The complete chloroplast genome of Marupa (Simarouba amara Aubl., Simaroubaceae).

Marupa (Simarouba amara Aublet 1775) is a tropical tree of the family Simaroubaceae. It is commonly used for its wood in the Amazonian forest, and it is an important species for restoring degraded environments. Yet, very little genetic resources are available to study this plant. In this paper, we sequenced for the first time the complete chloroplast genome of Marupa, using Oxford Nanopore long-read technology. The genome is 159,838 bp, includes 131 genes in total and presents a classic quadripartite structure. Its length and structure are similar to those of sister species of the Simaroubaceae family. A maximum likelihood phylogeny of the order Sapindale reveals that Simarouba amara is well positioned in its family. This complete plastome is a first step towards a better analysis of Marupa future evolution.

Species-level ichthyoplankton dynamics for 97 fishes in two major river basins of the Amazon using quantitative metabarcoding.

The Amazon basin holds the world's largest freshwater fish diversity. Information on the intensity and timing of reproductive ecology of Amazonian fish is scant. We use a metabarcoding method by capture using a single probe to quantify species-level ichthyoplankton dynamics. We sampled the Marañón and the Ucayali rivers in Peru monthly for 2 years. We identified 97 species that spawned mainly during the flood start, the flood end or the receding periods, although some species had spawning activity in more than one period. This information was new for 40 of the species in the Amazon basin and 80 species in Peru. Most species ceased spawning for a month during a strong hydrological anomaly in January 2016, demonstrating the rapidity with which they react to environmental modifications during the breeding season. We also document another unreported event in the Amazon basin, the inverse phenology of species belonging to one genus (Triportheus). Overall larval flow in the Marañón was more than twice that of the Ucayali, including for most commercial species (between two and 20 times higher), whereas the Ucayali accounts for ~80% of the fisheries landings in the region. Our results are discussed in the light of the main anthropogenic threats to fishes, hydropower dam construction and the Hidrovía Amazónica, and should serve as a pre-impact baseline.

The Digestive Function of Pseudoplatystoma punctifer Early Juveniles Is Differentially Modulated by Dietary Protein, Lipid and Carbohydrate Content and Their Ratios.

Pseudoplatystoma punctifer is an Amazonian catfish highly appreciated for its high flesh quality, size, and commercial value. Its aquaculture is pursued to satisfy the demands of an increasing population in the region. However, knowledge of the nutritional needs during the early life stages is necessary for improving growth and reducing the incidence of cannibalism, factors that limit the success of its commercial farming. This study aimed at evaluating the influence of four diets containing different protein and lipid levels (30:15, 30:10, 45:15, or 45:10 in %) in the digestive physiology and performance of early juveniles. The results showed that the dietary protein:lipid as well as carbohydrate levels and ratios influenced differently the whole-body proximate composition, the digestive physiology and development, and hence growth and survival. The 45:15 diet promoted the best growth, survival, and the most rapid development of the digestive system, as shown at histological (higher number of hepatocytes, goblet cells in the anterior intestine and enterocytes in all intestinal portions, and longer folds in the posterior intestine), molecular (highest amylase, lipoprotein lipase, phospholipase, trypsinogen, and pepsinogen gene expression), and biochemical (highest lipase and pepsin activities and higher alkaline phosphatase:leucine alanine peptidase activity ratio) levels. Lipids were favored over carbohydrates as source of energy, with lipids promoting a protein-sparing effect at adequate energy:protein ratio. Carbohydrate content higher than 25% was excessive for this species, leading to unbalanced lipid metabolism and fat deposition in the liver.

Molecular evidence for three genetic species of Dipteryx in the Peruvian Amazon.

There is a high international demand for timber from the genus Dipteryx, or "shihuahuaco" as it is known in Peru. Developing tools that allow the identification and discrimination of Dipteryx species is therefore important for supporting management of natural populations and to underpin legal trade of its timber. The objective of this study was the molecular characterization of Dipteryx species in the Peruvian Amazonia. Two plastid regions (cpDNA: trnH-psbA and matK) were sequenced and 11 microsatellite markers (nDNA) were genotyped for 32 individuals identified as Dipteryx charapilla, D. micrantha morphotype 1 and D. micrantha morphotype 2. Using the concatenated sequences of the plastid genes, we identified ten haplotypes that were not shared between the species or between the D. micrantha morphotypes. Haplotypic diversity was greater in D. micrantha morphotype 2 and D. charapilla than in D. micrantha morphotype 1, which presented only one haplotype with a wide distribution in Peru. The microsatellites allowed the discrimination of the same three clades and identified diagnostic alleles for each clade. These results allowed us to demonstrate that the two morphotypes of D. micrantha are different at both the plastid and nuclear markers, which supports the existence of three genetically distinct species in Peru. This study provides information for the genetic discrimination of Dipteryx species and emphasises the importance of conserving the genetic variability of this genus in the Peruvian Amazonia.

Molecular identification of a cryptic species in the Amazonian predatory catfish genus Pseudoplatystoma (Bleeker, 1962) from Peru.

Pseudoplatystoma species are highly prized South American Pimelodid migratory catfishes. Until recently, their taxonomy was not clearly established, with discrepancies between morphological and molecular analyses. Here, Pseudoplatystoma species from the Peruvian Amazon were characterized at the molecular level from a sample representing the observed range of their color pattern variations in the study area. Analyses were performed using seven microsatellite loci for 103 specimens and, for part of them (52), using sequences of two regions of their mitochondrial genome [Cytochrome Oxidase subunit I (COI) and Control Region (CR)]. Factorial correspondence analysis and assignment tests based on microsatellite polymorphism showed that the specimens originally identified as P. punctifer belonged to two different gene pools highly differentiated from P. tigrinum. Morphological examination identified two different morphotypes (with and without black stripes), suggesting the existence of two distinct taxa within P. punctifer. This result was corroborated by the ML tree based on CR sequences, where all individuals but four clustered in a similar way as in the FCA and Bayesian assignment tests. For these four individuals, mitochondrial introgression or retention of ancestral polymorphism was likely. In contrast, the ML tree based on COI sequences showed that reciprocal monophyly was not yet achieved for this marker for the two P. punctifer taxa. The existence of three sympatric species of Pseudoplatystoma in the Peruvian Amazon is discussed in relation to their molecular characteristics, color patterns and ecology. Evolutionary scenarios regarding their divergence are hypothesized.