Daniel Fidalgo

• PhD
• University of São Paulo

Based on dental morphology, it was recently suggested that the Southeast Coast of Brazil was inhabited by different biological groups throughout the Holocene. Among those that inhabited São Paulo state, coastal shellmound builders seem biologically distant from riverine shellmound builders. Additionally, individuals that later built ichthyological...

In this study, total mercury (THg) was analyzed in archaeological human bone from 23 sites dating to between the Middle Neolithic and the Antiquity. A total of 370 individuals from individual or collective burials were sampled, mostly using cortical bone from the humerus. These individuals were recovered from over 50 different funerary structures r...

RESUMO Aqui exploramos o potencial informativo da análise de remanescentes humanos quando o corpo é em si percepcionado enquanto tecnologia perecível. Essa é uma premissa básica da abordagem biocultural utilizada pela bioarqueologia, mas nem sempre é claramente evidente para arqueólogas e arqueólogos que não são especialistas nessa disciplina. Nest...

Dental wear is described as a limitation to dental morphological studies, as it obscures important crown trait features, resulting in significant differences on trait frequencies, an essential component for estimating biodistances. However, the actual impact of dental wear on biological distances still requires further characterization. We explore...

Objective The Southeast and South Coast of Brazil was inhabited during most of the Holocene by shellmound builders. Although there are cultural differences in the archaeological record between regions, it is still debatable how these differences may relate to different population histories. Here, we contribute to this discussion by exploring dental...

A middle-age adult male from the Bronze Age necropolis Torre Velha 3 (Serpa, Portugal) shows an enlarged right femoral head (coxa magna) with severe osteoarthrosis, and compatible changes on the right acetabulum. Using macroscopic and X-ray analysis, we discuss its possible aetiology as Legg-Calvé-Perthes, slipped femoral capital epiphysis, congeni...

Dental examination of 21 individuals (11 females, nine males and one undetermined sex) exhumed from the rock‐cut tombs of Torre Velha 3 (Serpa, Portugal), dating from the 2nd millennium BC, revealed dental wear features and oral lesions that can be linked to non‐masticatory activities and/or dietary habits. A total of 471 teeth were macroscopically...

Os Kaingang de São Paulo, entre os séculos XIX e XX, sofreram diversas ocupações no seu território pela frente de expansão colonialista. A deturpação de antigos cemitérios foi recorrente, mas alguns remanescentes foram parcialmente preservados e se encontram dispersos pelo Estado de São Paulo. Aqui se procurou rever, a partir da literatura, o poten...

We analyse new genomic data (0.05–2.95x) from 14 ancient individuals from Portugal distributed from the Middle Neolithic (4200–3500 BC) to the Middle Bronze Age (1740–1430 BC) and impute genomewide diploid genotypes in these together with published ancient Eurasians. While discontinuity is evident in the transition to agriculture across the region,...

Archaeological information. (DOCX)

Ancient DNA analysis. (DOCX)

CHROMOPAINTER and fineSTRUCTURE analyses. (DOCX)

X-chromosome contamination based on the number of mismatches at X-chromosome SNPs and adjacent sites. (XLSX)

List of ancient samples selected for genotype imputation. (XLSX)

Coancestry matrix obtained with CHROMOPAINTER for the analysis including 67 ancient samples. (XLSX)

Map and geographical locations of the archaeological locations of the samples sequenced in the present study. (TIF)

Affinity of imputed calls to reference panel populations, relative to pseudo-haploid and diploid calls, for five high coverage ancient samples. Results are shown for both all sites and just transversions in two separate panels. A world minor allele frequency of 25% has been applied. 1000 Genomes population and superpopulation names are noted along...

Affinity of imputed calls from five high coverage ancient samples to reference panel populations, relative to diploid calls, for a series of MAF filters. Results are shown for both all sites and just transversions in on left hand and right hand panels respectively. Top panels display world MAF filters of 25% and 5%. Bottom panels display European M...

Geographical and PC genetic coordinates for the Western_HG1 cluster. (TIF)

Geographical and PC genetic coordinates for the fineSTRUCTURE Yamnaya_Afanasievo cluster. (TIF)

Geographical and PC genetic coordinates for the fineSTRUCTURE Portugal_BA cluster. (TIF)

Geographical and PC genetic coordinates for the fineSTRUCTURE Russia_LBA cluster. (TIF)

CHROMOPAINTER haplotype donation vectors between each one of the imputed and non-imputed samples. (A) Correlation between imputed and non-imputed median haplotype donation from sample BR2 (1), Loschbour (2) and LBK (3). (B) Normal Quantile-Quantile plots and outlier detection (labelled populations). Coloured dots show populations present (red) or a...

Comparison of ancient samples with other ancient and modern datasets using genotype data. (DOCX)

D-statistics in the form of D(Mbuti, X; Y, Z) to test admixture between ancient populations. (XLSX)

Sex determination using Ry_compute. (TIF)

Proportion of correctly imputed genotypes grouped by minor allele frequency bins of 0.005. In this analysis, imputed genotypes were filtered by post imputation genotype probability ⋝ 0.99. (TIF)

Geographical and PC genetic coordinates for the fineSTRUCTURE cluster Caucasus Hunter-gatherers. (TIF)

Geographical and PC genetic coordinates for the fineSTRUCTURE HungarianMLN_SpainCardialEN cluster. (TIF)

Geographical and PC genetic coordinates for the fineSTRUCTURE CopperAge_to_AngloSaxon cluster. (TIF)

Geographical and PC genetic coordinates for the fineSTRUCTURE Hungary_BA cluster. (TIF)

Correlation between strands of ancestry and inferred polygenic risk score in present-day Europeans. Hunter-gatherer (WHG, EHG, CHG), Neolithic (Anatolian_EN) and Steppe (Yamnaya) Ancestry was measured by f4(Mbuti, Ancient_Ind1; Modern_WEurasian, Dai)/f4(Mbuti, Ancient_Ind1; Ancient_Ind2, Dai). Polygenic risk scores for height (92) were determined u...

Polygenic scores for pigmentation. SNPs with posterior genotype probability of less than 0.99 were excluded from analysis. (TIF)

Extended haplotype homozygosity (EHH) in regions under selection. Panels on the left represent the decay of EHH, or the probability of homozygosity at a certain base across 2 randomly chosen chromosomes in a population. Plots on the right represent existing haplotypes in a population, with the lower portion of the graph depicting haplotypes with th...

Extended haplotype homozygosity analysis. (DOCX)

X-chromosome contamination estimated with ANGSD (Korneliussen et al. 2014) and based on a previously published method (Rasmussen et al. 2011). (XLSX)

Selected D-statistics associated with Portuguese Neolithic and Bronze samples. (XLSX)

List of ancient individuals used in the F4 ratio test. This table contains the individuals which were used to estimate the approximate percentage ancestry in modern populations of five ancestral groups who have contributed to western Eurasian variation, using an F4 ratio test (Patterson 2012). (XLSX)

Post-mortem misincorporations in ancient samples. (TIF)

Outgroup F3-statistics in the form F3(Mbuti; X, modern European population). (TIF)

Estimation of imputation accuracy on chromosome 21. Comparison of variant calls obtained for BR2, NE1, Loschbour and Stuttgart at full coverage with genotypes from the same 4 individuals downsampled to 2x and subsequently imputed. Accuracy in (A) all 3 types of genotypes; (B) homozygous reference; (C) heterozygous and (D) homozygous alternate. (TIF...

Affinity of imputed calls from five high coverage ancient samples to reference panel populations, relative to diploid calls, for the final set of SNPs used in downstream analyses. 1000 Genomes population and superpopulation names are noted along the X axis. (TIF)

Geographical and PC genetic coordinates for the fineSTRUCTURE AegeanEN_HungarianLBK cluster. (TIF)

Geographical and PC genetic coordinates for the fineSTRUCTURE Atlantic_Neolithic cluster. (TIF)

Comparison between (A) unlinked and (B) linked CHROMOPAINTER/fineSTRUCTURE analyses. The unlinked analysis is only able to identify 10 populations, 9 less than when incorporating the linkage model. (TIF)

Bar plots illustrating polygenic risk scores across time, estimated for each one of the ancient population clusters. The traits chosen were: A) Height; B) Pigmentation; C) BMI and D) T2D. Polygenic scores were centered at the mean for the dataset. As in Fig 1 in the main text, each cluster is represented with a different colour. (TIF)

Polygenic risk scores estimated for height using genomewide summary statistics from the Wood 2014 dataset. (A) p = 0 (B) p<0.001. SNPs with posterior genotype probability of less than 0.99 were excluded from analysis. (TIF)

Polygenic risk scores estimated for height using genomewide summary statistics (Lango et al., 180 SNPs). (TIF)

Exploring ancient Iberian affinities through F- and D-statistics. (DOCX)

Imputation of missing genotypes in ancient samples. (DOCX)

Analysis of polygenic traits. (DOCX)

mtDNA lineages and contamination estimates based on mismatches at haplotype defining sites. (XLSX)

Y-chromosome lineages determined in the ancient Portuguese samples. (XLSX)

Coancestry matrix obtained with CHROMOPAINTER for the analysis of a dataset including 67 ancient samples and modern Eurasian genomes. (XLSX)

Principal component analysis of 604 modern West Eurasians onto which variation from 224 ancient genomes has been projected. The analysis is based on approximately 600,000 SNP positions. Moderns samples from the Human Origins dataset are represented in greyscale, with the exception of modern Iberians shown in green. Ancient samples are coloured by t...

Affinity of pseudo-haploid calls to reference panel populations, relative to diploid calls, for five high coverage ancient samples. Results are shown for world MAF filters of 25% and 5%. Only transversion SNPs are considered. 1000 Genomes population and superpopulation names are noted along the X axis. (TIF)

Geographical and PC genetic coordinates for the Western_HG2 cluster. (TIF)

Geographical and PC genetic coordinates for the fineSTRUCTURE Scandinavian_HG cluster. (TIF)

Geographical and PC genetic coordinates for the fineSTRUCTURE Sintashta_Andronovo cluster. (TIF)

Geographical and PC genetic coordinates for the fineSTRUCTURE Russia_LBA_IA cluster. (TIF)

Polygenic risk scores estimated for T2D using genomewide summary statistics. A) p = 0 B) p<0.001. SNPs with posterior genotype probability of less than 0.99 were excluded from analysis. (TIF)

fineSTRUCTURE tree comparison between each one of the imputed and non-imputed samples (BR2, Loschbour and LBK). The position of aDNA samples (shown in red) is very similar in both analyses. (TIF)

Height map and PCA. Red—increased genetic height scores, black—decreased genetic height. Broadly, hunter-gatherers and populations from Copper age and after present highest proportion of height increasing associated variants followed by Neolithic farmers. (TIF)

Polygenic risk scores estimated for BMI using genomewide summary statistics. (A) p = 0 (B) p<0.001. SNPs with posterior genotype probability of less than 0.99 were excluded from analysis. (TIF)

We analyse new genomic data (0.05-2.95x) from 14 ancient individuals from Portugal distributed from the Middle Neolithic (4200-3500 BC) to the Middle Bronze Age (1740-1430 BC) and impute genomewide diploid genotypes in these together with published ancient Eurasians. While discontinuity is evident in the transition to agriculture across the region,...

Resumo: O presente trabalho incide sobre a análise antropológica do espólio ósseo humano recuperado de 21 hipogeus do arqueossítio de Torre Velha 3 (TV3; São Salvador, Serpa), datados entre os meados e a segunda metade do II milénio a.C.. Dezasseis hipogeus são individuais, três duplos (uma inumação in situ com uma redução associada) e um triplo (e...

The present work focuses on the anthropological analysis of the human remains exhumed from 21 hypogea of the archaeological site of Torre Velha 3 (TV3; São Salvador, Serpa), which is dated between the middle and second half of the II millennium B.C. Sixteen hypogea were individual, three double (one in situ burial with an associated reduction) and...