Papers by Maria A Nieves Colon
Molecular Biology and Evolution, 2019
Indigenous peoples have occupied the island of Puerto Rico since at least 3000 BC. Due to the dem... more Indigenous peoples have occupied the island of Puerto Rico since at least 3000 BC. Due to the demographic shifts that occurred after European contact, the origin(s) of these ancient populations, and their genetic relationship to present-day islanders, are unclear. We use ancient DNA to characterize the population history and genetic legacies of precontact Indigenous communities from Puerto Rico. Bone, tooth, and dental calculus samples were collected from 124 individuals from three precontact archaeological sites: Tibes, Punta Candelero, and Paso del Indio. Despite poor DNA preservation, we used target enrichment and high-throughput sequencing to obtain complete mitochondrial genomes (mtDNA) from 45 individuals and autosomal genotypes from two individuals. We found a high proportion of Native American mtDNA haplogroups A2 and C1 in the precontact Puerto Rico sample (40% and 44%, respectively). This distribution, as well as the haplotypes represented, supports a primarily Amazonian South American origin for these populations and mirrors the Native American mtDNA diversity patterns found in present-day islanders. Three mtDNA haplotypes from precon-tact Puerto Rico persist among Puerto Ricans and other Caribbean islanders, indicating that present-day populations are reservoirs of precontact mtDNA diversity. Lastly, we find similarity in autosomal ancestry patterns between precontact individuals from Puerto Rico and the Bahamas, suggesting a shared component of Indigenous Caribbean ancestry with close affinity to South American populations. Our findings contribute to a more complete reconstruction of precontact Caribbean population history and explore the role of Indigenous peoples in shaping the biocultural diversity of present-day Puerto Ricans and other Caribbean islanders.
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Objectives: The tropics harbor a large part of the world's biodiversity and have a long history o... more Objectives: The tropics harbor a large part of the world's biodiversity and have a long history of human habitation. However, paleogenomics research in these climates has been constrained so far by poor ancient DNA yields. Here we compare the performance of two DNA extraction methods on ancient samples of teeth and petrous portions excavated from tropical and semi-tropical sites in
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Hispanic/Latino (H/L) populations, although linked by culture and aspects of shared history, refl... more Hispanic/Latino (H/L) populations, although linked by culture and aspects of shared history, reflect the complexity of history and migration influencing the Americas. The original settlement by indigenous Americans, followed by postcolonial admixture from multiple continents, has yielded localized genetic patterns. In addition, numerous H/L populations appear to have signatures of pre-colonization and post-colonization bottlenecks, indicating that tens of millions of H/ Ls may harbor signatures of founder effects today. Based on both population and medical genetic findings we highlight the extreme differentiation across the Americas, providing evidence for why H/Ls should not be considered a single population in modern human genetics. We highlight the need for additional sampling of understudied H/L groups, and ramifications of these findings for genomic medicine in one-tenth of the world's population.
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Background: As most ancient biological samples have low levels of endogenous DNA, it is advantage... more Background: As most ancient biological samples have low levels of endogenous DNA, it is advantageous to enrich for specific genomic regions prior to sequencing. One approach—in-solution capture-enrichment—retrieves sequences of interest and reduces the fraction of microbial DNA. In this work, we implement a capture-enrichment approach targeting informative regions of the Y chromosome in six human archaeological remains excavated in the Caribbean and dated between 200 and 3000 years BP. We compare the recovery rate of Y-chromosome capture (YCC) alone, whole-genome capture followed by YCC (WGC + YCC) versus non-enriched (pre-capture) libraries. Results: The six samples show different levels of initial endogenous content, with very low (< 0.05%, 4 samples) or low (0.1–1.54%, 2 samples) percentages of sequenced reads mapping to the human genome. We recover 12–9549 times more targeted unique Y-chromosome sequences after capture, where 0.0–6.2% (WGC + YCC) and 0.0–23.5% (YCC) of the sequence reads were on-target, compared to 0.0–0.00003% pre-capture. In samples with endogenous DNA content greater than 0.1%, we found that WGC followed by YCC (WGC + YCC) yields lower enrichment due to the loss of complexity in consecutive capture experiments, whereas in samples with lower endogenous content, the libraries' initial low complexity leads to minor proportions of Y-chromosome reads. Finally, increasing recovery of informative sites enabled us to assign Y-chromosome haplogroups to some of the archeological remains and gain insights about their paternal lineages and origins. Conclusions: We present to our knowledge the first in-solution capture-enrichment method targeting the human Y-chromosome in aDNA sequencing libraries. YCC and WGC + YCC enrichments lead to an increase in the amount of Y-DNA sequences, as compared to libraries not enriched for the Y-chromosome. Our probe design effectively recovers regions of the Y-chromosome bearing phylogenetically informative sites, allowing us to identify paternal lineages with less sequencing than needed for pre-capture libraries. Finally, we recommend considering the endogenous content in the experimental design and avoiding consecutive rounds of capture, as clonality increases considerably with each round.
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Objectives: The tropics harbor a large part of the world's biodiversity and have a long history o... more Objectives: The tropics harbor a large part of the world's biodiversity and have a long history of human habitation. However, paleogenomics research in these climates has been constrained so far by poor ancient DNA yields. Here we compare the performance of two DNA extraction methods on ancient samples of teeth and petrous portions excavated from tropical and semi-tropical sites in
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An archaeological assessment was carried out on an unprovenienced human skull recovered in easter... more An archaeological assessment was carried out on an unprovenienced human skull recovered in eastern Idaho, exhibiting cranial deformation and peri-mortem application of a red pigment. A combination of scanning electron microscopy (SEM), X-ray fluorescence (XRF), and energy-dispersive X-ray spectroscopy (EDS) identified the major and trace elements present in the red pigment as natural cinnabar. Carbon and oxygen stable isotopes from teeth and bone suggest a mostly C3 plant-based diet with subsidiary consumption of salmon or marine resources , and a regional geographic transition between early life and late adulthood. Radiocarbon dating determined the approximate age of the skull to be between 600 and 700 years old, and ancient mitochondrial DNA assessment identified characteristics of haplogroup B, one of four major Native American mitochondrial DNA lin-eages, which is consistent with the osteological analyses.
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American Journal of Physical Anthropology, 2016
Archaeological dental calculus is a rich source of host-associated biomolecules. Importantly, how... more Archaeological dental calculus is a rich source of host-associated biomolecules. Importantly, however, dental calculus is more accurately described as a calcified microbial biofilm than a host tissue. As such, concerns regarding destructive analysis of human remains may not apply as strongly to dental calculus, opening the possibility of obtaining human health and ancestry information from dental calculus in cases where destructive analysis of conventional skeletal remains is not permitted. Here we investigate the preservation of human mitochondrial DNA (mtDNA) in archaeological dental calculus and its potential for full mitochondrial genome (mitogenome) reconstruction in maternal lineage ancestry analysis. Extracted DNA from six individuals at the 700-year-old Norris Farms #36 cemetery in Illinois was enriched for mtDNA using in-solution capture techniques, followed by Illumina high-throughput sequencing. Full mitogenomes (7-34×) were successfully reconstructed from dental calculus for all six individuals, including three individuals who had previously tested negative for DNA preservation in bone using conventional PCR techniques. Mitochondrial haplogroup assignments were consistent with previously published findings, and additional comparative analysis of paired dental calculus and dentine from two individuals yielded equivalent haplotype results. All dental calculus samples exhibited damage patterns consistent with ancient DNA, and mitochondrial sequences were estimated to be 92-100% endogenous. DNA polymerase choice was found to impact error rates in downstream sequence analysis, but these effects can be mitigated by greater sequencing depth. Dental calculus is a viable alternative source of human DNA that can be used to reconstruct full mitogenomes from archaeological remains. Am J Phys Anthropol, 2016. © 2016 The Authors American Journal of Physical Anthropology Published by Wiley Periodicals, Inc.
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Objectives: Archaeological dental calculus is a rich source of host-associated biomolecules. Impo... more Objectives: Archaeological dental calculus is a rich source of host-associated biomolecules. Importantly, however, dental calculus is more accurately described as a calcified microbial biofilm than a host tissue. As such, concerns regarding destructive analysis of human remains may not apply as strongly to dental calculus, opening the possibility of obtaining human health and ancestry information from dental calculus in cases where destructive analysis of conventional skeletal remains is not permitted. Here we investigate the preservation of human mitochondrial DNA (mtDNA) in archaeological dental calculus and its potential for full mitochondrial genome (mitogenome) reconstruction in maternal lineage ancestry analysis. Materials and Methods: Extracted DNA from six individuals at the 700-year-old Norris Farms #36 cemetery in Illi-nois was enriched for mtDNA using in-solution capture techniques, followed by Illumina high-throughput sequencing. Results: Full mitogenomes (7–343) were successfully reconstructed from dental calculus for all six individuals, including three individuals who had previously tested negative for DNA preservation in bone using conventional PCR techniques. Mitochondrial haplogroup assignments were consistent with previously published findings, and additional comparative analysis of paired dental calculus and dentine from two individuals yielded equivalent haplo-type results. All dental calculus samples exhibited damage patterns consistent with ancient DNA, and mitochondrial sequences were estimated to be 92–100% endogenous. DNA polymerase choice was found to impact error rates in downstream sequence analysis, but these effects can be mitigated by greater sequencing depth. Discussion: Dental calculus is a viable alternative source of human DNA that can be used to reconstruct full mitogenomes from archaeological remains. Am J Phys Anthropol 000:000–
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Nieves-Colón MA and Martínez-Cruzado, JC. 2012. La contribución genética de África Sub-Sahariana... more Nieves-Colón MA and Martínez-Cruzado, JC. 2012. La contribución genética de África Sub-Sahariana a la población de la República Dominicana según el estudio de su ADN mitocondrial. Cuadernos de Investigación Histórica, 7: 28-41. Proceedings from Coloquio Africa y sus Identidades, University of Puerto Rico, Río Piedras Campus, San Juan, PR.
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In "Encyclopedia of Caribbean Archaeology" edited volume.
Basil A. Reid and R. Grant Gilmore III ... more In "Encyclopedia of Caribbean Archaeology" edited volume.
Basil A. Reid and R. Grant Gilmore III (Eds.), 2015. University Press of Florida.
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Conference Presentations by Maria A Nieves Colon
In recent years, dental calculus has emerged as an important source of ancient genetic material. ... more In recent years, dental calculus has emerged as an important source of ancient genetic material. However, calculus has not been extensively utilized as a source of endogenous host DNA when working with human skeletal remains. In this study we compare endogenous DNA yields obtained from extractions performed from both dental calculus and dental tooth roots for three pre-Columbian individuals, originating from three different archaeological sites of the island of Puerto Rico. Furthermore, in order to assess the effects of physical decontamination procedures on recovery of endogenous DNA, tooth root samples were further subdivided into two groups: one group was treated by removal of the cementum and the second group was left untreated. Extractions were then performed in three replicates for each individual, one from calculus, one from treated tooth roots and one from untreated tooth roots. DNA extracts were quantified, transformed into sequencing libraries, and enriched for the complete mitochondrial genome through in-solution hybridization capture. Preliminary results indicate that out of nine extracts obtained (three replicates for each individual) only seven were successfully built into libraries. Sequence data suggest that libraries made from treated tooth root extracts contain, on average, more sequence reads mapping to the reference and higher coverage than libraries built from untreated tooth root or calculus extracts. These results suggest that although calculus is a viable source of endogenous DNA, treated tooth root extractions result in higher overall endogenous DNA yields and a reduced presence of contaminant DNA molecules in these samples.
This work was supported by the ASU School of International Letters and Cultures Foster Latin American Studies Summer support Grant and the ASU Graduate Professional Student Association Travel Grant Program.
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Papers by Maria A Nieves Colon
Basil A. Reid and R. Grant Gilmore III (Eds.), 2015. University Press of Florida.
Conference Presentations by Maria A Nieves Colon
This work was supported by the ASU School of International Letters and Cultures Foster Latin American Studies Summer support Grant and the ASU Graduate Professional Student Association Travel Grant Program.
Basil A. Reid and R. Grant Gilmore III (Eds.), 2015. University Press of Florida.
This work was supported by the ASU School of International Letters and Cultures Foster Latin American Studies Summer support Grant and the ASU Graduate Professional Student Association Travel Grant Program.