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.

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.

Tempo and rates of diversification in the South American cichlid genus Apistogramma (Teleostei: Perciformes: Cichlidae).

Evaluating biodiversity and understanding the processes involved in diversification are noticeable conservation issues in fishes subject to large, sometimes illegal, ornamental trade purposes. Here, the diversity and evolutionary history of the Neotropical dwarf cichlid genus Apistogramma from several South American countries are investigated. Mitochondrial and nuclear markers are used to infer phylogenetic relationships between 31 genetically identified species. The monophyly of Apistogramma is suggested, and Apistogramma species are distributed into four clades, corresponding to three morphological lineages. Divergence times estimated with the Yule process and an uncorrelated lognormal clock dated the Apistogramma origin to the beginning of the Eocene (≈ 50 Myr) suggesting that diversification might be related to marine incursions. Our molecular dating also suggests that the Quaternary glacial cycles coincide with the phases leading to Apistogramma speciation. These past events did not influence diversification rates in the speciose genus Apistogramma, since diversification appeared low and constant through time. Further characterization of processes involved in recent Apistogramma diversity will be necessary.