Sequencing primate genomes: what have we learned?

We summarize the progress in whole-genome sequencing and analyses of primate genomes. These emerging genome datasets have broadened our understanding of primate genome evolution revealing unexpected and complex patterns of evolutionary change. This includes the characterization of genome structural variation, episodic changes in the repeat landscape, differences in gene expression, new models regarding speciation, and the ephemeral nature of the recombination landscape. The functional characterization of genomic differences important in primate speciation and adaptation remains a significant challenge. Limited access to biological materials, the lack of detailed phenotypic data and the endangered status of many critical primate species have significantly attenuated research into the genetic basis of primate evolution. Next-generation sequencing technologies promise to greatly expand the number of available primate genome sequences; however, such draft genome sequences will likely miss critical genetic differences within complex genomic regions unless dedicated efforts are put forward to understand the full spectrum of genetic variation.

The origins and impact of primate segmental duplications

Duplicated sequences are substrates for the emergence of new genes and are an important source of genetic instability associated with rare and common diseases. Analyses of primate genomes have shown an increase in the proportion of interspersed segmental duplications (SDs) within the genomes of humans and great apes. This contrasts with other mammalian genomes that seem to have their recently duplicated sequences organized in a tandem configuration. In this review, we focus on the mechanistic origin and impact of this difference with respect to evolution, genetic diversity and primate phenotype. Although many genomes will be sequenced in the future, resolution of this aspect of genomic architecture still requires high quality sequences and detailed analyses.

Fish colonization of artificial reefs in a large Neotropical reservoir: material type and successional changes

Artificial reefs have barely been used in Neotropical reservoirs (about five studies in three reservoirs), despite their potential as a fishery management tool to create new habitats and also to understand fish ecology. We experimentally assessed how reef material (ceramic, concrete, and PVC) and time modulated fish colonization of artificial reefs deployed in Itaipu Reservoir, a large reservoir of the mainstem Parana´ River, Brazil. Fish richness, abundance, and biomass were significantly greater in the reef treatments than at control sites. Among the experimental reefs, ceramic followed by the concrete treatments were the materials most effectively colonized, harboring the majority of the 13 fish species recorded. Although dependent on material type, many of the regularities of ecological successions were also observed in the artificial reefs, including decelerating increases in species richness, abundance, mean individual size, and species loss rates with time and decelerating decreases of species gain and turnover rates. Species composition also varied with material type and time, together with suites of life history traits: more equilibrium species (i.e., fishes of intermediate size that often exhibit parental care and produce fewer but larger offspring) of the Winemiller-Rose model of fish life histories prevailed in later successional stages. Overall, our study suggests that experimental reefs are a promising tool to understand ecological succession of fish assemblages, particularly in tropical ecosystems given their high species richness and low seasonality

Experimental assessment of the effects of a Neotropical nocturnal piscivore on juvenile native and invasive fishes

We experimentally examined the predator-prey relationships between juvenile spotted sorubim Pseudoplastystoma corruscans and young-of-the-year invasive and native fish species of the Paraná River basin, Brazil. Three invasive (peacock bass Cichla piquiti, Nile tilapia Oreochromis niloticus, and channel catfish Ictalurus punctatus) and two native (yellowtail tetra Astyanax altiparanae and streaked prochilod Prochilodus lineatus) fish species were offered as prey to P. corruscans in 300 L aquaria with three habitat complexity treatments (0%, 50% and 100% structure-covered). Prey survival was variable through time and among species (C. piquiti < O. niloticus < A. altiparanae < P. lineatus < I. punctatus), depending largely on species-specific prey behavior but also on prey size and morphological defenses. Habitat complexity did not directly affect P. corruscans piscivory but some prey species changed their microhabitat use and shoaling behavior among habitat treatments in predator’s presence. Pseudoplatystoma corruscans preyed preferentially on smaller individuals of those invasive species with weak morphological defensive features that persisted in a non-shoaling behavior. Overall, our results contrast with those in a companion experiment using a diurnal predator, suggesting that nocturnal piscivores preferentially prey on different (rather diurnal) fish species and are less affected by habitat complexity. Our findings suggest that recovering the native populations of P. corruscans might help controling some fish species introduced to the Paraná River basin, particularly C. piquiti and O. niloticus, whose parental care is expected to be weak or null at night