A Multilocus Approach to Understanding Historical and Contemporary Demography of the Keystone Floodplain Species Colossoma macropomum (Teleostei: Characiformes)

Spatial and temporal population genetic analysis of Semaprochilodus insignis (Prochilodontidae), an overexploited fish from the Amazon basin

Background

Semaprochilodus insignis is a migratory fish of commercial and subsistence importance to communities in the Amazon. Despite the high intensity of exploitation, recent studies have not been carried out to assess the genetic status of its stocks.

Methods

This study is the first to estimate genetic diversity and to test the existence of spatial and temporal structuring of S. insignis through sequencing of the mtDNA control region (n = 241) and eight microsatellite loci (n = 180) of individuals sampled at 11 sites distributed in the Brazilian Amazon basin.

Results

Results for both markers were congruent, revealing a homogeneous genetic diversity in all the sampled locations, in addition to the absence of spatial and temporal genetic structure, indicating that the species forms a large panmictic population in the Brazilian Amazon.

Discussion

Although overfishing does not yet appear to have affected the levels of genetic variability of S. insignis, signals of reduction of the effective population size and a bottleneck provide an early alert to the effects of overfishing. Thus, the ever-decreasing populations may threaten S. insignis in the future. Therefore, it is hoped that the results of this study may contribute to the elaboration of management plans or any other measures that aim at the management and conservation of this species of great importance for the Amazon basin.

Proactively averting the collapse of Amazon fisheries based on three migratory flagship species

Migratory species are the most important commercial fishes in the Amazon. They are also now the most threatened directly by some combination of overfishing, floodplain deforestation, and dam construction. Limited governmental monitoring and implemented regulations impede adequate management of the fisheries at adequate scale. We summarize the current stock status of the three most heavily exploited long-distance migratory species, which are two goliath catfishes (Brachyplatystoma rousseauxii and B. vaillantii) and the characiform Colossoma macropomum. In addition, we analyze impacts beyond overfishing on these species. Our results indicate: (i) the overfishing trends for these important species are either ominous or indicate the verge of collapse of the commercial fisheries based on them, and (ii) a dangerous synergy between overfishing, hydroelectric dams, and floodplain deforestation further challenge fisheries management of migratory species in the Amazon. We propose eight direct governmental actions as a proactive approach that addresses the main impacts on the fisheries. We consider that the most practical way to assess and manage overfishing of migratory species in the short run in an area as large as the main commercial fishing area in the Amazon is at market sites where enforced regulations can control fish catch. The management of the three species considered here has implications beyond just their sustainability. Their management would represent a paradigm shift where the governments assume their legal responsibilities in fishery management. These responsibilities include regulation enforcement, data collecting, inter-jurisdictional cooperation to protect migratory species at realistic life history scales, mitigation of the Madeira dams to assure goliath catfish passage to the largest western headwater region, and recognition of monitoring and managing wetland deforestation for the protection of fish and other aquatic and terrestrial biodiversity.

Mapping the hidden diversity of the Geophagus sensu stricto species group (Cichlidae: Geophagini) from the Amazon basin

South American freshwater ichthyofauna is taxonomically the most diverse on the planet, yet its diversity is still vastly underestimated. The Amazon basin alone holds more than half of this diversity. The evidence of this underestimation comes from the backlog of morphologically distinct, yet undescribed forms deposited in museum collections, and from DNA-based inventories which consistently identify large numbers of divergent lineages within even well-studied species groups. In the present study, we investigated lineage diversity within the Geophagus sensu stricto species group. To achieve these objectives, we analyzed 337 individuals sampled from 77 locations within and outside the Amazon basin representing 10 nominal and six morphologically distinct but undescribed species. We sequenced the mitochondrial cytochrome c oxidase subunit I (COI) and delimited lineages using four different single-locus species discovery methods (mPTP-15 lineages; LocMin-14 lineages; bGMYC-18 lineages; and GMYC-30 lineages). The six morphologically distinct but undescribed species were also delimited by the majority of the species discovery methods. Five of these lineages are restricted to a single collection site or a watershed and their habitats are threatened by human activities such as deforestation, agricultural activities and construction of hydroelectric plants. Our results also highlight the importance of combining DNA and morphological data in biodiversity assessment studies especially in taxonomically diverse tropical biotas.

The most important fishery resource in the Amazon, the migratory catfish Brachyplatystoma vaillantii (Siluriformes: Pimelodidae), is composed by an unique and genetically diverse population in the Solimões-Amazonas River System

ABSTRACT The migratory catfish Brachyplatystoma vaillantii is one of the most important fishery resources in the Amazon. Intense capture occurs associated to its life cycle. In order to know the genetic status, we sequenced the mitochondrial DNA control region from 150 individuals of B. vaillantii, collected in five fishing landing locations, covering the length of the Solimões-Amazonas River in Brazil. Genetic diversity parameters suggest there is no genetic differentiation between the five localities. Population’s expansion indicated by R 2 and Fu’s Fs tests was also confirmed by the high number of unique haplotypes found. The Analyses of molecular variance indicated that nearly all variability was contained within locations (99.86%), and estimates of gene flow among B. vaillantii were high (F ST = 0.0014). These results suggest that Brachyplatystoma vaillantii forms a panmitic population along the Solimões-Amazonas River and, has greater genetic variability than other species of the Brachyplatystoma genus available so far. Although the influence of different tributaries on B. vaillantii migration patterns remains uncertain, a single population in the main channel should be consider in future policies for management of this resource. However, since the species’ life cycle uses habitats in several countries, its management and conservation depend greatly of internationally joined efforts.

Molecular characterization and evaluation of virulence traits of Aeromonas spp. isolated from the tambaqui fish (Colossoma macropomum)

The present study was developed to characterize, at the species level, 34 strains of Aeromonas spp., previously isolated from stressed tambaqui fish (Colossoma macropomum), to elucidate virulence factors, as well as their antibiotic resistance profile. Amplification of the gyrB gene identified the strains as A. hydrophila, A. dhakensis, A. caviae, A. veronii and A. jandaei. Bacterial virulence was evaluated by enzymatic assays for phenotypical production of hemolysins, proteases and lipases followed by the search for genes codifying the enzymes β-hemolysin, serine protease and lipase. Phenotypical production of virulence factors was diversified and proteolytic activity demonstrated to be a common expression among the strains. On the other hand, the lip gene encoding extracellular lipase was the most expressed. Furthermore, A. hydrophila was the most prevalent species isolated from tambaqui in our work.

The largest fish in the world's biggest river: Genetic connectivity and conservation of Arapaima gigas in the Amazon and Araguaia-Tocantins drainages

Arapaima, pirarucu or paiche (Arapaima gigas) is one of the largest freshwater fish in the world, and has a long history of commercial exploitation in the Amazon region. To estimate levels of genetic variability and historical and recent connectivity in Arapaima, we examined variation in eleven microsatellite DNA markers in individuals from 22 localities in Brazil, Colombia, and Peru. The results of analysis of molecular variance, Bayesian clustering and discriminant analysis of principal components showed that Arapaima in our samples represents two major populations, one in the Amazonas and one in the Araguaia-Tocantins River basins. The Amazonas population is further structured by isolation-by-distance with the hydrologically largely unconnected Amapá locality representing the eastern-most extreme of this continuum; gene flow predominates at distances of less than 1500 km with localities separated by over 2000 km dominated by genetic drift and effectively forming different populations. We saw no evidence of multiple species of Arapaima in the Amazonas basin, and analysis of pairwise genetic divergence (F_ST) with Mantel tests and correlograms indicated that this largest population exhibits a large-scale pattern of isolation-by-distance, with which results from MIGRATE-N agreed. The degree and significance of genetic divergence indicates that most sampled localities represent demographically independent sub-populations, although we did identify several recent migration events between both proximal and more distant localities. The levels of genetic diversity were heterogeneous across sites, including low genetic diversity, effective population sizes, and evidence of genetic bottlenecks in several places. On average the levels of gene diversity and rarefied allelic richness were higher for localities along the Amazonas mainstem than in the tributaries, despite these being the areas of highest fishing pressure, while the lowest values were found in tributary headwaters, where landscape modification is a significant threat. We recommend that managers consider the regional and local threats to these populations and tailor strategies accordingly, strategies which should ensure the ability of young A. gigas to disperse through floodplain corridors to maintain genetic diversity among otherwise sedentary adult sub-populations.