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Fournier, R.

Publications and source records attributed to Fournier, R..

8 recordsLinked to original sources

Buried in two places: Lineages from elite Maya tombs also found in distant caves

Classic Maya societies (250-900 CE) carved out urban centers in the rainforest reaching population heights and political complexity previously unknown in the Mesoamerican tropics. Kinship was a central feature of the social fabric, and rulership was legitimized through claims of direct descent from mythical ancestors. Mortuary practices kept the dead close to the living, and ancestor veneration sometimes produced complex deposits of disarticulated remains that are difficult to identify and whose biological relationships to one another cannot be understood without genetic data. We screened 487 human tooth and bone samples and successfully generated genome-wide data for 430 of them. Of these, 341 samples representing 107 distinct individuals were recovered from both elite and non-elite tombs in a Classic period kingdom (250-900) CE in the rugged Maya Mountains of Belize. Remarkably, 24 of these individuals have skeletal elements in both an elite tomb and in a ritual tooth cache in a distant cave located 26.5km away on the other side of the Maya Mountains. These results indicate that elite lineages created ancestors from their deceased relatives in geographically expansive ways and highlights the importance of caves in the belief system of Classic Maya elites.

genetics↗

A SNP panel for co-analysis of capture and shotgun ancient DNA data

Advances in technology have decreased the cost of generating genetic variation data from ancient people, resulting in exponentially increasing numbers of individuals with whole genome data. However, each technology comes with platform-specific biases, limiting co-analyzability of individuals sequenced with different technologies as well as joint analysis of modern and ancient individuals. We present a method to identify single nucleotide polymorphisms (SNPs) with minimal technology-specific bias. Leveraging data from over 16,300 ancient individuals, we apply this method to identify a set of a million SNPs that we call the "Compatibility" panel, and which has been effectively assayed in a large fraction of ancient human DNA experiments published to date. We also identify a subset of these SNPs, the "Compatibility-HO" panel, which further restricts to positions that have been assayed in more than ten thousand modern individuals from more than a thousand diverse populations using the Affymetrix Human Origins (HO) genotyping array. The Compatibility panel reduces spurious Z-scores due to different sequencing platforms by nearly an order of magnitude, while retaining around 65-85% of statistical power for f-statistic analysis. We also provide a tool for users to select different tradeoffs between bias and power as well as sequencing platforms for their specific analyses.

bioinformatics↗

The Genetic Origin of the Indo-Europeans

The Yamnaya archaeological complex appeared around 3300BCE across the steppes north of the Black and Caspian Seas, and by 3000BCE reached its maximal extent from Hungary in the west to Kazakhstan in the east. To localize the ancestral and geographical origins of the Yamnaya among the diverse Eneolithic people that preceded them, we studied ancient DNA data from 428 individuals of which 299 are reported for the first time, demonstrating three previously unknown Eneolithic genetic clines. First, a "Caucasus-Lower Volga" (CLV) Cline suffused with Caucasus hunter-gatherer (CHG) ancestry extended between a Caucasus Neolithic southern end in Neolithic Armenia, and a steppe northern end in Berezhnovka in the Lower Volga. Bidirectional gene flow across the CLV cline created admixed intermediate populations in both the north Caucasus, such as the Maikop people, and on the steppe, such as those at the site of Remontnoye north of the Manych depression. CLV people also helped form two major riverine clines by admixing with distinct groups of European hunter-gatherers. A "Volga Cline" was formed as Lower Volga people mixed with upriver populations that had more Eastern hunter-gatherer (EHG) ancestry, creating genetically hyper-variable populations as at Khvalynsk in the Middle Volga. A "Dnipro Cline" was formed as CLV people bearing both Caucasus Neolithic and Lower Volga ancestry moved west and acquired Ukraine Neolithic hunter-gatherer (UNHG) ancestry to establish the population of the Serednii Stih culture from which the direct ancestors of the Yamnaya themselves were formed around 4000BCE. This population grew rapidly after 3750-3350BCE, precipitating the expansion of people of the Yamnaya culture who totally displaced previous groups on the Volga and further east, while admixing with more sedentary groups in the west. CLV cline people with Lower Volga ancestry contributed four fifths of the ancestry of the Yamnaya, but also, entering Anatolia from the east, contributed at least a tenth of the ancestry of Bronze Age Central Anatolians, where the Hittite language, related to the Indo-European languages spread by the Yamnaya, was spoken. We thus propose that the final unity of the speakers of the "Proto-Indo-Anatolian" ancestral language of both Anatolian and Indo-European languages can be traced to CLV cline people sometime between 4400-4000 BCE. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=115 SRC="FIGDIR/small/589597v1_ufig1.gif" ALT="Figure 1"> View larger version (91K): org.highwire.dtl.DTLVardef@127de98org.highwire.dtl.DTLVardef@87010aorg.highwire.dtl.DTLVardef@1554627org.highwire.dtl.DTLVardef@170dd63_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOSummary Figure:C_FLOATNO The origin of Indo-Anatolian and Indo-European languages. Genetic reconstruction of the ancestry of Pontic-Caspian steppe and West Asian populations points to the North Caucasus-Lower Volga area as the homeland of Indo-Anatolian languages and to the Serednii Stih archaeological culture of the Dnipro-Don area as the homeland of Indo-European languages. The Caucasus-Lower Volga people had diverse distal roots, estimated using the qpAdm software on the left barplot, as Caucasus hunter-gatherer (purple), Central Asian (red), Eastern hunter-gatherer (pink), and West Asian Neolithic (green). Caucasus-Lower Volga expansions, estimated using qpAdm on the right barplot as disseminated Caucasus Neolithic (blue)-Lower Volga Eneolithic (orange) proximal ancestries, mixing with the inhabitants of the North Pontic region (yellow), Volga region (yellow), and West Asia (green). C_FIG

genetics↗

Emo-FilM: A multimodal dataset for affective neuroscience using naturalistic stimuli

The extensive Emo-FilM dataset stands for Emotion research using Films and fMRI in healthy participants. This dataset includes detailed emotion annotations by 44 raters for 14 short films with a combined duration of over 2[1/2] hours, as well as recordings of respiration, heart rate, and functional magnetic resonance imaging (fMRI) from a different sample of 30 individuals watching the same films. The detailed annotations of experienced emotion evaluated 50 items including ratings of discrete emotions and emotion components from the domains of appraisal, motivation, motor expression, physiological response, and feeling. Quality assessment for the behavioural data shows a mean inter-rater agreement of 0.38. The parallel fMRI data was acquired at 3 Tesla in four sessions, accompanied with a high-resolution structural (T1) and resting state fMRI scans for each participant. Physiological recordings during fMRI included heart rate, respiration, and electrodermal activity (EDA). Quality assessment indicators confirm acceptable quality of the MRI data. This dataset is designed, but not limited, to studying the dynamic neural processes involved in emotion experience. A particular strength of this data is the high temporal resolution of behavioural annotations, as well as the inclusion of a validation study in the fMRI sample. This high-quality behavioural data in combination with continuous physiological and MRI measurements makes this dataset a treasure trove for researching human emotion in response to naturalistic stimulation in a multimodal framework.

neuroscience↗

Social and genetic diversity in first farmers of central Europe

The Linearbandkeramik (LBK) Neolithic communities were the first to spread farming across large parts of central Europe, settling fertile regions from Ukraine to France during the second half of the 6th millennium BCE. The LBK had a high degree of material culture uniformity, albeit with regional differences in settlement patterns, subsistence, and mortuary practices. To date, ancient DNA data from LBK individuals have been generated for a limited number of locations and often in small sample sizes, making it challenging to study variation within and across sites. We report genome-wide data for 178 LBK individuals, from the Alfold Linearbankeramik Culture (ALPC) eastern LBK site of Polgar-Ferenci-hat in Hungary, the western LBK site of Nitra in Slovakia, and the enclosed western LBK settlement and massacre site of Schletz in Austria, as well as 42 LBK individuals from 18 other sites. We also report genome-wide data for 28 Early Neolithic Koros and Star[c]evo individuals from 13 sites, viewed as the predecessors of the LBK. We observe a higher percentage of western hunter-gatherer (WHG) admixture among individuals in the eastern LBK than in the far more widely distributed western LBK, showing that these two archaeologically distinct cultures also had different genetic trajectories. Most WHG-farmer mixture occurred just before the dawn of the LBK culture and there is no evidence that the WHG ancestry came systematically more from males or females. However, we do find strong genetic evidence for patrilocality among the LBK, extending previous findings based on isotopic analysis, with more genetic structure across sites on the male than on the female line, and a higher rate of within-site relatives for males. At Schletz we detect almost no first-degree relatives despite reporting data from almost every skeleton present at the site, showing that this massacre involved people from a large population, not a small community.

genetics↗

Positive effects of projected climate change on post-disturbance forest regrowth rates in northeastern North American boreal forests

Forest anthropogenic and natural stand-replacing disturbances are increasing worldwide due to global change. Many uncertainties regarding the regeneration and growth of these young forests remain within the context of changing climate. In this study, we investigate the effects of climate, tree species composition, and other landscape-scale environmental variables upon boreal forest regrowth following clearcut logging in eastern Canada. Our main objective was to predict the effects of future climate changes upon post-logging forest height regrowth at a subcontinental scale using high spatial resolution remote sensing data. We modeled forest canopy height (estimated from airborne laser scanning [LiDAR] data over 20-m resolution virtual plots) as a function of time elapsed since the last clearcut along with climatic (i.e., temperature and moisture), tree species composition, and other environmental variables (e.g., topography and soil hydrology). Once trained and validated with [~]240,000 plots, the model that was developed in this study was used to predict potential post-logging canopy height regrowth at 20-m resolution across a 240,000 km2 area following scenarios depicting a range of projected changes in temperature and moisture across the region for 2041-2070. Our results predict an overall beneficial, but limited effect of projected climate changes upon forest regrowth rates in our study area. Stimulatory effects of projected climate change were more pronounced for conifer forests, with growth rates increasing between +5% and +50% over the study area, while mixed and broadleaved forests recorded changes that mostly ranged from -5% to +35%. Predicted increased regrowth rates were mainly associated with increased temperature, while changes in climate moisture had a minor effect. We conclude that such gains in regrowth rates may partially compensate for projected substantial increases in fire activity and other natural disturbances that are expected with climate change in these boreal forests.

ecology↗

Haplotype-based inference of recent effective population size in modern and ancient DNA samples

1Individuals sharing recent ancestors are likely to co-inherit large identical-by-descent (IBD) genomic regions. The distribution of these IBD segments in a population may be used to reconstruct past demographic events such as effective population size variation, but accurate IBD detection is difficult in ancient DNA (aDNA) data and in underrepresented populations with limited reference data. In this work, we introduce an accurate method for inferring effective population size variation during the past ~2,000 years in both modern and aDNA data, called HapNe. HapNe infers recent population size fluctuations using either IBD sharing (HapNe-IBD) or linkage disequilibrium (HapNe-LD), which does not require phasing and can be computed in low coverage data, including data sets with heterogeneous sampling times. HapNe showed improved accuracy in a range of simulated demographic scenarios compared to currently available methods for IBD-based and LD-based inference of recent effective population size, while requiring fewer computational resources. We applied HapNe to several modern populations from the 1, 000 Genomes Project, the UK Biobank, the Allen Ancient DNA Resource, and recently published samples from Iron Age Britain, detecting multiple instances of recent effective population size variation across these groups.

genetics↗

Cognitive exertion affects the appraisal of one's own and other people's pain

Correctly evaluating others pain is a crucial prosocial ability, especially relevant for the healthcare system. In clinical settings, caregivers assess their patients pain under high workload and fatigue, often while dealing with competing information/tasks. However, the effect played by such cognitive strain in the appraisal of others pain remains unclear. Following embodied accounts that posit a shared representational code between self and others states, it could be hypothesized that the representation of peoples pain might be influenced by cognitive exertion similarly to first-hand experiences. Fifty participants underwent one of two demanding tasks, involving either working memory (Experiment 1: N-Back task) or cognitive interference (Experiment 2: Stroop task). After each task, participants were exposed to painful laser stimulations at three intensity levels (low, medium, high), or video-clips of patients experiencing three intensity levels of pain (low, medium, high). Participants rated the intensity of each pain event on a visual analogue scale. We found that the two tasks influenced rating of both ones own and others pain, by decreasing the sensitivity to medium and high events. This was observed either when comparing the demanding condition to a control (Stroop), or when modelling linearly the difficulty/performance of each depleting task (N-Back). We provide converging evidence that cognitive exertion affects the subsequent appraisal of ones own and likewise others pain. Healthcare personnel should be aware that high workload might alter their cognitive abilities. Perspectivethis research shows that cognitive effort aftereffects impact negatively the assessment of of medium/high pain in others, reminiscently to what was observed in first-hand experiences. Healthcare professionals should be aware that high workload and severe cognitive fatigue could affect their diagnostic skills.

neuroscience↗