Despite the fishing activity in this lagoon that takes place most of the year, according to our results of taxonomic distinctness (Δ*) and average taxonomic distinctness (Δ+), there is no evidence of anthropogenic impact in this lagoon.


Taxonomic diversity; Coastal lagoon; Soft bottoms


The coastal and oceanic areas of México are highly diverse due to its position between the tropics (Lanza-Espino and Cáceres-Martínez, 1994). For example, the west coast of the Baja California peninsula has a high production of abalone, lobster, clam, snail, tuna and sardines (Ruiz-Duran, 1985). Coastal areas are strategically important because they are used for fishing, aquaculture, fossil fuel extraction, mining and tourism (Lanza-Espino and Cáceres-Martínez, 1994), and ecologically relevant because of their high biodiversity, they are used as shelter and breeding ground by many marine species, and they protect against erosion (Lanza-Espino and Cáceres-Martínez, 1994; Bocanegra-Castillo, 1998). México has more than 100 coastal systems (coastal lagoons and estuaries), and 22 of these are found in the Baja California peninsula (Lankford, 1977). Coastal lagoons on the northwest of México are characterized by an arid to semi-arid climate, with low precipitation (< 300 mm per year) and water runoff to coastal systems is intermittent, therefore, nutrient and sediment loads from land are limited (Lara et al., 1980; Camacho-Ibarra et al., 2003). Coastal systems are highly productive but are also highly threatened, not only from anthropogenic impacts, but also because of its inherent spatial and temporal variation of water temperature, salinity, oxygen concentration and turbidity (Yánez-Arancibia, 1977; Day et al., 1989; Lanza-Espino, 1994; Cáceres-Martínez, 1994). According to Moyle and Cech (1982), stability of the basic structure of fish communities of the lagoon-estuarine systems is attributable to four main conditions: 1) The regular distribution of the species, associated to environmental gradients of temperature, salinity and other variables; 2) migratory movements in and out of the system; 3) dominance of few species within the system; and 4) a very stable food web.


San Ignacio lagoon is the second most important lagoon on the Pacific side of the state of Baja California Sur. From the zoogeographical point of view, it is part of the Californian province (Briggs, 1974), geographically is in the temperate zone, inside the “Biosphere reserve El Vizcaíno”, which means is under special consideration regarding the use and management of its natural resources (CONANP, 2003). Studies carried out in this lagoon could be of potential interest because of its economic relevance to tourism and fisheries, and because of its major ecological role as shelter, breeding and feeding ground for many marine species. Therefore, the present study serves as reference to determine the variation of community structure and fish diversity associated to soft bottoms have changed through time.


1 Materials and Methods

The San Ignacio lagoon is located on the west coast of the Baja California peninsula between parallels 26°43' and 26°58' N and between meridians 113°08' and 113°16' W (Núñez-López, 1996). It has an approximate area of 17,500 km2, 35 km length and six km width (Ortega and Arriaga, 1991). It is a shallow water body with average depths from 2 to 4 meters and a maximum depth of 20 meters. It is divided into three zones: lower, connects the lagoon to the ocean with channels that reach depths from 10-20 m; medium, with three channels with average depths of 9 m; and upper, with depths of maximum 2 m (Figure 1) (Swart and Cummings, 1978). The tidal range in this lagoon is 1.6 m. It is considered a hypersaline lagoon, however, salinity ranges from 36 to 41 UPS because of seasonal changes in evaporation and mixing processes from the tidal cycle and wind (Núñez-López, 1998; Winant and Gutiérrez de Velasco, 1999).


Figure 1 Location of the 11 sampling sites in Laguna San Ignacio

Note: 1 = Canal del Cardón, 2 = La Freidera, 3 = La base, 4 = El Anegado, 5 = Norte Isla Garza, 6 = El Remate, 7 = Cantil Cristal, 8 = La Choya, 9 = Los Cerritos, 10 = Las Islitas, 11 = El Mapache


Six bi-monthly samplings were carried out in 11 localities from April 2013 to April 2014. An experimental trawl net with a length of 9.5 m, a vertical opening of 4.5 m, a mesh size of 1.75 inches, and metal doors of 95x50 cm, was used to catch the fish. The trawl speed was 3.5 km/h, sweeps lasted 20 minutes at an average depth of 5 m at each locality. A 25 feet boat with a 90 HP four stroke outboard motor was used as a trawler.


Geographic location was recorded at each locality using a Global Positioning System (GPS) (Table 1). Physicochemical variables (water temperature and salinity) were recorded using a YSI 2030 Pro multiparameter instrument. Organisms were identified to species level using specialized identification keys (Miller and Lea, 1972; Fischer et al., 1995; Thomson et al., 2000). Fish diversity was determined using the following ecological indexes: alpha diversity (α), beta diversity (β), gamma diversity (γ) and Fisher’s alpha diversity. Taxonomic diversity was determined using the following: taxonomic distinctness (TD Δ*) (Clarke and Warwick, 1998) and average taxonomic distinctness (AvTD Δ+) (Clarke and Warwick, 2001), considering six hierarchical taxonomic levels (phylum, class, order, family, genus and species), species richness and total abundance data, which were standardized by the square root (Clarke and Warwick, 1999). Ecological indexes were determined using the software PRIMER-E 6 & PERMANOVA+ v1.0.2. Statistical analysis (ANOVA and post-hoc Tukey test) to see whether there were significant differences between sites (spatial) and seasons (temporal) were performed using STATISTICA v8, considering a significance level of 0.05 and 95% confidence interval.


Table 1 Geographic coordinates of each site in San Ignacio lagoon, BCS


3 Results

According to the analysis of physicochemical variables, water temperature showed a seasonal pattern, there were significant differences between months (F (5,60) = 107.31, p=0.000012). The highest average temperature (25.2°C) was recorded in August and the lowest (16.3°C) in December, showing a thermal differential of 8.9°C (Table 2). No significant differences were found between sites (F (10,55) = 0.3163, p=0.9736). Salinity showed significant differences between months (F (5,60) = 18.3754, p=0.000016). Highest average value was recorded in June (38 UPS) and the lowest in April 2014 (31.1 UPS) (Table 2). There were no significant differences in salinity between sites (F (10,55) = 1.5622, p=0.1429).


Table 2 Average values (by site and by month) of physicochemical variables (temperature and salinity) and ecological indexes


A total of 66 sweeps were carried out, covering an area of 346,500 m2. A total of 2,887 organisms, belonging to 26 families, 38 genera and 46 species were captured. Families Haemullidae and Serranidae had the higher number of species, five species each, followed by Sciaenidae with four species, Paralichthydae and Clupeidae, with three species each, and other families with just one or two species each. Analysis of presence/absence showed differences during each season, with a high number of species with tropical affinity and a lower number of species with temperate affinity. Pleuronichthys guttulatus, Calamus brachysomus, Chaetodipterus zonatus and Sphoeroiedes annulatus were captured in every sampling, therefore, are considered resident species.


Fisher’s alpha diversity (α-Fisher) was significantly higher in warmer months (summer) than in colder months (winter) (F= (5,60) = 2.8749, p=0.0216), with August being significantly different from December and April 2014 (Table 2). Highest value was recorded in August (S=15.32) and the lowest value was recorded in December (S=4.41). Comparison of Fisher’s alpha diversity between sites showed no significant difference (F= (10,55) = 1.089, p=0.3866). Average values of alpha diversity (α) were obtained grouping all sites, resulting in monthly α values. The highest α value was recorded in August with 5.36 species, followed by October with 3.09 species, while December and April 2013 showed the lowest α values with 1.27 and 2.27 species, respectively. The highest beta diversity (β) was recorded in October with 19.9 species, and the lowest value was recorded in December with 8.7 species, followed by April 2014 with 11.3 species. Regarding gamma diversity (γ), the higher values were recorded in August and October with 23 species, and the lowest values was recorded in December with 10 species, followed by April 2014 with 14 species.


For the taxonomic distinctness (TD Δ*) analysis, total abundance data was used, which were standardized by its square root. The shortest value of taxonomic distinctness (taxonomic distance between two species) was recorded in April 2014 (Δ*=60.15), while the highest distance was recorded in December (Δ*=64.97) (Figure 2). TD Δ* was significantly different between months (F (5,60) = 2.7253, p=0.0277) with the highest taxonomic distance recorded in December (Δ*=64.9) and the shortest distance was recorded in April 2014 (Δ*=57.7). Comparison of Δ* between sites showed no significant differences (F (10,55) = 0.6723, p=0.7449). Highest taxonomic distance was recorded in site eight known as “La Choya” (∆*=65.33), while the shortest distance was recorded in site one known as “Canal del Cardón” (∆*=59.15) (Figure 3).


Figure 2 Temporal taxonomic distinctness (Δ*) of San Ignacio lagoon

Note: Central line is the mean and upper and lower lines correspond to 95% confidence interval


Figure 3 Spatial taxonomic distinctness (∆*) of San Ignacio lagoon

Note: Central line is the mean and upper and lower lines correspond to 95% confidence interval


For the average taxonomic distinctness (AvTD Δ+) analysis, presence/absence data was used. The higher taxonomic distance was recorded in August (∆+ = 67.65), while the shortest distance was recorded in April 2013 (∆+ = 61.90) (Figure 4). However, there were no significant differences between months (F (5,60) = 0.7298, p= 0.6039). Regarding the comparison of AvTD Δ+ between sites, the highest taxonomic distance was recorded for site three known as “La Base” (∆+ = 68.18), while the shortest distances were recorded for sites Cantil Cristal, Canal del Cardón and La Freidera with ∆+ values of 61.53, 60.64 y 60.04, respectively (Figure 5). However, there were no significant differences between sites (F (10,55) = 1.3429, p=0.2317).


Figure 4 Temporal average taxonomic distinctness (Δ+) of San Ignacio lagoon

Note: Central line is the mean and upper and lower lines correspond to 95% confidence interval


Figure 5 Spatial average taxonomic distinctness (Δ+) of San Ignacio lagoon

Note: Central line is the mean and upper and lower lines correspond to 95% confidence interval


4 Discussion

Variation of environmental parameters such as temperature and salinity, and water exchange patters determine the presence or absence of certain fish species in the lagoon (Horn and Allen, 1985; Sosa-López et al., 2005). According to Hubbs (1948) and Moore (1975), water temperature plays a major role in the distribution of marine species. Moreover, Galván-Piña et al. (2003) found that changes in the fish community structure of La Paz Bay are determined by the seasonal variation of water temperature. According to our results, temperature also influenced the distribution of fish in San Ignacio lagoon during the study period, recording high temperatures like those reported by Segura-Zarzosa et al. (1997) (28.5°C) during 1992-1993 and Barjau-González (2003) (25°C) during 1998-1999. The lowest temperature recorded in the present study was 16.3°C, while the lowest temperature reported by Segura-Zarzosa et al. (1997) during 1992-1993 was 15.8°C, and the lowest one reported by Barjau-González (2003) during 1998-1999 was 11.2°C. Based on these reports, and in contrast to those reported by Barjau-González et al. (2014), El Niño happened during the first half of 1998, while La Niña happened during the winter of 1999, contrasting to 2013-2014 considered neutral years. Therefore, water temperature variation could be influencing the variation of the fish community structure in San Ignacio lagoon throughout the years. In addition, Álvarez-Borrego and Granados-Guzmán (1982) reported a temperature variation from 13.5°C (lowest) to 26°C (highest) in Ojo de Liebre lagoon (also located in the Biosphere reserve El Vizcaíno), which compared to our results, there was a difference of 0.8°C with the lowest temperature, and a difference of 2.8°C with the highest temperature. A similar temperature variation pattern was reported by Gutiérrez-Sánchez (1997) in Magdalena Bay and by Barjau-González (2003) in San Ignacio lagoon, suggesting temperature changes throughout seasons, which increase from spring to summer, and decrease towards winter. In addition, our results showed a spatial variation of temperature, sites located closer to the mouth of the lagoon showed lower temperatures compared to those located inside the lagoon, away from the mouth, where higher temperatures were recorded. Similar results were reported by Gutiérrez-Sánchez (1997) in Magdalena Bay, Acevedo-Cervantes (1997) in Ojo de Liebre lagoon and Barjau-Gonzalez et al. (2015) in San Ignacio lagoon.


Regarding salinity, our results showed a spatial gradient from lower to higher salinity values. Sites located closer to the mouth of the lagoon, where water exchange is constant, showed lower salinity values than sites located inside the lagoon, away from the mouth, where water exchange takes more time. In addition, this is a shallow water body (two to four meters), with maximum depth of 18-20 meters only in the channel zones. It has a high evaporation rate and water runoff is low, therefore, freshwater input is low, resulting in high salinity values. Moreover, water exchange is slow, taking three to four months. Less dense water from the Pacific Ocean floats near the surface when it is being transported into the lagoon, while more dense water from the lagoon is directed towards the bottom when it is coming out of the lagoon (Barjau-González, 2003). Because of this, highest salinity (38 UPS) was recorded during summer (June) while the lowest salinity (31.1 UPS) was recorded during spring (April 2014). Similar results were reported by Nuñez-López et al. (1998) in 1992-1993, with a low salinity of 32 UPS during winter and 37 UPS during summer. However, Barjau-González (2003) reported a high salinity of 42 UPS during summer of 1998-1999, while the lowest salinity of 36 UPS was recorded during winter-spring. Likewise, Gutiérrez-Sánchez (1997) reported similar results for Magdalena Bay/Almejas Bay lagoon system, with lower salinity values on the sites near the mouth of the bay, increasing towards the channel zones in Almejas Bay. These reports and our results support Largier et al. (1995), who classified this type of lagoons as hypersaline lagoons because of their high evaporation rate, lower freshwater input and slow water exchange rate. Our results suggest a correlation between temperature and salinity, which influenced the presence/absence of certain species, which has been suggested by several authors. For example, De la Cruz Agüero (2000) suggested that temperature variations throughout time influence presence/absence of the ichthyofauna; Cognetti et al. (2006) also suggested that temperature is one of the most important environmental variables that determine distribution of many species that live above the thermocline.


Regarding fish species composition associated to soft bottoms, 46 species belonging to 38 genera, 26 families, nine orders and two classes, were recorded in this study, and have also been recorded in closer study areas such as Ojo de Liebre lagoon, Guerrero Negro and Magdalena Bay. For example, 18 species out of the 44-species recorded by Barjau-González (2003) were also recorded in the present study. Moreover, Acevedo-Cervantes (1997) reported 59 species in Ojo de Liebre lagoon, however, they used three different fishing techniques (gillnet, trawling net and cast net). Just considering trawling net (the same fishing technique used in the present study), they only captured 29 species, unlike the 46-species recorded in this study. Ramírez De Aguilar Azpiroz (2001) reported 43 species in the estuary El Coyote, where they also used three different fishing techniques, but only capturing 15 species with trawling net. Gutiérrez-Sánchez (1997) captured 75 species in Magdalena Bay using trawling net, however, 197 sweeps were carried out, while in the present study only 66 sweeps were carried out. Rodríguez-Romero et al. (1998) captured 55 species in Concepción Bay using a trawling net. Grijalva-Chon et al. (1996) suggested that different fishing techniques, sampling effort and characteristics of the sampling area can determine the record of species. 


According to Sosa-López et al., (2005), variation on the diversity values could indicate changes in the taxonomic structure of the fish community between different lagoons, resulting from different environmental variables that act as filters, selecting the presence of species phylogenetically related. Moreover, the loss of local heterogeneity, regarding habitat and resources, limits the number of available niches, resulting in a decline in diversity. There has been an intense critique on the limitations of ecological indexes (Shannon-Wienner, Pielou’s evenness and Simpson’s diversity index) commonly used to determine community structure and evaluate environmental impacts (Coleman et al., 1997; Pires et al., 2000). In contrast, Fisher’s alpha diversity (α-Fisher) (Fisher et al., 1943) is not commonly used to analyze diversity; however, it is biologically well supported because it is not depending on sample size and evaluates diversity more efficiently considering number of organisms and number of species (Condit et al., 1996; Moreno, 2001; Magurran, 2004). Lowest value of α-Fisher was recorded in December (S=2.41), while the highest value was recorded in August (S=17.32). Our results differ from the ones reported by Juaristi-Videgaray (2014), however, this makes sense because diversity is influenced by variation of temperature and salinity, substrate and depth difference throughout the lagoon (Allen and Horn, 1975; Amezcua-Linares, 1977; Quinn, 1980; Amezcua-Linares, 1996; Manjarrez-Acosta, 2001). According to Cognetti et al. (2006), temperature is the environmental variable that determined the distribution of many species. Fisher’s alpha diversity (α-Fisher) was not significantly different between sites. Moreover, sites that are located away from the mouth of the lagoon showed a higher α-Fisher value than the ones located near the mouth, which are directly influenced by the ocean.


Our results showed that when temperature and salinity increase on summer (June and August), alpha diversity also increases, and starts declining towards winter (December). In this sense, we can infer that the fish community probably uses this lagoon as feeding ground and shelter, therefore showing spatial and temporal variations (Yañez-Arancibia and Sánchez-Gil, 1986; Barjau-González, 2003).


This supports what has already been suggested by Juaristi-Videgaray (2014), fish are probably entering the lagoon during March and April, therefore, boosting species diversity during the warmer months (June, July and August), and leaving the lagoon during October and November, when temperature starts to decline, resulting in lower diversity during December. Measuring beta diversity (β) could help to understand ecosystem functioning (Legendre, 2007). According to our results, during the warmer months there is less replacement of species (8.72), unlike transition or colder months such as October (19.90) and April 2014 (11.36). Similar results were reported by Juaristi-Videgaray (2014) with 21.27 during spring and 14.73 during winter, and other study sites in México (Allen, 1982; Barjau-Gonzáez et al., 2012). Low beta diversity means that replacement or exchange of species between two sites is low, which could impact community structure, as suggested by Harrison (1992). Gamma diversity (γ), considered as the landscape diversity, showed similar values to those reported by Barjau-González (2003; 2012) and Juaristi-Videgaray (2014).


Taxonomic distinctness (TD Δ*), which is the average length between two organisms selected randomly that are taxonomically different. It is an index that measures pure taxonomic relatedness. Clarke and Warwick (1998) established the use of this index to infer if an ecosystem can be considered anthropogenically impacted or in pristine conditions. Values are adjusted depending on the number of hierarchy levels used; six levels were used for the present study. The use of this type of ecological indexes in México is relatively recent. Juaristi-Videgaray et al. (2014) reported spatial ∆* in San Ignacio lagoon with values from 49.95 to 66.67 units. Barjau-Gonzalez et al. (2012), reported spatial ∆* in San José island with values from 51.58 to 53.58 units. Barjau-González et al. (2014), reported spatial ∆* from eight sites of the west coast of La Paz Bay, with values from 53.58 to 59.29 units. Spatial ∆* recorded in the present study showed similar values (Table 2), even though Juaristi-Videgaray (2014) only carried out four samplings but used a trawling net, while other studies used visual census. When just presence/absence data are considered for analysis, taxonomic diversity (Δ) and taxonomic distinctness (Δ*) converge in the same index, average taxonomic distinctness (Δ+), which is the length of taxonomic relatedness between two random species (Sohier Charlotte, 2008). Our results, like those reported by Juaristi-Videgaray et al. (2014) in San Ignacio lagoon, by Barjau-Gonzalez et al. (2012) in San José Island, and Barjau-González et al. (2014) in La Paz Bay, with values close to the mean, and in some cases, close to the confidence intervals, suggest that san Ignacio lagoon is in good ecological condition.


Spatial average taxonomic distinctness (AvTD Δ+), showed a similar tendency to temporal AvTD Δ+, with values of 60.04 to 68.18 units (Figure 4; Figure 5; Table 2), like those previously reported, therefore suggesting San Ignacio lagoon is in good ecological condition, compared to other study areas. Regarding temporal AvTD Δ+, results showed values close to the mean (Figure 4; Table 2), with only April 2013 located near the lower confidence interval. This might be due to water sweeps (sweeps in which no capture was recorded) and because we used presence/absence data, April 2013 recorded 61.9 units, the lowest AvTD Δ+ value of all sampled months. AvTD Δ+ for all sampled sites and months are close to the mean and between the confidence intervals. Therefore, suggesting that despite fishing activity carried out throughout most of the year, this lagoon can be considered ecologically stable.


5 Conclusion

Despite the high fishing activity that happens in San Ignacio lagoon, in which many marine species such as fish, scallop, shrimp, lobster, and clams are captured, based on our results, this lagoon can be considered ecologically stable, probably because from December to April due to grey whale (Eschrichtius robustus) breeding season, all fishing activity is banned.


Authors contributions

JPC wrote the manuscript. EBG designed and carried out fish collection, analyzed data and revised the manuscript. JMLV revised the manuscript. JAAQ georeferenced the sampling sites. All authors read and approved the final manuscript. Likewise, they declare no conflict of interest.



Authors would like to acknowledge Departamento Académico de Ciencias Marinas y Costeras for funding the project in which this study took part and Universidad Autónoma de Baja California Sur (UABCS) for allowing the use of its facilities (Laboratorio de Ecología de Peces). MSc Myrna Barjau-Pérez Milicua for the english editing of the manuscript.



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