Genetic structure and gene flow in an endangered native tilapia fish (Oreochromis esculentus) compared to invasive Nile tilapia (Oreochromis niloticus) in Yala swamp, East Africa

The introduction of invasive Nile tilapia (Oreochromis niloticus), and the rapacious predator Nile perch (Lates niloticus), into Lake Victoria resulted in a decline in population sizes, genetic diversity and even extirpation of native species which were previously the mainstay of local fisheries. However, remnant populations of native fish species, including tilapia, still persist in satellite lakes around Lake Victoria where they may coexist with O. niloticus. In this study we assessed population genetic structure, diversity, and integrity of the native critically endangered Singidia tilapia (O. esculentus) in its refugial populations in the Yala swamp, Kenya, and contrasted this diversity with populations of the invasive tilapia O. niloticus in satellite lakes (Kanyaboli, Namboyo and Sare) and Lake Victoria. Based on mtDNA control region sequences and eight nuclear microsatellite loci, we did not detect any mtDNA introgression between the native and the invasive species in Lakes Kanyaboli and Namboyo, but did find low levels of nuclear admixture, primarily from O. niloticus to O. esculentus. Some genetic signal of O. esculentus in O. niloticus was found in Lake Sare, where O. esculentus is not found, suggesting it has recently been extirpated by the O. niloticus invasion. In both species, populations in the satellite lakes are significantly genetically isolated from each other, with private mtDNA haplotypes and microsatellite alleles. For O. niloticus, genetic diversity in satellite lakes was similar to that found in Lake Victoria. Our data imply a low frequency of immigration exchange between the two populations of O. esculentus and we suggest that the populations of this endangered species and important fisheries resource should be conserved separately in Lakes Kanyaboli and Namboyo and with high priority.     

Identifications of Captive and Wild Tilapia Species Existing in Hawaii by Mitochondrial DNA Control Region Sequence

Background

The tilapia family of the Cichlidae includes many fish species, which live in freshwater and saltwater environments. Several species, such as O. niloticus, O. aureus, and O. mossambicus, are excellent for aquaculture because these fish are easily reproduced and readily adapt to diverse environments. Historically, tilapia species, including O. mossambicus, S. melanotheron, and O. aureus, were introduced to Hawaii many decades ago, and the state of Hawaii uses the import permit policy to prevent O. niloticus from coming into the islands. However, hybrids produced from O. niloticus may already be present in the freshwater and marine environments of the islands. The purpose of this study was to identify tilapia species that exist in Hawaii using mitochondrial DNA analysis.

Methodology/Principal Findings

In this study, we analyzed 382 samples collected from 13 farm (captive) and wild tilapia populations in Oahu and the Hawaii Islands. Comparison of intraspecies variation between the mitochondrial DNA control region (mtDNA CR) and cytochrome c oxidase I (COI) gene from five populations indicated that mtDNA CR had higher nucleotide diversity than COI. A phylogenetic tree of all sampled tilapia was generated using mtDNA CR sequences. The neighbor-joining tree analysis identified seven distinctive tilapia species: O. aureus, O. mossambicus, O. niloticus, S. melanotheron, O. urolepies, T. redalli, and a hybrid of O. massambicus and O. niloticus. Of all the populations examined, 10 populations consisting of O. aureus, O. mossambicus, O. urolepis, and O. niloticus from the farmed sites were relatively pure, whereas three wild populations showed some degree of introgression and hybridization.

Conclusions/Significance

This DNA-based tilapia species identification is the first report that confirmed tilapia species identities in the wild and captive populations in Hawaii. The DNA sequence comparisons of mtDNA CR appear to be a valid method for tilapia species identification. The suspected tilapia hybrids that consist of O. niloticus are present in captive and wild populations in Hawaii.     

SNP marker detection and genotyping in tilapia

We have generated a unique resource consisting of nearly 175 000 short contig sequences and 3569 SNP markers from the widely cultured GIFT (Genetically Improved Farmed Tilapia) strain of Nile tilapia (Oreochromis niloticus). In total, 384 SNPs were selected to monitor the wider applicability of the SNPs by genotyping tilapia individuals from different strains and different geographical locations. In all strains and species tested (O. niloticus, O. aureus and O. mossambicus), the genotyping assay was working for a similar number of SNPs (288–305 SNPs). The actual number of polymorphic SNPs was, as expected, highest for individuals from the GIFT population (255 SNPs). In the individuals from an Egyptian strain and in individuals caught in the wild in the basin of the river Volta, 197 and 163 SNPs were polymorphic, respectively. A pairwise calculation of Nei’s genetic distance allowed the discrimination of the individual strains and species based on the genotypes determined with the SNP set. We expect that this set will be widely applicable for use in tilapia aquaculture, e.g. for pedigree reconstruction. In addition, this set is currently used for assaying the genetic diversity of native Nile tilapia in areas where tilapia is, or will be, introduced in aquaculture projects. This allows the tracing of escapees from aquaculture and the monitoring of effects of introgression and hybridization.     

Trophic Niche Segregation in the Nilotic Ichthyofauna of Lake Albert (Uganda, Africa)

Synopsis Nile perch, Lates niloticus, and Nile tilapia, Oreochromis niloticus, were originally transplanted from Lake Albert in western Uganda to the African Great Lakes, Lake Victoria and Lake Kyoga, where they are partially implicated in reduction of the fish species diversity. Lake Albert is facing multiple environmental changes, including declining fish species diversity, hyper-eutrophication, hypoxia, and reduced fish catches. To examine the role of Nile perch and Nile tilapia in the food web in their native Lake Albert, we estimated their diets using stable nitrogen and carbon isotopes. In Lake Albert, the tilapiine congeners (closely related species), Tilapia zillii, Oreochromis leucostictus, and Sarethorodon galilaeus, and the centropomid Nile perch congener, Lates macrophthalmus, have narrower diet breath in the presence of the native O. niloticus and L. niloticus. A computerized parameter search of dietary items for five commercially important fish species (Hydrocynus forskahlii, Bagrus bayad, L. niloticus, Alestes baremose and Brycinus nurse) was completed using a static isotopic mixing model. The outcome of the simulation for most fish species compared favorably to previously published stomach contents data for the Lake Albert fishes dating back to 1928, demonstrating agreement between stable isotope values and analyses of stomach contents. While there were some indications of changes in the diets of L. niloticus and A. baremose diets over the past 20 years in parallel with other changes in the lake, for the most part, food web structure in this lake remained stable since 1928. The Lake Albert fish assemblage provides insight into the invasion success of L. niloticus and O. niloticus.     

First records of Ambiphrya and Vorticella spp. (Protozoa,Ciliophora) in cultured Nile tilapia (Oreochromis niloticus) in the central region of Saudi Arabia

The present study was carried out as part of an ongoing general survey seeking to uncover protozoan parasites infecting cultured tilapia in the central region of Saudi Arabia. In the sample of 400 specimens of tilapia (Oreochromis niloticus) 30 were infested with Ambiphrya ameiuri simultaneously with Vorticella sp. Morphometric criteria were used to describe and identify these species and this study presents the first records of these species among cultured fish in Saudi Arabia.     

Shifts in the food of Nile tilapia, Oreochromis niloticus (L.) in Lake Victoria, Kenya

Studies of the food of introduced Nile tilapia, Oreochromis niloticus (L.) with respect to size, habitat and season were conducted between November 1998 and October 2000 in Kenyan waters of Lake Victoria. Stomach contents of 1980 specimens collected by demersal trawl and seining were analysed. Nile tilapia originally known to be herbivorous, feeding mostly on algae has diversified its diet to include insects, fish, algae and plant materials. The major diet of fish <5 cm total length was zooplankton whereas bigger fish included a wider range of food items in their diet. There was spatial variation in diet with insects and algae dominating in the gulf and open water habitats respectively. There was no seasonal variation in the food items ingested and diel feeding regime indicated that O. niloticus is a diurnal feeder. The shift in diet could be due to ecological and environmental changes in Lake Victoria, which have been associated with changes in composition and diversity of fish and invertebrate fauna, emergence and dominance of different flora including water hyacinth Eichhornia crassipes (Mart.) Solms‐Laub., and algae communities. The feeding habit of O. niloticus is discussed in the context of changes occurring in the lake.     

Utility of DNA barcoding in native Oreochromis species

The importance of Oreochromis in worldwide aquaculture and regional fisheries motivates the study of their genetic diversity in their native range. In this article, all mitochondrial cytochrome c oxidase subunit I gene (COI) sequences of Oreochromis species are retrieved from Barcode of Life Data system to quantify the available DNA barcoding information from wild individuals collected within the native ranges of the respective species. It is found that 70% of the known species in the genus still lack a COI barcode, and only 15% of the available sequences are from within the respective native ranges. Many of the available sequences have been produced from specimens acquired from aquaculture and introduced, naturalized populations, making the assessment of variation within the original native range challenging. Analyses of the wild-collected fraction of available sequences indicated the presence of cryptic lineages within Nile tilapia Oreochromis niloticus and O. schwebischi, the occurrence of potential introgressive hybridization between O. niloticus and blue tilapia O. aureus, and potential ancestral polymorphism between Karonga tilapia O. karongae and black tilapia O. placidus. This article also reports a case of misidentification of O. mweruensis as longfin tilapia O. macrochir. These results stress the importance of improving the knowledge of genetic variation within the native ranges of Oreochromis species for better-informed conservation of these natural resources.     

Analysis of VNTR loci in fish genomes using synthetic oligodeoxyribonucleotide probes

A set of synthetic oligodeoxyribonucleotide (oligo) probes, OAT18, OMS1 and OAT24 carrying the (TGG)₆, (GGAT)₄ and (GACA)₆ repeat motifs, respectively, was used to analyze the variable number tandem repeat (VNTR) loci in the genomes of Oncorhyncus mykiss (rainbow trout; family Salmonidae), Oreochromis mossambicus and Oreochromis niloticus (both tilapia belonging to family Cichlidae). Of all the oligos and enzymes (AluI, MboI, HaeIII and HinfI) used, the OAT18/HaeIII combination was found to be most informative for detecting DNA fingerprinting in rainbow trout, while the OMS1/MboI combination gave the most informative pattern for the Or. niloticus genome. In the rainbow trout genome, all three repeat loci were hypervariable, revealing varying degrees of polymorphism as compared to tilapia genomes. Startlingly, the OAT24 probe did not cross-hybridize with Or. mossambicus and lamprey salmon (Lampetra japonica) although GACA repeats have been reported to be evolutionarily conserved in all eukaryotes studied thus far. Cluster analysis with respect to GGAT repeat loci revealed that Or. niloticus diverged from Or. mossambicus before the separation of On. mykiss, suggesting the relatively recent evolution of these loci in rainbow trout, compared to the tilapia genomes. These highly informative probes will find application in various genetic studies of fishes.     

五个红罗非鱼群体的遗传多样性分析

实验采用微卫星标记技术,选用22对微卫星引物对5个红罗非鱼群体进行遗传多样性分析。经PCR扩增,16个微卫星位点扩增产物在关岛红罗非鱼（GD）、珍珠白红罗非鱼（ZZ）、佛罗里达红罗非鱼（FL）、明月红罗非鱼（MY）、马来西亚红罗非鱼（ML）中均获得了清晰稳定的条带。分析结果显示:16个微卫星标记共检测到146个等位基因。5个群体的平均等位基因数（N_a）在6.5625-8.5625,平均有效等位基因数（N_e）在4.1495-6.1330,平均杂合度（H_e）在0.7491-0.8247,平均多态信息含量（PIC）在0.6939-0.7840,说明它们的遗传多态性丰富。卡方检验表明5个红罗非鱼群体的大部分位点偏离Hardy-Weinberg平衡。在5个群体中,关岛红罗非鱼（GD）与珍珠白红罗非鱼（ZZ）遗传相似系数（0.6171）最小,遗传距离（0.4827）最大,说明两者亲缘关系最远;佛罗里达红罗非鱼（FL）与马来西亚红罗非鱼（ML）遗传相似系数（0.9069）最大,遗传距离（0.0977）最小,可推断两者亲缘关系最近。采用UPGMA进行聚类分析,结果表明:佛罗里达与马来西亚先聚成一支,二者再与珍珠白聚在一起,接着三者与明月聚在一起,最后,四者与关岛聚到一起。聚类结果说明关岛群体与其他4个群体亲缘关系最远;佛罗里达与马来西亚亲缘关系最近,珍珠白群体次之,明月群体再次之。以上结果可推断5个红罗非鱼群体遗传多态性丰富,具有较大的选育潜力。     

Diel vertical migration of major fish-species in Lake Victoria, East Africa

Understanding of migration patterns is essential in the interpretation of hydro-acoustic stock assessment data of partly demersal partly pelagic fish stocks. In this paper we provide this kind of information for some species that were common in the Mwanza Gulf of Lake Victoria in the 1980s, before and after the upsurge of introduced Nile perch (Lates niloticus). Detritivorous haplochromines and Nile tilapia (Oreochromis niloticus), both stay near the bottom during day and night. Feeding seems to occur predominantly during the day. The zooplanktivorous haplochromines and dagaa (Rastrineobola argentea) dwell near the bottom by day and migrate towards the surface during the night. They seem to follow their prey, zooplankton and lake-fly larvae. Piscivorous nembe (Schilbe intermedius) show similar migration patterns to zooplanktivorous fishes, but their behaviour cannot be unambiguously explained by pursuit of prey. Nile perch to some extend migrate into the column at night, though the majority remains near the bottom. Feeding takes place during day and night.     

A place preference test in the fish Nile tilapia

The Nile tilapia fish (Oreochromis niloticus) has a high potential to be used as a model in neuroscience studies. In the present study, the preference of the Nile tilapia between a gravel-enriched (GEE), a shelter-enriched (SEE) or a non-enriched (NEE) environment was determined, for developing a place preference model. Nile tilapia had an initial preference for GEE, but after 1 day of observation, the fish stabilized their frequency of visits among compartments. Hence, any stimulus motivating tilapia increase in compartment visiting indicates a positively reinforcing effect. This feature is very useful for the development of new behavioural paradigms for fish in tests using environmental discrimination, such as the conditioning place preference test.     

Comparative age and growth of Nile tilapia (<Emphasis Type="Italic">Oreochromis niloticus</Emphasis> L.) in lakes Nabugabo and Wamala,Uganda

Age and growth of Nile tilapia (Oreochromis niloticus) from Lake Nabugabo and Lake Wamala, Uganda, were determined using cross-sectioned sagittal otoliths. Marginal-increment and edge analyses of Nile tilapia otoliths from Lake Nabugabo indicated formation of two annuli per 12-month period. Opaque zones associated with faster growth were observed between April and June and between September and December, coincident with the two rainy seasons of the year. Within both lakes, males were larger at age than females. Nile tilapia from Lake Nabugabo, however, had faster growth rates than Nile tilapia from Lake Wamala, and fish >3 years old from Lake Nabugabo were larger at age than those from Lake Wamala. Ages ranged from 0 to 8.0 years for Nile tilapia from Lake Nabugabo, and from 0.5 to 6.5 years for tilapia from Lake Wamala. Differences in the patterns of growth in Nile tilapia between lakes may reflect, at least in part, the relatively energy-rich omnivorous diet of Nile tilapia in Lake Nabugabo versus a phytoplanktivorous diet in Lake Wamala. Diet differences of Nile tilapia between the two lakes are ascribed to trophic changes in the lakes due to the introduction of Nile perch (Lates niloticus) into Lake Nabugabo but not Lake Wamala. Alternatively, the greater exploitation of Nile tilapia in Lake Nabugabo may have resulted in increased growth rates, whereas Nile tilapia in Lake Wamala may be subject to slower, density-dependent growth. Handling editor: J. Cambray     

Mitotic chromosomal abnormalities and DNA polymorphism in the Nile tilapia (Oreochromis niloticus,Linnaeus, 1758) as a biomarker for water pollution by heavy metals

Mitotic chromosomal aberrations and DNA polymorphism (RAPD marker) were carried out on the Nile tilapia Oreochromis niloticus collected from five sites in Minia governorate, Egypt to test their applicability as biomonitors for heavy metal contaminants of water. The diploid chromosome number of O. niloticus population was 2 n = 44. Different types of chromosomal aberrations were recorded (e.g., deletion, ring, centromeric attenuation, end-to-end association, dicentric chromosome, stickiness chromosomes, endomitosis, fragments and chromatid gap). The chromosomal aberrations varied between O. niloticus population collected from five sites, and the most common type was ring (R) chromosomes. Samples obtained from Bahr Yousef and Irrigation drain exhibited the highest aberration frequency. The frequency of chromosomal aberration was positively correlated with the concentration of heavy metals where their concentration in the surface water of Irrigation drain and Bahr Yousef exceeded the limits defined by WHO as well as the concentration of Pb in muscles. The RAPD marker was also used to identify genetic variation among Nile tilapia samples collected from five different water sources. It created polymorphic and unique bands that can be used as genetic markers to track DNA variations. The dendrogram also revealed that exposure to heavy metal pollution causes gradual accumulation of variance, whereas areas subjected to environmental stress showed higher genetic variation and clustered together.     

Genetic diversity and population structure of Chrysichthys nigrodigitatus from Niger Delta based on AFLP analysis

The silver catfish, Chrysichthys nigrodigitatus is an important food fish in the Niger Delta. To understand the genetic variations and population structure in Nigeria’s Niger Delta, eighty-eight individuals collected from 7 locations were analyzed based on amplified fragment length polymorphism (AFLP) analysis. A total of 243 bands were identified using 4 AFLP primer combinations. The average gene diversity was 0.1708 ± 0.1547 and Shannon’s information index was 0.2792 ± 0.2224. The pairwise F_st values ranged from 0.133 to 0.796. The results of AMOVA analysis indicated that 19.03% of the genetic variation was contained among three groups. The gene flow estimates (Nm) demonstrated that different degrees of gene flow existed among populations ranging from 0.064 to 1.630. Two clades were recognized on the UPGMA tree. The results supported that freshwater or brackishwater habitat, limited long-distance dispersal of the adult and juveniles and physical barriers may be responsible for the current genetic structure.     

Genetic diversity and geographic distribution of variation of Hordeum murinum as revealed by retroelement insertional polymorphisms in Iran

Hordem murinum is a widespread weedy/wild species, growing in different ecological conditions in Iran. Populations of H. murinum subsp. glaucum (2n = 2x = 14) and subsp. leporinum (2n = 4x, 6x = 28, 42) are found in this region. Inter-retroelement amplified polymorphism (IRAP) markers were used to analyse the genetic diversity of 57 accessions of H. murinum from different regions of Iran, and to examine patterns of diversity related to the taxonomy and geography. Eight IRAP primer combinations amplified a total of 241 distinct DNA fragments sized 150-1400 bp, from which 236 (97.9%) were polymorphic. On average, each primer combination amplified about 30.12 fragments (ranged from 23 to 34) in PCR. The patterns of genetic diversity were closely correlated with taxonomic groups, ploidy levels and geographic origin. Along with the high genetic diversity, three geographic sub-genepools were evident, 1: in the North-Northeast region along the Alborz Mountains, 2: in the West-Northwest region along the Zagros Mountains, and 3: in the Central — Southern region. The genetic diversity in diploids was higher than polyploids. Also genetic diversity in W-NW region along the Zagros Mountains was considerably higher than that of the other regions.     

Interactions between Nile tilapia (Oreochromis niloticus) and cladocerans in ponds (Khartoum,Sudan)

Juvenile Nile tilapia (Oreochromis niloticus) are omnivorous, and the question asked in this study is how they affect on their environment? Do they mainly act as predators on the cladoceran zooplankton or do they compete with the cladocerans for phytoplankton? This problem was studied in three ponds with and three ponds without small tilapia (3–5 cm). The fish growth rate, the succession of plankton species and the changes in abiotic conditions, were monitored over a period of 67 days. The fish biomass was kept low and the mean was approximately constant (12.6 g m^?2) during the experiment. Phosphate was added to avoid phytoplankton nutrient limitation. Although the diet of Nile tilapia contained both phytoplankton and zooplankton, the fish affected the ecosystem in a similar way as zooplanktivorous fish. The fish ponds got more phytoplankton due to increase of Chlorophyta. Effects on the other phytoplankton groups Euglenophyta, Bacillariophyta, Cryptophyta and Cyanophyta could not be registered. The ponds without fish had higher densities of Daphnia lumholtzi and D. barbata. The other Cladocerans seemed less influenced by fish presence. The relative fish growth rate was most positively correlated with the density of Daphnia lumholtzi, Diaphanosmoa excisum and Bosmina longirostris. Tilapia seemes to have two feeding modes: (1) preying on large zooplankton and (2) unselective filtration of small planktonic organisms such as phytoplankton. In our experiment the first feeding mode affected the ecosystem more than the second.     

Evaluation of copper, lead and arsenic level in tilapia fish in Cempaka Lake (Bangi, Malaysia) and human daily/weekly intake

In recent years, many studies have stated the nutritional benefits of fish consumption: vitamins, proteins and omega-3 fatty acids, which may protect humans from adverse health effects, including heart disease and stroke. This study aimed to evaluate the concentration of Cu, Pb and As in the liver, gills and muscles of tilapia fish (Oreochromis niloticus) and to calculate the weekly intake from eating tilapia collected from Cempaka Lake, Selangor — Peninsular Malaysia during the period between April 2009 to February 2010. The elemental concentrations were determined using inductively — coupled plasma mass spectrometry (ICP-MS). The results showed that all heavy metal concentrations were significantly different among fish organs, and between calendar months. The data showed that Cu levels in liver, gills and muscles were 491.30, 3.70 and 1.82 μg/g dry weight (dw), respectively. Meanwhile Pb levels were 2.71, 1.04 and 0.48 μg/g dw, respectively and As levels were 6.26, 4.18 and 1.79 μg/g dw, respectively. Significant changes occurred in Cu, Pb and As levels in tilapia fish organs in Cempaka Lake over the period of 11 months. Tilapia weekly intake was calculated based on mean Cu, Pb and As concentrations in the muscle of tilapia fish and adult consumption of tilapia in Malaysia which averages at 160 grams per day. Furthermore, tilapia weekly and daily human intakes for Cu, Pb and As were compared with the Provisional Tolerable Weekly Intake (PTWI) established by the JECFA (WHO/FAO) presenting values below the PTWI. Metal levels in fish muscle were found to be lower than the maximum permitted concentrations recommended by various authorities; hence, consumption of tilapia fish from Cempaka Lake is currently safe for humans.     

Establishment and application of a microsatellite-based parentage identification method for Oreochromis niloticus,O. aureus,and O. niloticus × O. aureus

In genetic fish breeding research, clear pedigree information is of great significance for breeding and parental management. In order to establish a stable, highly accurate, and widely applicable parentage identification method for tilapia, 13 highly polymorphic microsatellite loci within populations of Oreochromis niloticus, O. aureus, O. niloticus × O. aureus, and their mixed population were screened. Four groups of fluorescent-labeled multiple capillary electrophoresis were established for allelic genotyping. The assignment success rate reached 100% when 7, 9, 8 and 12 loci were used in the population of O. niloticus, O. aureus, O. niloticus × O. aureus, and their mixed population, respectively. All 175 progeny individuals of “Yuemin No. 1” tilapia were exclusively assigned to their parental pairs when the 12 loci for the mixed population were used. This study established a fluorescent-labeled microsatellite-based parentage assignment method for O. niloticus, O. aureus, O. niloticus × O. aureus, and their mixed population with high identification accuracy and efficiency, which lays a foundation for pedigree information and population genetic management in tilapia breeding.     

Allozyme and RAPD polymorphism in Tylophora indica (Burm.f.) Merr.

Tylophora indica (Burm.f.) Merr (syn. T. asthmatica), is being indiscriminately collected for medicinal use which is not sustainable. Conservation of the species requires information on existing genetic content and its distribution in different populations. In the present study, polymorphism in allozyme and RAPD profiles of five populations were analysed using six enzyme systems and ten random primers. Genetic content in terms of allozymes and RAPDs as revealed by Shannon-Weiner index was more or less same in all the populations. Evenness as calculated from observed diversity (Shannon-Weiner index, H’) and the maximum expected diversity (H^max) for the allozymes and RAPDs was high for individual populations indicating that the distribution of genetic content was fairly uniform. From the results, it was concluded that collection of few genotypes from geographically distinct locations rather than intensive collection within one or two locations would be representative of the genetic variability present in this species.