Remediation of a marine shore tailings deposit and the importance of water-rock interaction on element cycling in the coastal aquifer

We present the study of the geochemical processes associated with the first successful remediation of a marine shore tailings deposit in a coastal desert environment (Bahia de Ite, in the Atacama Desert of Peru). The remediation approach implemented a wetland on top of the oxidized tailings. The site is characterized by a high hydrauliz gradient produced by agricultural irrigation on upstream gravel terraces that pushed river water (similar to 500 mg/L SO(4)) toward the sea and through the tailings deposit. The geochemical and isotopic (delta(2)H(water) and delta(18)O(water), delta(34)S(sulfate) , delta(18)O(sulfate)) approach applied here revealed that evaporite horizons (anhydrite and halite) in the gravel terraces are the source of increased concentrations of SO(4), Cl, and Na up to similar to 1500 mg/L in the springs at the base of the gravel terraces. Deeper groundwater interacting with underlying marine sequences increased the concentrations of SO(4), Cl, and Na up to 6000 mg/L and increased the alkalinity up to 923 mg/L CaCO(3) eq. in the coastal aquifer. These waters infiltrated into the tailings deposit at the shelf-tailings interface. Nonremediated tailings had a low-pH oxidation zone (pH 1-4) with significant accumulations of efflorescent salts (10-20 cm thick) at the surface because of upward capillary transport of metal cations in the arid climate. Remediated tailings were characterized by neutral pH and reducing conditions (pH similar to 7, Eh similar to 100 mV). As a result, most bivalent metals such as Cu, Zn, and Ni had very low concentrations (around 0.01 mg/L or below detection limit) because of reduction and sorption processes. In contrast, these reducing conditions increased the mobility of iron from two sources in this system: (1) The originally Fe(III)-rich oxidation zone, where Fe(II) was reduced during the remediation process and formed an Fe(II) plume, and (2) reductive dissolution of Fe(III) oxides present in the original shelf lithology formed an Fe-Mn plume at 10-m depth. These two Fe-rich plumes were pushed toward the shoreline where more oxidizing and higher pH conditions triggered the precipitation of Fe(HI)hydroxide coatings on silicates. These coatings acted as a filter for the arsenic, which naturally infiltrated with the river water (similar to 500 mu g/L As natural background) into the tailings deposit.

The life history of retrocopies illuminates the evolution of new mammalian genes.

New genes contribute substantially to adaptive evolutionary innovation, but the functional evolution of new mammalian genes has been little explored at a broad scale. Previous work established mRNA-derived gene duplicates, known as retrocopies, as models for the study of new gene origination. Here we combine mammalian transcriptomic and epigenomic data to unveil the processes underlying the evolution of stripped-down retrocopies into complex new genes. We show that although some robustly expressed retrocopies are transcribed from preexisting promoters, most evolved new promoters from scratch or recruited proto-promoters in their genomic vicinity. In particular, many retrocopy promoters emerged from ancestral enhancers (or bivalent regulatory elements) or are located in CpG islands not associated with other genes. We detected 88-280 selectively preserved retrocopies per mammalian species, illustrating that these mechanisms facilitated the birth of many functional retrogenes during mammalian evolution. The regulatory evolution of originally monoexonic retrocopies was frequently accompanied by exon gain, which facilitated co-option of distant promoters and allowed expression of alternative isoforms. While young retrogenes are often initially expressed in the testis, increased regulatory and structural complexities allowed retrogenes to functionally diversify and evolve somatic organ functions, sometimes as complex as those of their parents. Thus, some retrogenes evolved the capacity to temporarily substitute for their parents during the process of male meiotic X inactivation, while others rendered parental functions superfluous, allowing for parental gene loss. Overall, our reconstruction of the "life history" of mammalian retrogenes highlights retroposition as a general model for understanding new gene birth and functional evolution.