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Genome-wide Ancestry and Demographic History of African-Descendant Maroon Communities from French Guiana and Suriname

Fortes Lima, César Augusto; Gessain, Antoine; Ruiz Linares, Andrés; Bortolini, Maria Cátira; Migot Nabias, Florence; Bellis, Gil; Moreno Mayar, José Víctor; Restrepo Jaramillo, Berta Nelly; Rojas Montoya, Winston; Avendaño Tamayo, Efrén De Jesús; Bedoya Berrío, Gabriel de Jesús; Orlando, Ludovic; Salas Ellacuriaga, Antonio; Helgason, Agnar; Pius Gilbert, Marcus Thomas; Sikora, Martin; Schroeder, Hannes; Dugoujon, Jean Michel (Cell PressEstados Unidos, 2017)

The transatlantic slave trade was the largest forced migration in world history. However, the origins of the enslaved Africans and their admixture dynamics remain unclear. To investigate the demographic history of ...
Predicting haplogroups using a versatile machine learning program (PredYMaLe) on a new mutationally balanced 32 Y-STR multiplex (CombYplex): Unlocking the full potential of the human STR mutation rate spectrum to estimate forensic parameters

Bouakaze, Caroline; Delehelle, Franklin; Sáenz Oyhéréguy, Nancy; Moreira, Andreia; Schiavinato, Stéphanie; Croze, Myriam; Delon, Solène; Fortes Lima, Cesar Augusto; Gibert, Morgane; Bujan, Louis; Huyghe, Éric; Bellis, Gil; Calderón Fernández, María del Rosario; Hernández de la Fuente, Candela Lucía; Avendaño Tamayo, Efrén De Jesús; Bedoya Berrío, Gabriel de Jesús; Salas Ellacuriaga, Antonio; Mazières, Stéphane; Charioni, Jacques; Migot Nabias, Florence; Ruiz Linarès, Andrés; Dugoujon, Jean Michel H.; Thèves, Catherine; Mollereau Manaute, Catherine; Noûs, Camille; Poulet, Nicolas; King, Turi; D'Amato, María Eugenia; Balaresque, Patricia L. (Elsevier BVNetherlands, 2020)

We developed a new mutationally well-balanced 32 Y-STR multiplex (CombYplex) together with a machine learning (ML) program PredYMaLe to assess the impact of STR mutability on haplogourp prediction, while respecting forensic ...

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Genome-wide Ancestry and Demographic History of African-Descendant Maroon Communities from French Guiana and Suriname
...
Fortes Lima, César Augusto | 2017

The transatlantic slave trade was the largest forced migration in world history. However, the origins of the enslaved Africans and their admixture dynamics remain unclear. To investigate the demographic history of African-descendant Marron populations, we generated genome-wide data (4.3 million markers) from 107 individuals from three African-descendant populations in South America, as well as 124 individuals from six west African populations. Throughout the Americas, thousands of enslaved Africans managed to escape captivity and establish lasting communities, such as the Noir Marron. We find that this population has the highest proportion of African ancestry ( 98%) of any African-descendant population analyzed to date, presumably because of centuries of genetic isolation. By contrast, African-descendant populations in Brazil and Colombia harbor substantially more European and Native American ancestry as a result of their complex admixture histories. Using ancestry tract-length analysis, we detect different dates for the European admixture events in the African-Colombian (1749 CE; confidence interval [CI]: 1737–1764) and African-Brazilian (1796 CE; CI: 1789–1804) populations in our dataset, consistent with the historically attested earlier influx of Africans into Colombia. Furthermore, we find evidence for sex-specific admixture patterns, resulting from predominantly European paternal gene flow. Finally, we detect strong genetic links between the African-descendant populations and specific source populations in Africa on the basis of haplotype sharing patterns. Although the Noir Marron and African-Colombians show stronger affinities with African populations from the Bight of Benin and the Gold Coast, the African-Brazilian population from Rio de Janeiro has greater genetic affinity with Bantu-speaking populations from the Bight of Biafra and west central Africa.

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Predicting haplogroups using a versatile machine learning program (PredYMaLe) on a new mutationally balanced 32 Y-STR multiplex (CombYplex): Unlocking the full potential of the human STR mutation rate spectrum to estimate forensic parameters
...
Bouakaze, Caroline | 2020

We developed a new mutationally well-balanced 32 Y-STR multiplex (CombYplex) together with a machine learning (ML) program PredYMaLe to assess the impact of STR mutability on haplogourp prediction, while respecting forensic community criteria (high DC/HD). We designed CombYplex around two sub-panels M1 and M2 characterized by average and high-mutation STR panels. Using these two sub-panels, we tested how our program PredYmale reacts to mutability when considering basal branches and, moving down, terminal branches. We tested first the discrimination capacity of CombYplex on 996 human samples using various forensic and statistical parameters and showed that its resolution is sufficient to separate haplogroup classes. In parallel, PredYMaLe was designed and used to test whether a ML approach can predict haplogroup classes from Y-STR profiles. Applied to our kit, SVM and Random Forest classifiers perform very well (average 97 %), better than Neural Network (average 91 %) and Bayesian methods (< 90 %). We observe heterogeneity in haplogroup assignation accuracy among classes, with most haplogroups having high prediction scores (99–100 %) and two (E1b1b and G) having lower scores (67 %). The small sample sizes of these classes explain the high tendency to misclassify the Y-profiles of these haplogroups; results were measurably improved as soon as more training data were added. We provide evidence that our ML approach is a robust method to accurately predict haplogroups when it is combined with a sufficient number of markers, well-balanced mutation rate Y-STR panels, and large ML training sets. Further research on confounding factors (such as CNV-STR or gene conversion) and ideal STR panels in regard to the branches analysed can be developed to help classifiers further optimize prediction scores.

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Browsing by Author "Salas Ellacuriaga, Antonio"

Genome-wide Ancestry and Demographic History of African-Descendant Maroon Communities from French Guiana and Suriname

Predicting haplogroups using a versatile machine learning program (PredYMaLe) on a new mutationally balanced 32 Y-STR multiplex (CombYplex): Unlocking the full potential of the human STR mutation rate spectrum to estimate forensic parameters

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Genome-wide Ancestry and Demographic History of African-Descendant Maroon Communities from French Guiana and Suriname

Predicting haplogroups using a versatile machine learning program (PredYMaLe) on a new mutationally balanced 32 Y-STR multiplex (CombYplex): Unlocking the full potential of the human STR mutation rate spectrum to estimate forensic parameters

Browsing by Author "Salas Ellacuriaga, Antonio"

Genome-wide Ancestry and Demographic History of African-Descendant Maroon Communities from French Guiana and Suriname ﻿

Predicting haplogroups using a versatile machine learning program (PredYMaLe) on a new mutationally balanced 32 Y-STR multiplex (CombYplex): Unlocking the full potential of the human STR mutation rate spectrum to estimate forensic parameters ﻿

Envíos recientes

Genome-wide Ancestry and Demographic History of African-Descendant Maroon Communities from French Guiana and Suriname

Predicting haplogroups using a versatile machine learning program (PredYMaLe) on a new mutationally balanced 32 Y-STR multiplex (CombYplex): Unlocking the full potential of the human STR mutation rate spectrum to estimate forensic parameters

Genome-wide Ancestry and Demographic History of African-Descendant Maroon Communities from French Guiana and Suriname

Predicting haplogroups using a versatile machine learning program (PredYMaLe) on a new mutationally balanced 32 Y-STR multiplex (CombYplex): Unlocking the full potential of the human STR mutation rate spectrum to estimate forensic parameters