**3. Environmental impacts and risks for Neotropical fish**

Neotropical fish are currently being threatened by anthropogenic activities that are showing visible effects on freshwater ecosystems. These effects are related to overfishing; non-native species introduction; dam construction for hydropower; river contamination from mining activities; and industrial and agricultural pollution and deforestation [45].

In Neotropical areas, the limits of exploitation of the majority of commercially valued fish stocks are close to the maximum sustainable yield [46]. Aquaculture would indirectly alleviate pressures on threatened wild stocks and, therefore, needs to be carried out in a sustainable way with the least possible impact on natural populations [47]. In 2015, of the 25 countries with the highest production from aquaculture (97.1% of total production), three Neotropical countries were included (Chile, Brazil and Ecuador). Moreover, with regard to freshwater aquaculture, Brazil leads this ranking, producing 474,300 tons, followed by Chile producing around 68.7 tons and Ecuador 28.2 tons [48].

In 2016, according to IBGE (Brazilian Institute of Geography and Statistics) data, Brazilian aquaculture had continued to grow and reached a total of 580,000 tons, with a production value of R\$ 4.2 billion. A total of 77.32% of this production originated from fish farms followed by shrimp farms (21.5%). The development of farming technologies directed at the native species has helped to accelerate fish production, and relieve the pressure exerted by extractive fisheries.

Despite the advantages of aquaculture, uncontrolled fish production and lack of proper inspection by government agencies can be problematic for the Neotropical ichthyofauna. Uncontrolled hybridisation of fish, introduction of non-native species and loading of excess nutrients originating from effluents from aquaculture production can become a serious threat to wild fish populations.

Currently, the production of fish hybrids involves many Neotropical species resulting in viable products of high interest for farmers [49]. Nevertheless, the main threat caused by hybridisation is the genetic introgression on wild populations [50, 51]. If fertile, hybrids can genetically contaminate natural and farmed stocks by genetic homogeneisation and compete with the native parental lineages (in sexual behaviour, territory, food, etc.) [52].

Brazil plays an important role in the conservation of its rich diversity of Neotropical fish. However, policy initiatives have threatened the biodiversity of these species and the functioning of their ecosystems. In some countries, there is specific legislation for hybridisation (in contrast to the Brazilian legislation, which does not require a licence for hybrid production); for example, in the state of California, there are laws prohibiting unlicensed fish hybridisation [53]. In Brazil, most commercial establishments are unlicensed, and there are few legislative proposals to regulate the activity [54]. According to Hashimoto et al., legislation is necessary to guarantee the safety of hybridisation techniques used in Brazil [55].

There is a particularly high concentration of hydroelectric dams in the Upper Paraná and São Francisco rivers (many of the rivers in South America are so heavily dammed they become a chain of reservoirs) [6]. The largest dams in Latin America are Itaipu (Paraná River, Paraguay-Brazil), Guri (Rio Caroni, Venezuela), Tucuruí (Rio Tocantins, Brazil) and Yacyretá (Paraná River, Argentina-Brazil). Currently, 90% of the energy consumed in Brazil originates from hydroelectric plants, with an annual output of 78,000 MW [6]. Dams have been built in almost all hydrographic basins with consequent formation of reservoirs. These reservoirs alter the natural distribution of seasonal flows and nutrients, leading to the formation of new ecosystems with specific structures and functioning [56]. These new ecosystems have several factors that affect the local ichthyofauna have a serious impact on the life cycle of the fish [57]. Dams act as barriers to the natural flow of rivers. They are built mainly to produce electricity, but also to supply water to residential, agricultural and industrial areas. The change and/or loss in water flow impacts the distribution of aquatic life biodiversity [58]. Dams also affect the watershed and lower the water quality, impacting not only the river itself but also its tributaries. This may also be harmful to native species by destabilising the ecosystem and the living communities [57]. For example, migratory fish suffer due to the interruption to their migratory routes and require a different habitat to complete their life cycle. These species generally migrate upstream to spawn during the wet season producing numerous small eggs. These eggs and larvae are transported with the current to nurseries downstream without any parental care, where they find ideal conditions for initial development and protection from predators [59, 60]. The consequences of blocking migratory fish routes is observed in their reproductive cycle for years, leading to the depletion of natural stocks and extinction of the species [61].

due to environmental conditions. For example, the "traíra" (*Hoplias malabaricus*), which has the ability to reproduce throughout the year or to follow a defined seasonal cycle depending

Neotropical fish are currently being threatened by anthropogenic activities that are showing visible effects on freshwater ecosystems. These effects are related to overfishing; non-native species introduction; dam construction for hydropower; river contamination from mining

In Neotropical areas, the limits of exploitation of the majority of commercially valued fish stocks are close to the maximum sustainable yield [46]. Aquaculture would indirectly alleviate pressures on threatened wild stocks and, therefore, needs to be carried out in a sustainable way with the least possible impact on natural populations [47]. In 2015, of the 25 countries with the highest production from aquaculture (97.1% of total production), three Neotropical countries were included (Chile, Brazil and Ecuador). Moreover, with regard to freshwater aquaculture, Brazil leads this ranking, producing 474,300 tons, followed by Chile producing

In 2016, according to IBGE (Brazilian Institute of Geography and Statistics) data, Brazilian aquaculture had continued to grow and reached a total of 580,000 tons, with a production value of R\$ 4.2 billion. A total of 77.32% of this production originated from fish farms followed by shrimp farms (21.5%). The development of farming technologies directed at the native species has helped to accelerate fish production, and relieve the pressure exerted by extractive fisheries. Despite the advantages of aquaculture, uncontrolled fish production and lack of proper inspection by government agencies can be problematic for the Neotropical ichthyofauna. Uncontrolled hybridisation of fish, introduction of non-native species and loading of excess nutrients originating from effluents from aquaculture production can become a serious threat

Currently, the production of fish hybrids involves many Neotropical species resulting in viable products of high interest for farmers [49]. Nevertheless, the main threat caused by hybridisation is the genetic introgression on wild populations [50, 51]. If fertile, hybrids can genetically contaminate natural and farmed stocks by genetic homogeneisation and compete

Brazil plays an important role in the conservation of its rich diversity of Neotropical fish. However, policy initiatives have threatened the biodiversity of these species and the functioning of their ecosystems. In some countries, there is specific legislation for hybridisation (in contrast to the Brazilian legislation, which does not require a licence for hybrid production); for example, in the state of California, there are laws prohibiting unlicensed fish hybridisation [53]. In Brazil, most commercial establishments are unlicensed, and there are few legislative proposals to regulate the activity [54]. According to Hashimoto et al., legislation is necessary

with the native parental lineages (in sexual behaviour, territory, food, etc.) [52].

to guarantee the safety of hybridisation techniques used in Brazil [55].

**3. Environmental impacts and risks for Neotropical fish**

activities; and industrial and agricultural pollution and deforestation [45].

on their environment [21].

254 Biological Resources of Water

around 68.7 tons and Ecuador 28.2 tons [48].

to wild fish populations.

The new ecosystem formed modifies the structure of fish communities that inhabit the river, and the establishment of new communities depends on the physical, chemical, hydrological and geomorphological changes as a result of the spatial and temporal redistribution of the river flow [62–65]. Changes in species composition and abundance can increase the numbers of some species and eliminate others, causing collapse of the ecosystem [66].

In order to mitigate such effects, management measures have been put in place to preserve the Neotropical ichthyofauna [67]. Until the 1950s, the main objective of management programmes was to ensure that species could migrate through the reservoirs to complete their life cycle. Transposition mechanisms (fish ladders) were created in the main Brazilian dams. In the 1990s, dozens of fish transposition systems were constructed, even with few studies into the efficacy of the method and despite the costs and effort required [68]. Most of these mechanisms are based on ladders, structures that reduce the velocity and gradient of the water so that fish can climb and pass through the dam [21].

However, these mechanisms have species selectivity and allow the movement of only some species of fish. This divergence between species can cause dramatic imbalances in the population and the Neotropical ecosystem [59]. The main process of passage is recognition of the entrance [69]. If the fish cannot recognise the entrance to the passage, they remain where they are, which delays migration and spawning and interferes significantly with their reproductive process [70].

Storage and repopulation of fish are alternative methods to mitigate the impacts of hydroelectric dams [57]. Several breeding programmes were implemented aimed at the production of fish to restock the reservoirs, mainly to improve fishing activities. Some non-native species were introduced to southern and southeastern regions of Brazil over 20 years (1970–1990) due to the difficulty of producing native species [71], a trend that has declined in recent years, though it still exists [21]. Hydroelectric companies have begun to produce native species for restocking (repopulation), but for this to be successful, evaluation of the efficiency and genetic quality of the parents is essential [21, 72]. In repopulation programmes, genetic monitoring is a fundamental step, since a reduction in genetic variability reduces the adaptability of the species to different environmental conditions and interferes significantly with the survival of young fish [66, 73]. The use of molecular markers has been shown to be effective for genetic management in order to maximise diversity and reduce inbreeding in the repopulation centres [67, 68, 74].

spreading across the Atlantic coast [85, 86]. This affected the ichthyofauna by fragmentation and destruction of habitats, water contamination, change in water flow, impact on estuaries and mangroves at the mouth of the River Doce [87], destruction of fish breeding areas, destruction of the nurseries of the ichthyofauna (feeding areas for larvae and juveniles), disruption of the gene flow between different areas, loss of species with habitat specificity and collapse of

Genetic Applications in the Conservation of Neotropical Freshwater Fish

http://dx.doi.org/10.5772/intechopen.73207

257

Genetic tools are important resources for the conservation of Neotropical fish species. The biology and population dynamics of the species are still unknown due to insufficient research. In spite of the high diversity that characterises Neotropical fish, there are many species with a large geographical distribution and differing population structure. Along a hydrographic basin, one can find many populations, from panmictic populations of long-distance migratory species, characterised by large gene flow, to restricted populations of local organisms with well-defined population structures [88]. Research into the verification of variability and genetic structure of populations belonging to different river basins will aid the construction of policies and management measures for the maintenance of natural populations. In addition, genetic tools are increasingly being used to molecularly identify new species that was previously impossible due to morphological similarities. Furthermore, various anthropogenic activities in aquaculture and pollution have been increasingly studied at the molecular level,

particularly with respect to research into hybrid fish and the effects of contaminants.

adapt to environmental changes and anthropogenic activities [90].

Biodiversity is conceptualised into distinct biological levels (genetic, species, community and ecosystem) that have each been impacted by human activities. The impact on genetic diversity is one of the biggest concerns, affecting species adaptation and taxa speciation [89, 90]. Knowledge of how the genetic diversity of Neotropical fish is maintained and how the populations are structured is important to determine how these species can be conserved. Many species of freshwater fish display genetic variation with adaptive traits that enhance survival and reproduction in particular environments and increase the capability of the organisms to

Genetic variability in populations can be measured by the allele number and heterozygosity [91]. Intrapopulation variability is influenced by factors such as mutation, genetic drift and natural selection. Genetic variation originates from mutations and decreases in genetic drift that increases the interpopulation differentiation due to a finite population size, with gene flow occurring between populations [92]. Conversely, natural selection can reduce genetic variation by allele fixation [93]. Anthropogenic activities, such as habitat fragmentation, increase the risks of genetic drift and gene flow reduction, diminishing the genetic variability of populations and interrupting flow of the adaptive genes leading to extinction of some species [90]. Molecular genetic markers have emerged as a powerful tool to identify genetic variability in populations [94] and have had a substantial impact on the fields of ecology,

fish stocks [85].

**4. Genetic applications**

evolution and conservation [95].

Aquatic organisms are fragile and sensitive to a wide range of stressors. Reproduction, growth and population survival are highly dependent on water quality. Environmental pollutants such as metals and pesticides present a serious risk to local ichthyofauna. The physiological effects of toxicants include disruption of hormonal, neurological and metabolic systems and elimination of behaviours that are essential to fitness and survival in natural ecosystems [75]. Studies into many Neotropical fish have corroborated this. *Prochilodus lineatus* subjected to 7 days of *in-situ* tests in a contaminated urban stream suffered a series of epithelial lesions, lamellar fusion and aneurysms in the gills [76]. Another study carried out with *Rhamdia quelen* exposed to herbicides (Roundup® Original, Primoleo® and Facet®) showed harmful effects in the gills, liver, kidneys and muscle [77]. *A. altiparanae* and *P. lineatus* exposed to biodegradable detergents in an urban lake showed various changes in gill function such as lamellar fusions, aneurysms, mucous and chlorine cell proliferation [78]. A study involving *A. altiparanae* showed that the level if DNA breaks was most sensitive biomarker to contamination with pesticides [79]. *P. lineatus* showed nickel accumulation in different tissues (kidneys, liver, gills and muscle) with DNA damage [80].

Mining activities impact the aquatic ecosystem in the basins of Upper Paraguay and in the Colombian, Brazilian and Peruvian Amazon [6]. Mercury, the main compound released during gold mining, accumulates in the sediment and in the muscle and tissues of fish (bioaccumulation). This means that through the trophic chain, the predators that are high in the food chain tend to accumulate more metals (biomagnification). Fish in the rivers of Madre de Dios city (Perú), affected by illegal mining, revealed that the species *Calophysus macropterus*, *Pseudoplatystoma punctifer*, *P. fasciatum*, *H. malabaricus*, *Prochilodus nigricans*, *Hydrolycus pectoralis*, *Plagioscion squamosissimus* and *Zungaro zungaro* showed high levels of mercury accumulation in tissues that exceeded the maximum limit permitted by the World Health Organisation (500 μgHg/kg) [81]. The same was found in the Upper Pantanal (Brazil), in the Poconé and Nossa Senhora do Livramento regions (Upper Paraguay River), where piscivorous or detritivorous species such as *Pimelodus muculatus*, *P. fasciatum*, *P. lineatus*, *Salminus maxillosus*, *P. corruscans*, *Acestrorhynchus altus*, *Serrasalmus nattereri* and *H. malabaricus* also had high levels of mercury [82, 83]. Other metals that accumulate in fish organs are nickel and copper [80, 84], causing significant damage to the fish species and its consumers.

Mining can also lead to the collapse of dams, as occurred in Mariana city (Minas Gerais state, Brazil) in 2015 that was considered the biggest environmental disaster in Brazil that released approximately 55–62 million m3 of mining waste directly into the watershed of the River Doce, spreading across the Atlantic coast [85, 86]. This affected the ichthyofauna by fragmentation and destruction of habitats, water contamination, change in water flow, impact on estuaries and mangroves at the mouth of the River Doce [87], destruction of fish breeding areas, destruction of the nurseries of the ichthyofauna (feeding areas for larvae and juveniles), disruption of the gene flow between different areas, loss of species with habitat specificity and collapse of fish stocks [85].
