The sharpnose shark (Rhizoprionodon longurio) is among the top three shark species captured by artisanal fisheries of the Gulf of California. This study includes information regarding the feeding habits of this species using the stomach contents of 70 individuals ranged from 54 to 109 cm in total length (TL). Out of the 16 prey items identified, fish of the families Scombridae (Scomber japonicus; prey-specific relative importance index [%PSIRI] = 6.3) and Batrachoididae (%PSIRI = 5.5), the cephalopod Lolliguncula spp. (%PSIRI = 6.3), and the crustacean Pleuroncodes planipes (%PSIRI = 4.3) were the most important prey. Only female stomachs were obtained (N = 19) in the central area of the gulf, and the PSIRI indicated that the preferred prey were the cephalopod Lolliguncula spp. (%PSIRI = 10.5) and fish of the Sparidae family (Calamus brachysomus; %PSIRI = 5.8). The number of stomachs was not sufficient to analyse differences by sex. Regarding its trophic position, R. longurio was a tertiary consumer (TLK = 4.4). A TLK = 4.4 was calculated for the central area, and a TLK = 4.3 for the southern area. According to Levin's index (Bi), this shark is a specialist predator in the whole study area (Bi = 0.19), including the centre (Bi = 0.29). Conversely, it was considered a generalist predator in the southern area (Bi = 0.63). The high quantity of empty stomachs could relate to the time the sharks were caught in fishing a gear.

Marine ecosystems are exposed to a wide variety of factors that may produce disturbances in their structure and functioning. The Gulf of California supports fisheries, tourism, intensive agriculture, mining, and more recently, shrimp aquaculture. Under such conditions, animals are forced to cope with several changes in their environment that can contribute to animal welfare problems. Serum cortisol level analysis may be a particularly useful means of assessing the physiological status of mammals potentially affected by increasing human activity in the Gulf of California, such as the California sea lion (Zalophus californianus californianus). In this study, we report for the first time the serum cortisol concentration of free-living, wild California sea lion pups. The analysis was performed in eleven rookeries along the Gulf of California. Two consecutive blood samples (S1 and S2) were obtained from 56 sea lion pups following a capture, handling and anaesthesia regime, and cortisol was measured by radioimmunoassay. Female pups showed higher serum cortisol than males in the first sample. In males, the second sample was significantly higher than the first. Cortisol levels in the two samples of both sexes combined differed between the Southern and Midriff-region rookeries. This information could be useful to assess welfare in wild populations of sea lions and to determine anthropogenic factors in the Gulf of California that may contribute to stress and reduced welfare.

Ficopomatus Southern, 1921 is a serpulid genus currently composed of six species, two of which (F. enigmaticus and F. miamiensis) are reef-builders. The former has invaded subtropical and warm-temperate estuaries worldwide, causing environmental and economic harm. In this study, Ficopomatus miamiensis and F. uschakovi are reported from brackish-water coastal localities in both Atlantic and Pacific sides of Mexico, including a Biosphere Reserve, estuaries, as well as shrimp and oyster farms. Ficopomatus miamiensis is reported from Veracruz (southern Gulf of Mexico, Mexico territory) and Sinaloa (southern Gulf of California). Ficopomatus uschakovi is reported for the first time in the southern Gulf of Mexico (Mexico territory) and repeatedly recorded in Chiapas (southern Mexican Pacific). There are no phenotypic differences between specimens of F. miamiensis from both coasts of Mexico. Comparison of mitochondrial cytochrome b (Cytb) DNA sequences further support the notion that F. miamiensis from the type locality (Florida) and Atlantic coasts of Mexico is also found along the Pacific coast of Mexico. Morphological variability within specimens of F. uschakovi from a single locality (either Laguna del Ostión or La Encrucijada) in Mexico suggest potential presence of multiple cryptic species. Molecular genetics studies are needed to confirm the taxonomic and invasive status of F. uschakovi.

The hawksbill sea turtle Eretmochelys imbricata is categorized as Critically Endangered on the IUCN Red List and its population has declined by over 80% in the last century. The Eastern Pacific population is one of the most threatened hawksbill populations globally. Western Mexico is the northern distribution limit for hawksbill sea turtles in the Eastern Pacific and recent research indicates that the Mexican Pacific portion of the population is a separate management unit because of the restricted movements of these turtles. Here we use the most complete database of sighting records in the north-west Pacific of Mexico to identify sites where hawksbill turtles are present. We also develop a conservation index to determine the conservation status of hawksbill turtle sites. Our results demonstrate the importance of this region for juveniles and the relevance of rocky reefs and mangrove estuaries as habitats for hawksbill turtles. We identified 52 sites with records of hawksbill turtles. Most of these sites (71%) are not protected; however, sites with high conservation value included islands and coastal sites along the Baja California peninsula that are established as marine protected areas. Reefs and mangrove estuaries relevant for hawksbill turtles are probably also significant fish nursery areas that are important for local fishing communities, creating opportunities for conservation strategies that combine science, local engagement and policy to benefit both local fishing communities and hawksbill sea turtle conservation.

Of the five nominal species in the genus Caranx Lacepède 1801 distributed throughout the Eastern Central Pacific, Caranx caballus and Caranx sexfasciatus are the only two that have formal fish larval descriptions based on diagnostic characteristics (morphology, meristics and pigmentation). In this study, the diagnostic characteristics of three Caranx species larvae were validated using DNA barcoding analysis cytochrome c oxidase subunit I (COI; 651 bp). For the first time, the morphological taxonomic assignation of C. caballus fish larvae was confirmed using COI gene partial sequences of adults, with a genetic similarity between 99.8–100%. However, molecular evidence demonstrated that fish larvae previously described as C. sexfasciatus had high genetic similarity (99.7–100%) and low genetic distance (<1%) to Caranx caninus adults. An undescribed larval morphotype collected in the present study genetically matched (100%) with COI sequences of C. sexfasciatus adults. The diagnostic characteristics of this new morphotype were a lack of pigmentation in the supraoccipital crest, over the gut, and at the terminal region of the gut. The combination of diagnostic characteristics and DNA barcoding evidence allowed the discrimination and validation of C. caballus, C. caninus and C. sexfasciatus larvae. The diagnostic characteristics and COI sequences of Caranx lugubris and Caranx melampygus larvae, which are also distributed in the Eastern Central Pacific, remain to be investigated.

In order to determine the sex of Chelonia mydas individuals found within one of the principal foraging areas of the Gulf of California during any given stage of ontogeny, 529 individuals were sampled in Bahía de los Ángeles from 1995–2012, and their morphometric data were collected. A principal component analysis (PCA) was performed for the morphometric variables, and two principal components were obtained that unambiguously separated sexes and ontogenetic stages. The first component was defined by straight carapace length (SCL), curve carapace length (CCL), plastron length (PL) and carapace depth (CD), while the second factor was represented by total tail length (TTL). Allometric models were fitted with the most important variables determined by the PCA. The model PL = αSCLβ was able to distinguish between adults and immature individuals. For adult organisms, the model that best separated males from females was TTL = αSCLβ. Adult females had SCL values of 66–96.7 cm and TTL values of 16.3–25 cm, while adult males had SCL values of 66.4–12.5 cm and TTL values > 25 cm. As the organisms were considered immature only if SCL < 77.3, we were able to determine the TTL values for immature individuals by using elemental mathematics and solving for SCL in the equation TTL = αSCLβ for each group (i.e. adult females, adult males and immatures). So, considering the mathematical approach and acknowledging the lack of background information, immature individuals may be considered potential females if the TTL value is between 7.04–17.8 cm and potential males if the TTL value > 17.8 cm.

The loggerhead turtle (Caretta caretta) is a circumglobal species and is listed as vulnerable globally. The North Pacific population nests in Japan and migrates to the Central North Pacific and Pacific coast of North America to feed. In the Mexican Pacific, records of loggerhead presence are largely restricted to the Gulf of Ulloa along the Baja California Peninsula, where very high fisheries by-catch mortality has been reported. Records of loggerhead turtles within the Sea of Cortez also known as the Gulf of California (GC) exist; however, their ecology in this region is poorly understood. We used satellite tracking and an environmental variable analysis (chlorophyll-a (Chl-a) and sea surface temperature (SST)) to determine movements and habitat use of five juvenile loggerhead turtles ranging in straight carapace length from 62.7–68.3 cm (mean: 66.7 ± 2.3 cm). Satellite tracking durations ranged from 73–293 days (mean: 149 ± 62.5 days), transmissions per turtle from 14–1006 (mean: 462 ± 379.5 transmissions) and total travel distance from 1237–5222 km (mean: 3118 ± 1490.7 km). We used travel rate analyses to identify five foraging areas in the GC, which occurred mainly in waters from 10–80 m deep, with mean Chl-a concentrations ranging from 0.28–13.14 mg m−3 and SST ranging from 27.8–34.4°C. This is the first study to describe loggerhead movements in the Gulf of California and our data suggest that loggerhead foraging movements are performed in areas with eutrophic levels of Chl-a.

Endemic insular species are particularly vulnerable to anthropogenic threats. The fish-eating bat Myotis vivesi is restricted mainly to the islands of the Gulf of California in Mexico and although several aspects of its biology have been studied there are no recent accounts of its current distribution. We conducted several expeditions during 2001–2016 to verify the current geographical distribution of this bat, and to record the presence of introduced predators. We identified the localities in which maternity colonies occur, estimated the size of the bat population on Partida Norte Island in 2003, and monitored bat presence on this island during 2004–2016. We found fish-eating bats on 36 islands and maternity colonies on 19 islands. Introduced rats Rattus rattus or cats Felis catus were captured on seven islands where the bats were present, and on five islands where they were absent. We estimated a population of c. 30,000 fish-eating bats in May 2003 and we confirmed the species’ presence on Partida Norte Island during 2004–2016. Based on the information compiled from our surveys and previous studies, we discuss the adequacy of the species’ current categorization as Vulnerable on the IUCN Red List, and its conservation status conferred by Mexican conservation authorities.

Spatial variations of polychaetes along the Baja California Peninsula continental shelf were analysed in two ways: (1) by evaluating the species richness and defining the faunal assemblages from local sampling, and (2) by characterizing the latitudinal variation of beta-diversity based on the distribution of all polychaetes reported up to now. Twenty-seven stations from three oceanographic expeditions were sampled, and 2858 individuals from 38 families and 231 species were identified. Polychaetes were abundant (mean = 37.5 ind 0.1 m−2) and diversified (mean = 15 species station−1). Differences in species composition defined seven faunal assemblages, but their number of species did not show significant latitudinal changes. The beta-diversity analysis was based on distribution data of 730 species from 47 families. The presence of a group of islands in the middle Gulf could have a negative effect on the species distribution, since the lowest values of β T-diversity (0.39) were found in the northern Gulf, but their species were different from those recorded in the central region. The wide variation in β T-diversity (0.5–0.87) showed latitudinal changes in the species composition, mainly in the Gulf mouth (0.86–0.87), which indicated that the fauna inside the Gulf was different from that inhabiting the Pacific coasts. The ICE and Chao2 estimators showed that the polychaetes in the study area are relatively well known (>80%), and that most species (415) have small distribution ranges. The effects of these infrequent species were similar at each latitudinal band, which suggested that the observed β T-diversity pattern could represent a suitable estimation.

This study investigates changes in precipitation patterns and variations in paleoproductivity in the tropical Pacific region associated with the North American Monsoon, Intertropical Convergence Zone (ITCZ) latitudinal migration, and changes in insolation during the middle and late Holocene. Major and trace element records (Al, Ba, C, K, Si and Ti) and Zr/Al and Ba/Al ratios in a core from Alfonso Basin, southern Gulf of California, are used as proxies of terrigenous input and bio-productivity. Records reveal an increase in precipitation and low bio-productivity ca. 6200 to 2400 cal yr BP, associated with the strengthening of monsoonal precipitation and northward shift of the ITCZ mean position in the eastern tropical Pacific. A multi-centennial drought from ca. 2400 to 1900 cal yr BP, and a dry and cold interval ca. 700 and 500 cal yr BP, are characterized by strong aeolian input and enhanced productivity, associated with diminution of the summer monsoonal precipitation and reduced insolation in the Northern Hemisphere and more southerly ITCZ position. Correlation of Alfonso Basin records with other records in the Gulf of California and the Pigmy and Cariaco basins in the Gulf of Mexico and central Atlantic provides constraints on NAM, ITCZ migration, and insolation-driven changes.

A laminated sequence (core BAP96-CP 24°38.12′N, 110°33.24′W; 390 m depth) from the Alfonso Basin in Bay of La Paz, southern Gulf of California, contains a record of paleoceanographic and paleoclimatic changes of the past 7900 yr. Radiolarian assemblages and magnetic susceptibility are used as proxies of oceanographic and climatic variability. The records provide a regional scenario of the middle and late Holocene, suggesting two major climatic regimes and several millennial-scale events. Conditions relatively warmer and drier than today occurred from ∼7700 to 2500 cal yr BP, promoting the intensification of evaporation processes and the prevalence of the Gulf of California water in the Basin. These conditions correlate with strong droughts in the middle Holocene of North America and with minimal incursion of tropical waters into the Gulf of California. Proxies indicate a warm scenario and the dominance of the Equatorial Surface Water in the Alfonso Basin from ∼2400 to 700 cal yr BP, suggesting the intensification of ENSO cycles. A climatic signal between ∼1038 and 963 cal yr BP may be correlated with global signal of the “Medieval Warm Period.” Several cooling events are recognized at 5730, 3360, 2700, 1280 and 820 cal yr BP and are associated with intensification of northwest winds leading to upwellings and enhanced productivity in the Basin.

The diet and feeding pattern of scyphomedusa Stomolophus meleagris (Rhizostomeae) was studied, by comparing stomach samples from different developmental stages and environmental zooplankton with the aim to determine diet composition, trophic niche breadth, selectivity and feeding overlap of this edible jellyfish species. Samplings were performed during April and December 2010 and in January 2011, in the coastal lagoon Las Guásimas (27°49′–27°54′N 110°40′–110°35′W), central Gulf of California, which consisted of zooplankton tows and jellyfish collections for stomach content. More than 39 prey items were identified in the gut contents (N = 69), from which eight taxa formed over 90% of the total. Fish eggs were considered main prey (58.6%), copepods (10.8%), veliger larvae of gastropod (13.0%) and bivalve (12.7%) were secondary prey while cirriped and decapod larvae were incidental prey (<3%). However, these proportions varied significantly between small, medium and large size classes of medusa as well as number and type of prey increasing as a function of medusa size. Values of Levin's index confirmed S. meleagris is a specialist predator and Pearre's index showed positive selection of fish eggs, gastropods, bivalves and cirripeds while selectivity was negative for copepods and appendicularians. The relative timing of these changes suggests that ontogenetic processes are closely related with shift in the diet, which indicates increasing predation pressure during development of the medusoid stage of this species, thus emphasizing their ecological importance in coastal ecosystems.

Latitudinal patterns of composition, biogeographic affinity and indicators of taxonomic diversity are described for the by-catch fish community in five typical shrimping areas in the Mexican Pacific (Upper Gulf of California, Sinaloa-Nayarit, Jalisco-Colima, Michoacán-Guerrero and Gulf of Tehuantepec). The taxonomic composition included two classes, 20 orders, 65 families, 147 genera and 292 species. The family Sciaenidae was the best represented with 33 species, whereas at the genus level, Anchoa was represented with eight species. A high percentage of the species showed wide distribution ranges (30.2% for Cortez Province ~ Panamic Province; 21.3% for San Diego Province ~ Panamic Province); nevertheless, each ecosystem included a characteristic combination of species, apparently related to the physiographic conditions of the ecosystems. Species richness showed a pronounced decrease from the Upper Gulf of California, which has warm-temperate features, to the Gulf of Tehuantepec, which has tropical conditions; this is an opposite trend to that observed in the taxonomic diversity indicators, suggesting that a taxonomic redundancy was present in tropical areas and higher taxonomic diversity was present in the Upper Gulf of California, despite the lower species richness. This is explained by the prevailing environmental conditions and isolation processes generated during the formation of the Gulf of California.

The trophic spectrum of both Eucinostomus entomelas and Micropogonias megalops, the two most abundant fish species in Laguna Las Guásimas, Sonora, México is described in our study. A total of 21 types of prey were identified belonging to seven taxonomic groups (Crustacea, Mollusca, Annelida, Rhodophyta, Copepoda, Echinodermata and Chordata) to analyse the feeding spectra and diet breadth. The preferred prey items of Eucinostomus entomelas (Dark-spot mojarra) were Polichaeta (index of relative importance = 46.7%), followed by bivalves (36.6%), and Luidia columbia (5.6%), while those of Micropogonias megalops (Bigeye croaker) were Portunidae (22.8%) followed by Gammaridae (20.55%) and Crustacea (18.37%). The trophic spectrum for male E. entomela was composed of Bivalvia and Polychaeta. Both predators showed low values in diet breadth (E. entomelas (Levin's index Bi = 0.14) and M. megalops (Levins's index Bi = 0.43)). The low trophic overlap (Cλ = 0.14) between predators suggests that both fish are not competing with each other for food resources in Laguna Las Guásimas.

We examined the effect of a tidal-mixing front on the three-dimensional distribution of larval fish habitats (LFHs) in the Midriff Archipelago Region in the Gulf of California during winter. Zooplankton and environmental variables were sampled from 0 to 200 m in 50 m strata. Four LFHs were defined in association with the front, two on the northern side and two on the southern side. The northern LFHs were: (1) the Mainland Shelf Habitat, located from the surface to 100 m depth on the north-east mainland shelf, characterized mainly by the presence of Citharichtys fragilis; and (2) the Wide Distribution Habitat, extending from north-west to south across the front from the surface to 200 m depth, dominated by the ubiquitous Engraulis mordax. The southern LFHs were: (3) the Eddy Zone Habitat, defined nearly on an anticyclonic eddy, with the highest larval abundance and richness from the surface to 100 m depth, dominated by Leuroglossus stilbius; and (4) the Southern Gulf Habitat, associated with low temperature waters from the southern Gulf of California, dominated by southern-gulf species (e.g. Scomber japonicus and Sardinops sagax). Despite the weak stratification and low thermal contrast (~1.5°C) across the south front compared to summer (~3°C), our results demonstrate that the frontal zone may influence the formation of planktonic habitats even during generally homogeneous periods, which may also be relevant in other regions of the world.

Concentrations of cadmium (Cd), lead (Pb), copper (Cu), zinc (Zn) and iron (Fe) were measured in three macroalgal species, Codium simulans, Sargassum sinicola and Gracilaria pachydermatica, and in the sea slug Elysia diomedea, living in marine ecosystems dominated by Sargassum species and located near exploited phosphorite deposits. Metal concentrations in macroalgae and sea slugs were significantly different among sites. The highest concentrations of Cd recorded in C. simulans and S. sinicola, as well as in E. diomedea were recorded at the site closest to the phosphorite deposit. In general, Cd and Zn concentrations in E. diomedea were higher than those recorded in specimens of C. simulans, S. sinicola and G. pachydermatica. In contrast, Pb, Cu, and Fe concentrations in E. diomedea were lower than or similar to those in macroalgae from all sampled sites. The information generated contributes to the knowledge about potential mobility and metal bioaccumulation at lower trophic levels in marine eco systems.

Two species of limid clams, Acesta sphoni and Acesta mori, were observed and sampled from seven localities in the Gulf of California, Mexico. The two species are known to occur on seamounts and escarpments along the north-eastern Pacific margin of the United States. This report provides the first records of each species in the Gulf of California and the greatest depth records for both species. Though they occasionally overlap geographically, the two species are clearly stratified by depth, with A. sphoni occupying shallower and warmer, hypoxic waters, and A. mori occupying deeper and colder, oxic waters. The species are easily distinguished morphologically. The shells of A. mori have very fine radial ribbing for a smooth appearance and are more rounded and inflated, whereas those of A. sphoni are narrower and more elongate with 31 to 77 strong radial ribs. The largest individuals sampled were A. sphoni. For each species, DNA analyses revealed arrays of mitochondrial haplotypes similar to those found previously at north-eastern Pacific localities along the California, Oregon and Washington margins, providing no evidence for geographical subdivision throughout this newly extended range.

The Pacific sharpnose shark Rhizoprionodon longurio is caught seasonally by inshore artisanal fisheries in the Mexican Pacific. Our study focuses on the feeding ecology of this shark species in the southern Gulf of California. The prey species obtained from stomach contents were identified and quantified, and variations between sexes and maturity stages were determined. A total of 98 stomachs were analysed during two periods (2000–2001 and 2003–2004); 64% of stomachs contained food. The trophic spectrum was composed of four cephalopod species, three crustacean species, and 13 pelagic and benthic fish species. According to the index of relative importance (%IRI), the fish Echiophis brunneus (IRI = 14.4%), Opisthopterus dovii (IRI = 12.2%) and Scomber japonicus (IRI = 9.6%) were the main prey items. Based on diversity values, IRI values and diet breadth, R. longurio is an opportunistic predator. The trophic position of R. longurio was above four in all categories, which indicates that this shark is a tertiary consumer.

The presence of a shrimp necrotizing hepatopancreatitis bacterium (NHP) in zooplankton samples from the Gulf of California was confirmed by qPCR and DNA sequences analysis. Samples of zooplankton were collected from stations located on the eastern shore of the Gulf of California, an area adjacent geographically to the coast of Sonora, Mexico. Three zooplankton samples (NHP S3, S23 and S24) were detected. These samples were collected in Bahía de Agiabampo and Bahía de Guasimas, an area distributed along the length of the coast in the vicinity of a shrimp farm area. These results clearly indicate that NHP-B may be associated or colonizing zooplankton, which may serve as a potential vector of potential importance in the spread of this disease. The biological meaning of this finding is discussed.

A new species of deep water Epimeria is described based on material collected in 1526–1586 m depth during the TALUD X expedition in the central Gulf of California, Mexico. It is the sixth species of this genus reported for the East Pacific. Epimeria morronei sp. nov. is morphologically similar to E. norfanzi Lörz, 2011 (New Zealand, 1268 m depth) and E. cora J.L. Barnard, 1971 (off Oregon, USA, 2086 m depth). Epimeria morronei sp. nov., however, differs from these two species by a combination of several characters, including: vestigial eyes; multidentate mandibular lacinia mobilis; a distinct setae arrangement in palm and dactylus of gnathopods 1–2; the shape and relative size of coxae 1–5; and the shape of the telson.