Late Pleistocene landscape changes and habitat specialization as promoters of population genomic divergence in Amazonian floodplain birds.

Although vicariant processes are expected to leave similar genomic signatures among codistributed taxa, ecological traits such as habitat and stratum can influence genetic divergence within species. Here, we combined landscape history and habitat specialization to understand the historical and ecological factors responsible for current levels of genetic divergence in three species of birds specialized in seasonally flooded habitats in muddy rivers and which are widespread in the Amazon basin but have isolated populations in the Rio Branco. Populations of the white-bellied spinetail (Mazaria propinqua), lesser wagtail-tyrant (Stigmatura napensis) and bicolored conebill (Conirostrum bicolor) are currently isolated in the Rio Branco by the black-waters of the lower Rio Negro, offering a unique opportunity to test the effect of river colour as a barrier to gene flow. We used ultraconserved elements (UCEs) to test alternative hypotheses of population history in a comparative phylogeographical approach by modelling genetic structure, demographic history and testing for shared divergence time among codistributed taxa. Our analyses revealed that (i) all three populations from the Rio Branco floodplains are genetically distinct from other populations along the Amazon River floodplains; (ii) these divergences are the result of at least two distinct events, consistent with species habitat specialization; and (iii) the most likely model of population evolution includes lower population connectivity during the Late Pleistocene transition (~250,000 years ago), with gene flow being completely disrupted after the Last Glacial Maximum (~21,000 years ago). Our findings highlight how landscape evolution modulates population connectivity in habitat specialist species and how organisms can have different responses to the same historical processes of environmental change, depending on their habitat affinity.

Phylogeography of Baryancistrus xanthellus (Siluriformes: Loricariidae), a rheophilic catfish endemic to the Xingu River basin in eastern Amazonia.

Baryancistrus xanthellus (Loricariidae) is an endemic fish species from the Xingu River basin with its life history in the shallow rapid waters flowing over bedrock substrates. In order to investigate the genetic diversity and demographic history of B. xanthellus we analyzed sequence data for one mitochondrial gene (Cyt b) and introns 1 and 5 of nuclear genes Prolactin (Prl) and Ribosomal Protein L3 (RPL3). The analyses contain 358 specimens of B. xanthellus from 39 localities distributed throughout its range. The number of genetically diverged groups was estimated using Bayesian inference on Cyt b haplotypes. Haplotype networks, AMOVA and pairwise fixation index was used to evaluate population structure and gene flow. Historical demography was inferred through neutrality tests and the Extended Bayesian Skyline Plot (EBSP) method. Five longitudinally distributed Cyt b haplogroups for B. xanthellus were identified in the Xingu River and its major tributaries, the Bacajá and Iriri. The demographic analysis suggests that rapids habitats have expanded in the Iriri and Lower Xingu rivers since 200 ka (thousand years) ago. This expansion is possibly related to an increase in water discharge as a consequence of higher rainfall across eastern Amazonia. Conversely, this climate shift also would have promoted zones of sediment trapping and reduction of rocky habitats in the Xingu River channel upstream of the Iriri River mouth. Populations of B. xanthellus showed strong genetic structure along the free-flowing river channels of the Xingu and its major tributaries, the Bacajá and Iriri. The recent impoundment of the Middle Xingu channel for the Belo Monte hydroelectric dam may isolate populations at the downstream limit of the species distribution. Therefore, future conservation plans must consider the genetic diversity of B. xanthellus throughout its range.

Microplastics in sediments from Amazon rivers, Brazil.

We assessed the concentrations of microplastics in sediment samples collected in seven sites from Solimões, Negro and Amazon rivers, upstream and downstream the metropolitan region of Manaus. Concentrations ranged from 417 to 8178 particles/kg of dried sediment (microplastics: 0.063-5 mm), and from 0 to 5725 particles/kg of dried sediment (microplastics: 0.063-1 mm). The highest microplastics concentrations were observed in samples from shallow water (water depth of 5-7 m) sites with lower water velocity of the Negro river surrounding Manaus, and the lowest concentration in farthest sample collected in deeper zone (water depth of 34 m) of the Amazon river around 110 km downstream Manaus. The variation of microplastics concentrations within the studied area can be related to hydraulic characteristics defining the erosive-depositional behavior of the sampling sites and their proximity to Manaus. Our results represent the first report to show the ubiquitous presence and widespread distribution of microplastics in sediments from the lower Solimões, lower Negro and upper Amazon rivers.

Shut down of the South American summer monsoon during the penultimate glacial.

We analysed changes in mean annual air temperature (MAAT), vegetation and biomass burning on a long and continuous lake-peat sediment record from the Colônia basin, southeastern Brazil, examining the responses of a wet tropical rainforest over the last 180 ka. Stronger southern atmospheric circulation up to the latitude of Colônia was found for the penultimate glacial with lower temperatures than during the last glacial, while strengthening of the South American summer monsoon (SASM) circulation started during the last interglacial and progressively enhanced a longer wet summer season from 95 ka until the present. Past MAAT variations and fire history were possibly modulated by eccentricity, although with signatures which differ in average and in amplitude between the last 180 ka. Vegetation responses were driven by the interplay between the SASM and southern circulation linked to Antarctic ice volume, inferred by the presence of a cool mixed evergreen forest from 180 to 45 ka progressively replaced by a rainforest. We report cooler temperatures during the marine isotope stage 3 (MIS 3: 57-29 ka) than during the Last Glacial Maximum (LGM: 23-19 ka). Our findings show that tropical forest dynamics display different patterns than mid-latitude during the last 180 ka.

Optically Stimulated Luminescence Sensitivity of Quartz for Provenance Analysis.

Finding the source or provenance of quartz grains occurring in a specific location allows us to constrain their transport pathway, which is crucial information to solve diverse problems in geosciences and related fields. The optically stimulated luminescence (OSL) sensitivity (light intensity per unit mass per unit radiation dose) has a high capacity for discrimination of quartz sediment grains and represents a promising technique for provenance analysis. In this study, we tested the use of quartz OSL sensitivity (ultraviolet emission) measured under different preheating temperatures and with blue light stimulation at room temperature (~20 °C) for sediment provenance analysis. Quartz OSL sensitivity measured at 20 °C is positively correlated with the sensitivity of an OSL signal measured using procedures (preheat at 190 °C for 10 s, blue stimulation at 125 °C and initial 1 s of light emission) to increase the contribution of the fast OSL component, which has been successfully applied for sediment provenance analysis. The higher OSL signal intensity measured without preheating and with light stimulation at room temperature allows the use of lower given doses, thus reducing measurement time. Additionally, the OSL sensitivity measured at 20 °C in polymineral silt samples of a marine sediment core is also suitable for provenance analysis, as demonstrated by comparison with other independent proxies. OSL signals obtained through light stimulation at room temperature have thus the potential to considerably expand measurement possibilities, including in situ measurements using portable OSL readers.

New Archaeological Evidence for an Early Human Presence at Monte Verde, Chile.

Questions surrounding the chronology, place, and character of the initial human colonization of the Americas are a long-standing focus of debate. Interdisciplinary debate continues over the timing of entry, the rapidity and direction of dispersion, the variety of human responses to diverse habitats, the criteria for evaluating the validity of early sites, and the differences and similarities between colonization in North and South America. Despite recent advances in our understanding of these issues, archaeology still faces challenges in defining interdisciplinary research problems, assessing the reliability of the data, and applying new interpretative models. As the debates and challenges continue, new studies take place and previous research reexamined. Here we discuss recent exploratory excavation at and interdisciplinary data from the Monte Verde area in Chile to further our understanding of the first peopling of the Americas. New evidence of stone artifacts, faunal remains, and burned areas suggests discrete horizons of ephemeral human activity in a sandur plain setting radiocarbon and luminescence dated between at least ~18,500 and 14,500 cal BP. Based on multiple lines of evidence, including sedimentary proxies and artifact analysis, we present the probable anthropogenic origins and wider implications of this evidence. In a non-glacial cold climate environment of the south-central Andes, which is challenging for human occupation and for the preservation of hunter-gatherer sites, these horizons provide insight into an earlier context of late Pleistocene human behavior in northern Patagonia.