Origins, Admixture Dynamics, and Homogenization of the African Gene Pool in the Americas

The Transatlantic Slave Trade transported more than 9 million Africans to the Americas between the early 16th and the mid-19th centuries. We performed a genome-wide analysis using 6,267 individuals from 25 populations to infer how different African groups contributed to North-, South-American, and Caribbean populations, in the context of geographic and geopolitical factors, and compared genetic data with demographic history records of the Transatlantic Slave Trade. We observed that West-Central Africa and Western Africa-associated ancestry clusters are more prevalent in northern latitudes of the Americas, whereas the South/East Africa-associated ancestry cluster is more prevalent in southern latitudes of the Americas. This pattern results from geographic and geopolitical factors leading to population differentiation. However, there is a substantial decrease in the between-population differentiation of the African gene pool within the Americas, when compared with the regions of origin from Africa, underscoring the importance of historical factors favoring admixture between individuals with different African origins in the New World. This between-population homogenization in the Americas is consistent with the excess of West-Central Africa ancestry (the most prevalent in the Americas) in the United States and Southeast-Brazil, with respect to historical-demography expectations. We also inferred that in most of the Americas, intercontinental admixture intensification occurred between 1750 and 1850, which correlates strongly with the peak of arrivals from Africa. This study contributes with a population genetics perspective to the ongoing social, cultural, and political debate regarding ancestry, admixture, and the mestizaje process in the Americas.

Use of an Integrated Geochemical and Ecotoxicological Approach to Evaluate Sediment Metal Contamination in Three Protected Estuarine Areas Along the Coast of São Paulo State, Brazil

We compared sediment quality in estuaries at three locations along the coast of São Paulo State, Brazil, using geochemical analyses and whole sediment toxicity tests, during the southern summer and winter of 2013. Each locality is afforded a distinct degree of legal protection, and exhibits a different level of metal pollution: overall, Rio Diana (RD, the most polluted, a Permanent Protection Area) > Rio Itapanhaú (RI, intermediate contamination, an Environmental Protection Area) > Rio Picinguaba (RP, pristine, a State Park). Chronic sediment toxicity tests evaluated reproductive rates of the copepod Nitokra sp. RI sediments showed the highest metal concentrations and toxicity in both seasons. Metal concentrations at RD were low but toxic in summer. RP sediments were not contaminated, suggesting effective legal protection from pollution at this locality. RI and RD, although provided some legal protection, showed clear signs of environmental degradation, emphasizing the need for more effective pollution control.

Metal-Associated Biomarker Responses in Crabs from a Marine Protected Area in Southeastern Brazil

The environmental quality of a Ramsar wetland site located at the Cananéia-Iguape-Peruíbe Protected Area (CIP-PA), in São Paulo, Brazil, was assessed by geochemical analyses and biomarker assessments (GPx, GST, GSH, GST, MT, LPO, DNA damage) performed in swimming crab Callinectes danae Smith, 1869 organs (posterior and anterior gills and hepatopancreas) to estimate sediment contaminant bioavailability. The results indicated that two sampling stations, PT and PM, exhibited the worst environmental conditions, as sediments collected at both points contained metal contamination, while crabs exhibited significant responses for GPx, GST, and LPO (mostly during winter). Sediment contamination tended to be associated to fine sediments (both seasons) and organic matter (winter). During the summer survey, Pb concentrations in sediments of station PT exceeded the Brazilian Sediment Quality Guidelines (SQGs) and the Canadian Interim Marine Sediment Quality Guidelines. Metal concentrations in sediments sampled in winter were higher compared with summer, with Co, Ni, and Pb exceeding SQGs levels at PT, whereas Co, Ni, Hg, Zn, and Pb exceeded SQGs at PM. Biomarker induction during summer appeared to be caused by natural variables (water salinity and temperature, and molting cycle), whereas oxidative stress and tissue damage during winter appeared to be more clearly linked to metal contamination. Anterior gills presented the clearest signs of seasonal variability, being more responsive to sediment contamination. The results suggest that metals originated from the upper Ribeira de Iguape River are transported toward the estuarine system, causing effects on C. danae individuals. Additionally, seasonality is a strong factor concerning CIP-PA toxicity, since the rainfall regime significantly modifies the freshwater flow and, consequently, estuarine water salinity, suspended particle and metal inputs, as well as the location of depositional areas. Thus, efforts to mitigate CIP-PA contamination should be based on the control of upstream pollution sources.

Multi-generational effects under single and pulse exposure scenarios in two monophyletic Daphnia species

Anthropogenic activities commonly relate to a set of diffuse and point contamination sources, from industrial, domestic or agricultural outputs, characterized by a chemical cocktail exposure and consequent disturbances of natural ecosystems. Different species may present different sensitivities to contaminants, even when phylogenetically close. This study used two monophyletic Daphnia species from tropical and temperate environments, Daphnia similis and Daphnia magna respectively, to evaluate the variation of their sensitivity to Pb (if any) and fitness during a multi-generational exposure and recovery. To accomplish that, standard acute immobilization tests were done on specific generations. Tests were carried out with exposures to 1) potassium dichromate (K₂Cr₂O₇) to evaluate organisms' sensitivity/fitness, 2) Pb, to monitor variation on Pb sensitivity and 3) the fungicide mancozeb, providing a pulse toxicity approach on generational Pb acclimated daphnids. Since growth is an important trait related to organisms' fitness, organisms' size measurements were also monitored. In addition, organisms were maintained under two different dietary regimes. Our results indicate no variation on daphnids sensitivity to K₂Cr₂O₇, except for D. similis from a recovery period under food restriction. However, a lower Pb sensitivity was seen for both species throughout generations. Both species also showed that under food restriction neonates' sizes were larger than those kept under regular food, while reproduction was considerably reduced. Food restriction also generated opposite outcomes on both species, such as D. magna epigenetic changes and D. similis phenotypic acclimation to Pb. Besides, D. magna pre-exposed to Pb presented lower sensitivity to mancozeb, while the contrary was shown by D. similis. This study indicates that daphnids are capable of acquiring a lower sensitivity to Pb across a long-term exposure, and that Pb pre-exposure can affect the sensitivity to other chemicals. Also, different patterns in multi-generational responses from monophyletic species (especially under oligotrophic media, common on natural habitats) acknowledge the use of representative or native species to assess the effect of contaminants, since monophyletic species can provide different toxicity outputs.

Phylogeny of the comb-tooth blenny genus Scartella (Blenniiformes: Blenniidae) reveals several cryptic lineages and a trans-Atlantic relationship

Here we present the first phylogeny of the genus Scartella based on mitochondrial data. The analysis strongly corroborates the validity of all species of the genus and shows that Scartella cristata, a species with a disjunct distribution, is a lineage complex comprising five clades: two in Caribbean waters, another in the East Atlantic/Mediterranean and two in Brazil. Brazilian clades occur in sympatry from Rio de Janeiro to Rio Grande do Sul states (southern Brazil). One clade (BRA 1) is unique to Brazil, while the other (BRA 2) is closely related to the eastern Atlantic lineage. Possible explanations for this pattern include both natural and anthropic mechanisms.

Toxicity of lead and mancozeb differs in two monophyletic Daphnia species

Lead and mancozeb are two important chemicals used for different human purposes and activities worldwide. Hazard assessment in different areas of the world is carried out with different but phylogenetically similar species, adapted to different climatic conditions, in order to increase relevance. This study evaluated the sensitivity of two monophyletic species, the tropical species Daphnia similis and the temperate species Daphnia magna, to the two chemicals lead and mancozeb. Standard acute and chronic ecotoxicological tests (reproduction and growth), as well as other sublethal measurements such as the intrinsic rate of population increase (r), feeding rate (FR) and O₂ consumption, were recorded along with the analysis of the AChE activity to determine the neurotoxicity of both contaminants. Albeit their similar evolutionary status, D. magna generally presented a lower sensitivity to Pb in comparison to D. similis. Despite the differences in sensitivity, both species presented similar patterns of response under Pb exposure, with diminished reproductive outputs, feeding impairment, reduced O₂ consumption and no effect on AChE activity. Mancozeb decreased the reproduction, rate of population increase and feeding rate, increased the AChE activity in both species and increased O₂ consumption only in D. magna. While D. magna increased O₂ consumption under mancozeb exposure, no effects were observed for D. similis. Thus, species may present different responses and sensitivities to different pollutants, regardless of their phylogeny. Therefore, the use of ecotoxicological assays with native species is crucial for a better ecological risk assessment in contaminated areas.

Multi-generational exposure to Pb in two monophyletic Daphnia species: Individual, functional and population related endpoints

To better evaluate chemical damage in chronically contaminated habitats, a nine-generational exposure to Lead (Pb) was done with two monophyletic Daphnia species, from temperate (Daphnia magna) and tropical (Daphnia similis) environments. The multi-generational test consisted generally of a continuous Pb exposed set of organisms, plus an extra control set running simultaneously. To assess daphnids recovery after Pb exposure, some organisms from the sixth generation were transferred to clean media for three extra generations (recovery period; F6 to F9), while others were keep Pb exposed. All setups (control, Pb exposure and recovery period) were submitted to two different dietary regimes, the standard (3 × 10⁵ cells/mL) and restricted food (1.5 × 10⁵ cells/mL) regimes. To evaluate the effects of generational Pb exposure and food regimes, individual, functional and population related endpoints were assessed (number of offspring, body length and rate of population increase (r) and feeding rate (FR)). The tests were conducted on the first (F0) and last generations (F9). No differences were shown on number of offspring and feeding among F9 control and continuous Pb exposed D. magna, although a higher r was shown for F9 Pb exposed organisms. F9 Pb exposed D. similis also presented a higher r than F9 control, however, lethality was induced at high Pb exposure levels. At food restriction the patterns were opposite and D. magna died at high Pb exposure while Pb exposed D. similis was the only setup (compared to control and recovery period) to survive at high Pb exposure levels. Regarding the recovery period, D. magna (standard food) did not cope well with the Pb re-exposure and lethality was induced, while D. similis indicate a decreased Pb sensitivity (only setup that survived high Pb exposure levels). Under food restriction, both species presented a decreased Pb sensitivity and consequent failed recovery (possibly due to epigenetic changes). Both species presented similar patterns regarding generations. Organisms from F0 presented enhanced reproductive outputs in comparison to F9 and the contrary occurred to the FR (even in control organisms). Data show an acclimation under a generational Pb exposure, which could increase the population of adapted organisms in natural habitats. And, since there was not a full recovery after three generations in clean media, an indication of epigenetic changes for both species may also be considered.

Bioaccumulation and morphological traits in a multi-generation test with two Daphnia species exposed to lead

Anthropic pressure negatively affects natural environments. Lead (Pb) is a non-essential highly toxic metal that is present in aquatic ecosystems. Two daphnid species from two different latitudes, the temperate Daphnia magna and the tropical Daphnia similis were used as test-organisms to evaluate a long-term Pb exposure. Both species were exposed for nine generations to a chronic concentration of Pb (50 μg/L) and the effects were explored, considering some endpoints not commonly used in toxicity tests: body burden of Pb and presence of granules in the dorsal region of neonates, hemoglobin contents, carapace deformation and morphology, production of males and ephippia (or dormant haploid egg), changes in the eggs' colour and eggs abortion. This multi-generation test was conducted under two food regimes, the usual (3 × 10⁵ cells/mL) and the restricted (1.5 × 10⁵ cells/mL) regime. On generation F6, Pb acclimated neonates were changed to a clean media for three generations, to evaluate exposure retrieval (recovery period). Negative and adverse effects occurred through generations, but no disparity was shown between D. magna and D. similis. The D. magna Pb accumulation showed different patterns regarding food regime. Bioaccumulation was faster under usual food, rapidly reaching a saturation point, whereas a gradual increase occurred under food restriction. A successful retrieval happened regarding Pb in D. magna, since no difference between control and recovering organisms was evidenced regarding their Pb body burdens. Generational Pb exposure led to carapace malformations, Pb aggregation in neonates' dorsal region, reddish extremities, production of males, ephippia (or dormant haploid egg), and aborted eggs, and changes in the eggs' colour (green and white). Food restriction also induced the production of males. Reddish extremities disappeared in recovering organisms and ephippia (or dormant haploid egg) did not occurred during the recovery period. Existent males revealed a shorter lifespan than females (under stress). D. magna and D. similis presented similar responses, for the endpoints analysed; however, it does not mean that this lack of sensitivity difference will be observed when other endpoints (e.g. survival, reproduction) are considered. Bioaccumulation of Pb and adverse effects occurred at the tested concentration of 50μg/L, although higher Pb levels are allowed in the environment as safe concentrations, as reported by the Brazilian legislation and the literature where effects are evidences above 400 μg/L of Pb. Pb effects on reproduction, respiration, malformation, and other adverse effects suggest that a chronic generational exposure can be harmful to both D. magna and D. similis, and that such chronic contaminated environments should not be disregarded when it comes to environmental monitoring.

EPIGEN-Brazil Initiative resources: a Latin American imputation panel and the Scientific Workflow

EPIGEN-Brazil is one of the largest Latin American initiatives at the interface of human genomics, public health, and computational biology. Here, we present two resources to address two challenges to the global dissemination of precision medicine and the development of the bioinformatics know-how to support it. To address the underrepresentation of non-European individuals in human genome diversity studies, we present the EPIGEN-5M+1KGP imputation panel—the fusion of the public 1000 Genomes Project (1KGP) Phase 3 imputation panel with haplotypes derived from the EPIGEN-5M data set (a product of the genotyping of 4.3 million SNPs in 265 admixed individuals from the EPIGEN-Brazil Initiative). When we imputed a target SNPs data set (6487 admixed individuals genotyped for 2.2 million SNPs from the EPIGEN-Brazil project) with the EPIGEN-5M+1KGP panel, we gained 140,452 more SNPs in total than when using the 1KGP Phase 3 panel alone and 788,873 additional high confidence SNPs (info score ≥ 0.8). Thus, the major effect of the inclusion of the EPIGEN-5M data set in this new imputation panel is not only to gain more SNPs but also to improve the quality of imputation. To address the lack of transparency and reproducibility of bioinformatics protocols, we present a conceptual Scientific Workflow in the form of a website that models the scientific process (by including publications, flowcharts, masterscripts, documents, and bioinformatics protocols), making it accessible and interactive. Its applicability is shown in the context of the development of our EPIGEN-5M+1KGP imputation panel. The Scientific Workflow also serves as a repository of bioinformatics resources.

Ecotoxicological assessment of sediments from an urban marine protected area (Xixová-Japuí State Park, SP, Brazil)

This study aimed to evaluate the environmental quality of the marine portion of Xixová-Japuí State Park (XJSP), an urban marine protected area, which is influenced by multiple contamination sources, by using ecotoxicological and geochemical analyses. Sediments were predominantly sandy, with low CaCO3 and organic matter contents, and presented contamination by metals (Cd,Cu,Zn). Acute toxicity was detected in three tested samples, and copepod exposed to sediments from four stations exhibited lower fecundities, despite the absence of significant effects. Contamination and toxicity seemed to be associated, suggesting that the environment is degraded and presents risks to the biota. Whole sediment TIE indicated ammonia as a main responsible for toxicity, suggesting sewage is a main contributor to sediment degradation. As external contamination sources seem to be negatively influencing the sediment quality, the park conservation objectives are not being fully reached, demanding actions to mitigate impacts.

Viability of impacted bone allografts under metal mesh at the calcar in revision surgery of the hip

Metal meshes are used in revision surgery of the hip to contain impacted bone grafts in cases with cortical or calcar defects in order to provide rotational stability to the stem. However, the viability of bone allografts under these metal meshes has been uncertain. We describe the histological appearances of biopsies obtained from impacted bone allografts to the calcar contained by a metal mesh in two femoral reconstructions which needed further surgery at 24 and 33 months after the revision procedure. A line of osteoid and viable new bone was observed on the surface of necrotic trabeculae. Active bone marrow between these trabeculae showed necrotic areas in some medullary spaces with reparative fibrous tissue and isolated reactive lymphocytes. This is interpreted as reparative changes after revascularisation of the cancellous allografts. These pathological findings are similar to those reported in allografts contained by cortical host bone and support the hypothesis that incorporation of morcellised bone under metal meshes is not affected by these devices.