Molecular identification of evolutionarily significant units in the Amazon River dolphin Inia sp. (Cetacea: Iniidae)

The Amazon river dolphin, genus Inia, is endemic to the major river basins of northern South America. No previous studies have focused on the genetic structure of this genus. In this work, 96 DNA samples from specimens of this genus were collected in the Orinoco basin (four rivers), the Putumayo River, a tributary of the Colombian Amazon and the Mamoré, and the Tijamuchí and Ipurupuru rivers in theBolivian Amazon. These samples were used to amplify a fragment of 400 bp of the mitochondrial DNA (mtDNA) control region. In addition, 38 of these samples were also used to sequence 600 bp of the mitochondrial cytochrome b gene. The analysis of the population structure subdivision with an analysis of molecular variance (AMOVA) revealed important aspects about the genetic structure of Inia groups fromthese three geographically separate regions. By comparing the control region DNA and cytochrome b sequences, distinct types of nonshared haplotypes were observed. The net genetic divergence of control region sequences was 6.53% between the Orinoco and Bolivian rivers, 5.32% between the Putumayo and Bolivian rivers, and 2.50% between the Orinoco and Putumayo rivers. For the cytochrome b gene, these values were 2.48%, 2.98%, and 0.06%, respectively. The nucleotide sequences were analyzed phylogenetically using several genetic distance matrices and applying neighbor-joining, maximum likelihood, and maximum parsimony procedures. The results support the proposal to subdivide the Inia genus into at least two evolutionarily significant units: one confined to the Bolivian river basin and the other widely distributed across the Amazon and Orinoco basins.     

Phylogeography and intraspecific genetic variation of prochilodontid fishes endemic to rivers of northern South America

Phylogeography and intraspecific genetic variation were studied in prochilodontids endemic to the Orinoco, Essequibo and Amazon River basins of northern South America. Portions of two protein‐encoding mitochondrial (mt) DNA genes, ND4 and COI, were examined using single‐strand conformational polymorphisms (SSCPs) and nucleotide sequencing. Phylogeographic analysis indicated that the geographically widespread Prochilodus rubrotaeniatus is paraphyletic, with individuals from the Orinoco sharing most recent common ancestry with co‐occurring Prochilodus mariae . A second Prochilodus rubrotaeniatus clade was composed of haplotypes found in the Rio Cuyuní(Essequibo Basin) and tributaries of the Rio Negro (Amazon Basin). Intraspecific genetic analysis suggested that a complex set of processes have influenced patterns of genetic variation in prochilodontid lineages. Prochilodus rubrotaeniatus is monomorphic at both loci in the Rio Negro and probably recently colonized this basin from the Rio Essequibo. Only two of 55 P. mariae exhibited variant haplotypes, and both had resulted from non‐synonymous changes in the ND4 region. These observations were counter to neutral expectation and consistent with the action of natural selection on the mitochondrion. Overall, these analyses implicate vicariance, demography and selection for driving diversification of prochilodontids in northern South America.     

Transcontinental dispersal,ecological opportunity and origins of an adaptive radiation in the Neotropical catfish genus Hypostomus (Siluriformes: Loricariidae)

Ecological opportunity is often proposed as a driver of accelerated diversification, but evidence has been largely derived from either contemporary island radiations or the fossil record. Here, we investigate the potential influence of ecological opportunity on a transcontinental radiation of South American freshwater fishes. We generate a species‐dense, time‐calibrated molecular phylogeny for the suckermouth armored catfish subfamily Hypostominae, with a focus on the species‐rich and geographically widespread genus Hypostomus. We use the resulting chronogram to estimate ancestral geographical ranges, infer historical rates of cladogenesis and diversification in habitat and body size and shape, and test the hypothesis that invasions of previously unoccupied river drainages accelerated evolution and contributed to adaptive radiation. Both the subfamily Hypostominae and the included genus Hypostomus originated in the Amazon/Orinoco ecoregion. Hypostomus subsequently dispersed throughout tropical South America east of the Andes Mountains. Consequent to invasion of the peripheral, low‐diversity Paraná River basin in southeastern Brazil approximately 12.5 Mya, Paraná lineages of Hypostomus, experienced increased rates of cladogenesis and ecological and morphological diversification. Contemporary lineages of Paraná Hypostomus are less species rich but more phenotypically diverse than their congeners elsewhere. Accelerated speciation and morphological diversification rates within Paraná basin Hypostomus are consistent with adaptive radiation. The geographical remoteness of the Paraná River basin, its recent history of marine incursion, and its continuing exclusion of many species that are widespread in other tropical South American rivers suggest that ecological opportunity played an important role in facilitating the observed accelerations in diversification.     

Phylogenetic status of brown trout Salmo trutta populations in five rivers from the southern Caspian Sea and two inland lake basins,Iran: a morphogenetic approach

Interrelationships, origin and phylogenetic affinities of brown trout Salmo trutta populations from the southern Caspian Sea basin, Orumieh and Namak Lake basins in Iran were analysed from complete mtDNA control region sequences, 12 microsatellite loci and morphological characters. Among 129 specimens from six populations, seven haplotypes were observed. Based on mtDNA haplotype data, the Orumieh and southern Caspian populations did not differ significantly, but the Namak basin–Karaj population presented a unique haplotype closely related to the haplotypes of the other populations (0·1% Kimura two‐parameter, K2P divergence). All Iranian haplotypes clustered as a distinct group within the Danube phylogenetic grouping, with an average K2P distance of 0·41% relative to other Danubian haplotypes. The Karaj haplotype in the Namak basin was related to a haplotype (Da26) formerly identified in the Tigris basin in Turkey, to a Salmo trutta oxianus haplotype from the Aral Sea basin, and to haplotype Da1a with two mutational steps, as well as to other Iranian haplotypes with one to two mutational steps, which may indicate a centre of origin in the Caspian basin. In contrast to results of the mtDNA analysis, more pronounced differentiation was observed among the populations studied in the morphological and microsatellite DNA data, except for the two populations from the Orumieh basin, which were similar, possibly due to anthropogenic causes.     

Cytogenetic studies on Apareiodon affinis (Pisces, Characiformes) from Paraná river basin: sex chromosomes and polymorphism

Comparative cytogenetic studies were carried out on Apareiodon affinis from an important hydrographic system at South America, the Paraná river basin. Two distant regions were chosen, which were separated by Guaíra Falls (formerly Sete Quedas); the region in the upper part of the hydrographic basin is called Upper Paraná (Brazil), whereas and the other in the lower part is called Lower Paraná (Argentina). Individuals from Upper Paraná have diploid numbers of 2n = 54 (NF = 108) for males and 2n = 55 (NF = 110) for females, showing female heterogamety with a ZZ/ZW₁W₂ multiple sex chromosomes system that is endemic for the region. In different localities at Lower Paraná, the specimens presented diploid number of 2n = 54 for both sexes, without any sex chromosomes heteromorphism. However, they have an accentuated polymorphism characterized by variation in number of acrocentric chromosomes, constituting something new for family Parodontidae. The most likely hypothesis to explain the origin of such polymorphism is based on successive pericentric inversions giving rise to acrocentric chromosomes. Thus, it was possible to detect 10 cytotypes along the Lower Paraná basin. Such chromosomal variations possibly are the consequence of an adaptative process. Our data probably indicate the occurrence of distinct species in each region that share the same denomination. This revised version was published online in July 2006 with corrections to the Cover Date.     

The Amazon River system as an ecological barrier driving genetic differentiation of the pink dolphin (Inia geoffrensis)

The pink dolphin (Inia geoffrensis) is widely distributed along the Amazon and Orinoco basins, covering an area of approximately 7 million km². Previous morphological and genetic studies have proposed the existence of at least two evolutionary significant units: one distributed across the Orinoco and Amazon basins and another confined to the Bolivian Amazon. The presence of barriers in the riverine environment has been suggested to play a significant role in shaping present‐day patterns of ecological and genetic structure for this species. In the present study, we examined the phylogeographic structure, lineage divergence time and historical demography using mitochondrial (mt)DNA sequences in different pink dolphin populations distributed in large and small spatial scales, including two neighbouring Brazilian Amazon populations. mtDNA control region (CR) analysis revealed that the Brazilian haplotypes occupy an intermediate position compared to three previously studied geographic locations: the Colombian Amazon, the Colombian Orinoco, and the Bolivian Amazon. On a local scale, we have identified a pattern of maternal isolation between two neighbouring populations from Brazil. Six mtDNA CR haplotypes were identified in Brazil with no sharing between the two populations, as well as specific cytochrome b (cyt b) haplotypes identified in each locality. In addition, we analyzed autosomal microsatellites to investigate male‐mediated gene flow and demographic changes within the study area in Brazil. Data analysis of 14 microsatellite loci failed to detect significant population subdivision, suggesting that male‐mediated gene flow may maintain homogeneity between these two locations. Moreover, both mtDNA and microsatellite data indicate a major demographic collapse within Brazil in the late Pleistocene. Bayesian skyline plots (BSP) of mtDNA data revealed a stable population for Colombian and Brazilian Amazon lineages through time, whereas a population decline was demonstrated in the Colombian Orinoco lineage. Moreover, BSP and Tajima's D and Fu's F_s tests revealed a recent population expansion exclusively in the Bolivian sample. Finally, we estimated that the diversification of the Inia sp. lineage began in the Late Pliocene (approximately 3.1 Mya) and continued throughout the Pleistocene. Published 2011. This article is a US Government work and is in the public domain in the USA. © 2011 The Linnean Society of London, Biological Journal of the Linnean Society, 2011, 102 , 812–827.     

Taxonomic revision of Hypostomus albopunctatus (Siluriformes: Loricariidae) reveals a new piece of the Hypostomus jigsaw in the upper Rio Paraná basin

Hypostomus albopunctatus was described from the Rio Piracicaba, a tributary of the Rio Tietê, upper Rio Paraná basin. Nevertheless, specimens attributed to this species are commonly found throughout other river systems in the upper Rio Paraná basin and present varying degrees of morphological variation. A taxonomic review of H. albopunctatus based on large series of specimens from many localities throughout the upper Rio Paraná basin was carried out. Results support H. lexi, H. niger and H. scaphyceps as junior synonyms. Hypostomus albopunctatus differs from all congeners except H. heraldoi by having pectoral-fin spine equal to or shorter than pelvic-fin spine (v. longer); it differs from H. heraldoi by having white or light yellow spots on the body and fins (v. dark brown or black spots). Despite conspicuous variation related to the shape and size of the spots and snout morphology, both spot and snout patterns overlapped among the examined populations, thus this variation was inferred to be intraspecific within a widely distributed H. albopunctatus.     

Acoustic homogeneity in the piranha Serrasalmus maculatus

Different studies suggest some social calls could be used in fish identification if their specificity is unambiguously assessed. Sounds of different populations of piranhas Serrasalmus maculatus Kner, 1858 were recorded to determine their homogeneity between rivers inside a single basin (Araguari and Grande River, upper Paraná River basin) and between separated basins (Amazon and Paraná basins). All fish from the different populations produced sounds with similar acoustic features. Consequently, the populations were not discernible based on individual sound characteristics. This high homogeneity between sounds from different populations indicates their usefulness for conservation projects using passive acoustic monitoring in piranhas. Moreover, it supports the use of acoustic features as complementary key characteristics in taxonomic studies.     

First record of non‐native hybrid catfish Pseudoplatystoma reticulatum × Leiarius marmoratus in the Upper Paraná River basin,Brazil

The aim of this study is to report the presence of a three non‐native hybrid long‐whiskered catfishes (family Pimelodidae) in the Upper Paraná River basin, Brazil. Genetic analyses demonstrated that the three presumptive hybrids were a result of the crossbreeding of Pseudoplatystoma reticulatum (central Amazonas River basin and Lower Paraná River) and Leiarius marmoratus (Amazonas, Essequibo and Orinoco rivers), producing a hybrid commonly known in Brazil as cachandiá. The potential threat to biodiversity, due to possible genetic contamination, competition and predation of wild stocks, of such artificially produced hybrid fishes is discussed.     

Population genetic structure of the Amazonian black flannelmouth characin (Characiformes,Prochilodontidae: <Emphasis Type="Italic">Prochilodus nigricans</Emphasis> Spix &amp; Agassiz, 1829): contemporary and historical gene flow of a migratory and abundant fishery species

In the present study, sequences of the mtDNA control region (834 bp) were analyzed from 337 specimens of Prochilodus nigricans from sites along the main channel of the Amazonas River and three major tributaries, Madeira, Purus, and Juruá. The results of the analysis of molecular variance revealed that a large part of the genetic variation occurred within the populations analyzed (~85 %). Analysis with SAMOVA and Barriers suggested that the upper Madeira River and Purus Rivers had diverged genetically from the other samples, indicating restricted gene flow among these areas, while sites within the remaining range exhibited relatively little population structure. The high degree of structuring observed in the Madeira River basin population may be attributed to the presence of rapids along its upper course, while the genetic divergence found in the upper Purus River suggests historical connection between the upper Purus and upper Madeira Rivers followed by slow genetic drift due to large effective population sizes. However, given the life history and hypothesized evolutionary strategy of this species, we urge caution in interpreting that this targeted species is not at risk of overexploitation due to contemporary abundance. In order to preserve genetic diversity, we recommend enforcement of management regimes for regional stocks.     

Lack of mtDNA variation among remote middle Volga and upper Ural brown trout suggests recent and rapid recolonization

Brown trout populations from the middle Volga and upper Ural drainages in the Russian Federation were analyzed with respect to their inter‐relationships and phylogenetic status using complete mtDNA control region sequences and 10 microsatellite loci. Among 56 individuals from eight populations (six from the middle Volga and two from the upper Ural drainages) only one haplotype was detected: Iran1 from the Danube phylogenetic lineage. This haplotype is very frequent in the southern Caspian basin in Iran. Given the high diversity of haplotypes in northern Iran, in contrast to the complete domination of the Iran1 haplotype in our study, it seems likely that Iran1 reached the middle Volga and upper Ural drainages as a consequence of colonization from the southern Caspian basin. In contrast to the mtDNA analysis, a more pronounced differentiation was observed among the studied populations on the basis of microsatellite DNA data. Based on this result, it is proposed that each population should be treated as a distinct management unit in the context of future conservation activities.     

Phylogeography and Pleistocene demographic history of the endangered marsh deer (Blastocerus dichotomus) from the Río de la Plata Basin

The marsh deer is the largest neotropical cervid with morphological and ecological adaptations to wetlands and riparian habitats. Historically, this now endangered species occupied habitats along the major river basins in South America, ranging from southern Amazonia into northern Argentina to the Paraná river delta. This particularly close association with wetlands makes marsh deer an excellent species for studying the effects of Pleistocene climatic changes on their demographic and phylogeographic patterns. We examined mitochondrial DNA variation in 127 marsh deer from 4 areas distributed throughout the Río de la Plata basin. We found 17 haplotypes in marsh deer from Brazil, Bolivia and Argentina that differed by 1–8 substitutions in a 601 bp fragment of mitochondrial control region sequence, and 486 bp of cytochrome b revealed only 3 variable sites that defined 4 haplotypes. Phylogeny and distribution of control region haplotypes suggest that populations close to the Pantanal area in central Brazil underwent a rapid population expansion and that this occurred approximately 28,000–25,000 years BP. Paleoclimatic data from this period suggests that there was a dramatic increase for precipitation in the medium latitudes in South America and these conditions may have fostered marsh deer’s population growth.     

Patterns of population differentiation in annual killifishes from the Paraná–Uruguay–La Plata Basin: the role of vicariance and dispersal

Aim To elucidate the role of vicariance versus dispersal at the microevolutionary scale in annual killifish populations belonging to the Austrolebias bellottii species complex (Rivulidae). Within this complex, A. bellottii and A. apaii have low vagility and occur widely within the study area, making them excellent models for testing biogeographic hypotheses of differentiation. Location South America, in the Paraná–Uruguay–La Plata river basin. Methods Molecular data and morphometric analyses were used to reconstruct the phylogeographic history and morphological variation of 24 populations of two taxa of the A. bellottii species complex. Phylogenetic analyses using maximum likelihood (ML) and Bayesian inference (BI) model‐based methods, estimates of clade divergence times implemented in beast , non‐metric multidimensional scaling, analysis of molecular variance results, and morphological analyses elucidated the role of vicariance versus dispersal hypotheses in population differentiation in the aforementioned river basin. Results In the A. bellottii species complex from the Paraná–Uruguay–La Plata river basin, past allopatric fragmentation from vicariance events seems to be the most plausible scenario for diversification since the Late Miocene and more recently since the Plio‐Pleistocene. The Plio‐Pleistocene vicariance produced the differentiation of three major clades in A. bellottii populations. One clade from the eastern Uruguay River drainage was separated from another in western Uruguay and the Paraná–La Plata River drainages. A later vicariance event split populations to the south (lower Paraná–La Plata Basin) and north (middle Paraná) of the western Paraná River drainage. However, our results do not exclude the possibility of dispersal events among A. bellottii populations from both the Uruguay and Paraná river drainages, which could occur in these river basins during hypothesized connectivity cycles of the Late Pliocene and Pleistocene. Main conclusions Past allopatric fragmentation caused by different vicariance events seems to be the main driver of diversification in the A. bellottii species complex since the Plio‐Pleistocene. However, the current molecular data suggest that populations from both drainages of the Paraná–Uruguay rivers may have experienced cycles of connectivity during the Pleistocene, perhaps including multiple vicariance or dispersal events from populations located in the western lower Uruguay River drainage, which encompassed climatic and geological changes in the Paraná–Uruguay–La Plata Basin.     

Molecular phylogeography of the Amazonian Chagas disease vectors Rhodnius prolixus and R. robustus

The phylogeographical structure of the closely related species Rhodnius prolixus and R. robustus is presented based on a 663-base pair (bp) fragment of the mitochondrial cytochrome b gene. Twenty haplotypes were recovered from 84 samples examined, representing 26 populations from seven Latin American countries. The resulting phylogenetic tree is composed of five major reciprocally monophyletic clades, one representing R. prolixus and four representing R. robustus. While R. prolixus is a very homogeneous assemblage, R. robustus has deeper clades and is paraphyletic, with the clade comprising R. robustus from Venezuela (Orinoco region) more closely related to the R. prolixus clade than to the other R. robustus populations from the Amazon region. The R. robustus paraphyly was supported further by the analysis of a nuclear gene (D2 region of the 28S RNA) for a subset of specimens. The data support the view that R. robustus represents a species complex. Levels of sequence divergence between clades within each region are compatible with a Pleistocene origin. Nucleotide diversity (pi) for all R. prolixus populations was extremely low (0.0008), suggesting that this species went through a recent bottleneck, and was subsequently dispersed by man.     

Isolation and characterization of microsatellite loci in Piaractus mesopotamicus and their applicability in other Serrasalminae fish

The subfamily Serrasalminae (Characidae, Teleostei) is an endemic Neotropical group of fishes distributed along the Amazon, Paraná‐Paraguay and Orinoco Basins. The pacu (Piaractus mesopotamicus) is found in all major rivers that comprise the Pantanal of Mato Grosso. In order to investigate population genetic structure within the group, an enriched microsatellite library was constructed. Eight polymorphic were loci screened, with an average of 6.5 alleles per locus. Five loci exhibited greater than 60% heterozygosity. Additionally, a high level of cross‐species amplification was obtained.     

Distribution of non‐native suckermouth armoured catfish Pterygoplichthys ambrosettii in the upper Paraná River basin,Brazil

This study describes the invasion of the upper Paraná River basin by Pterygoplichthys ambrosettii based on a literature review and field samples. Pterygoplichthys ambrosettii has been reported in 42 localities throughout the upper Paraná River basin, including the Tietê, Paranapanema, Paraná, Grande and Aguapeí rivers. The ascent of P. ambrosettii after the inundation of the Sete Quedas Falls on the Paraná River and the release of individuals by aquarium hobbyists were the primary drivers of this invasion.     

Molecular analysis reveals hidden diversity in <Emphasis Type="Italic">Zungaro</Emphasis> (Siluriformes: Pimelodidade): a genus of giant South American catfish

The genus Zungaro contains some of the largest catfish in South America. Two valid species are currently recognized: Zungaro jahu, inhabiting the Paraná and Paraguay basins, and Zungaro zungaro, occurring in the Amazonas and Orinoco basins. Analysing Zungaro specimens from the Amazonas, Orinoco, Paraguay and Paraná basins, based on the sequencing of COI and D-loop, we found at least three MOTUs, indicating the existence of hidden diversity within this fish group. Considering the ecological and economic values of this fish, our results are surely welcomed for its conservation, disclosing new findings on its diversity and pointing out the necessity for a detailed taxonomic revision.     

Yellow-eyed piranhas produce louder sounds than red-eyed piranhas in an invasive population of Serrasalmus marginatus

Serrasalmus marginatus is a piranha species native from the lower Paraná River basin and has been invasive in the upper Paraná River basin since the 1980s. In piranhas, sounds of different species have different features. The aim of this study was to investigate if the sounds produced by this species could be used to distinguish two morphotypes: red- and yellow-eyed S. marginatus from the Araguari River (upper Paraná River basin). All the temporal and frequency features of the sounds were equivalent in both groups of eye colour; it corresponds to the species-specific signature described for S. marginatus. Nonetheless, the amplitude features were all statistically different between red- and yellow-eyed piranhas. Yellow-eyed specimens produced louder sounds. In different fish species, colour change in eyes can be due to the absence or the presence of a dominant allele. It can also be involved in social rank or during reproduction. Different hormones and neuropeptides can modulate vocal features. It is hypothesized that a mutation or different hormonal concentrations could explain both sound amplitude and eye colour playing a role in animal communication in S. marginatus.     

Fatty acid alterations in the detritivorous Prochilodus lineatus promoted by opportunistic feeding on sewage discharges in the Río de la Plata estuary

Muscle fatty acid profiles and PCB contents of the detritivorous species Prochilodus lineatus and its diet (stomach contents, settling particles and sediments) were analysed from reference and polluted areas of the Paraná‐Rio de la Plata basin, to evaluate the alterations produced by opportunistic feeding on sewage discharges. Overall muscle fatty acid composition was dominated by saturated and monounsaturated 16 and 18 carbon (18 C‐FA) components with reduced long‐chain polyunsaturated fatty acids (LC‐PUFA). Compared to sediments, settling particles and stomach contents were enriched in lipids and had a similar fatty acid composition. Opportunistic feeding on sewage detritus at Buenos Aires resulted in enhanced PCB and triglyceride accumulation, with higher proportions of 18 C‐FA and lower proportions of 16:1 and LC‐PUFA compared to fish from northern pristine reaches of the basin. Mid‐Paraná showed intermediate values reflecting mixing of the North stock with migrating Buenos Aires P. lineatus identified by their lipid and contaminant profile. According to multivariate analyses, this geographical variation of fatty acid composition was strongly influenced by PCB concentration. Prochilodus lineatus assimilates the energy subsidy of sewage inputs through enhanced lipogenesis with dominant 18 C‐FA and significant amounts of valuable LC‐PUFA. This lipid alteration facilitates the bioaccumulation of PCBs which in turn may reinforce the adipogenic effect of sewage feeding.