Genomic insights into the early peopling of the Caribbean

Nägele, Kathrin; Posth, Cosimo; Orbegozo, Miren Iraeta; Armas, Yadira Chinique de; Godoy, Silvia Teresita Hernández; Herrera, Ulises M. González; Nieves-Colón, María A.; Sandoval-Velasco, Marcela; Mylopotamitaki, Dorothea; Radzevičiūtė, Rita; Laffoon, Jason E.; Pestle, William J.; Ramos‐Madrigal, Jazmín; Lamnidis, Thiseas Christos; Schaffer, William C.; Carr, Robert; Day, Jane; Antúnez, Carlos Arredondo; Rivero, Armando Rangel; Martínez-Fuentes, Antonio J.; Crespo-Torres, Edwin; Roksandic, Ivan; Stone, Anne C.; Lalueza‐Fox, Carles; Hoogland, Menno L. P.; Roksandić, Mirjana; Hofman, Corinne L.; Krause, Johannes; Schroeder, Hannes

doi:10.1126/science.aba8697

Cited by 49 publications

(47 citation statements)

References 73 publications

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“…Significance values are consistent with pairs of Isthmian and non-Isthmian groups deriving from at least two separate streams of ancestry, as attested by Rank1 p-value <0.01 in most comparisons, especially for the Guna (Figure S30). This finding demonstrates that the distinctiveness of the Isthmo-Colombian area cannot be explained by genetic drift alone, as recently inferred in other population contexts (Nägele et al, 2020). The Guna also show lower values (mostly <25 th percentile) of shared genetic history with ancient genomes representative of well-known Indigenous ancestries than the average of the one shared by other IA populations (Figure S31).…”

Section: Resultssupporting

confidence: 84%

“…We retained only populations with more than 30K overlapping SNPs and significant Z-scores (>3.3) in all comparisons. This distance matrix was used to generate a neighbor joining tree ( Figure S19) with the program PHYLIP 3.6 (Nägele et al, 2020). The tree was visualized with FigTree 1.4.4 (https://github.com/rambaut/figtree).…”

Section: Admixture Tests (F-statistics)mentioning

confidence: 99%

“…• Mbuti, Papuan, CHB, Malta_24000 and USR_11500 as non-IA sources (Nägele et al, 2020;Posth et al, 2018) • ASO_4000 and Chipewyan for NNA • LagoaSanta_10400 for SNA1…”

Section: Ancestry Modelling With Qpwavementioning

confidence: 99%

“…We used ANGSD (Korneliussen et al, 2014) to estimate contamination on reads with mapping quality greater than 30 and base quality greater than 20. We considered at least 100 sites with depth greater than or equal to 2 (Nägele et al, 2020) matching the HapMap CEU allele frequencies (Altshuler, 2010) as potential contaminants, after excluding pseudo-autosomal regions on chromosome X. We then applied the tool presented in (Moreno-Mayar et al, 2020) to estimate contamination using low-depth X-chromosome data, setting to 1,000 the maximum number of jackknife samples used for estimating standard errors and considering the estimates from the Two-consensus method.…”

Section: Supplementary Informationmentioning

confidence: 99%

“…However, the demographic dynamics underlying many of these events are still uncharacterized, especially at the regional level before and after European contact (Lindo et al, 2017; Nakatsuka et al, 2020; Nägele et al, 2020). The Panamanian land bridge lies between the Atlantic and Pacific Oceans and connects the two American continents.…”

Section: Introductionmentioning

confidence: 99%

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Archaeogenomic Distinctiveness of the Isthmo-Colombian Area

Capodiferro

Aram

Raveane

et al. 2020

Preprint

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The recently enriched genomic history of Indigenous groups in the Americas is still meagre concerning continental Central America. Here, we report ten pre-Hispanic (plus two early colonial) genomes and 84 genome-wide profiles from seven groups presently living in Panama. Our analyses reveal that pre-Hispanic demographic changes and isolation events contributed to create the extensive genetic structure currently seen in the area, which is also characterized by a distinctive Isthmo-Colombian Indigenous component. This component drives these populations on a specific variability axis and derives from the local admixture of different ancestries of northern North American origin(s). Two of these ancestries were differentially associated to Pleistocene Indigenous groups that also moved into South America leaving heterogenous footprints. An additional Pleistocene ancestry was brought by UPopI, a still unsampled population that remained restricted to the Isthmian area, expanded locally during the early Holocene, and left genomic traces up to the present.

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Section: Resultssupporting

confidence: 84%

Section: Admixture Tests (F-statistics)mentioning

confidence: 99%

“…• Mbuti, Papuan, CHB, Malta_24000 and USR_11500 as non-IA sources (Nägele et al, 2020;Posth et al, 2018) • ASO_4000 and Chipewyan for NNA • LagoaSanta_10400 for SNA1…”

Section: Ancestry Modelling With Qpwavementioning

confidence: 99%

Section: Supplementary Informationmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Archaeogenomic Distinctiveness of the Isthmo-Colombian Area

Capodiferro

Aram

Raveane

et al. 2020

Preprint

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A population history of indigenous Bahamian islanders: Insights from ancient DNA

Forbes‐Pateman

Yardumian

Vilar

et al. 2022

American Journal of Biological Anthropology

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Objectives: The Bahamas is an archipelago in the western Atlantic Ocean that stretches over 1000 km, just north of Cuba and east of the Florida Peninsula. Modern DNA studies show that contemporary Bahamians are genetic descendants of European and African ancestors, unlike Cuba, Dominican Republic, and Puerto Rico, where Indigenous descendancy is well documented. For The Bahamas little was known about the genetic ancestry of the Indigenous Lucayans (AD 700-1600) and their relationship to other Indigenous Caribbean populations. In this study, we investigated genetic diversity in Indigenous Lucayans from the Bahamas Archipelago to better understand the phylogeography of their genetic lineages, and to determine their relationship with other Indigenous Caribbean populations. Materials and methods:We characterized genetic diversity across two uniparental markers in 31 ancient individuals from burial sites on seven Bahamian islands. Results:We observed significant homogeneity in Lucayan paternal lineages, with only two haplogroups (Q-M902 and Q-Z781) found among them. Mitochondrial lineages were more diverse, with individuals belonging to haplogroup A2, B2, C1b, and C1d1. Four were assigned to a previously unidentified C1d lineage. Of the B2 samples, 7 of 11 belonged to the rare South America/Caribbean haplogroup B2e. This haplogroup was the most prevalent in the Northwest Bahamas while C1, particularly C1d, was more prevalent in the Central and Southern Bahamas.Discussion: These findings document a complex genetic history with an initial migration from Hispaniola beginning 1300 years ago, and possible gene flow from Cuba to Andros in late Bahamian prehistory.

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The devil is in the details

Bravi

Motti

Beltramo

et al. 2022

American Journal of Biological Anthropology

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We read with great interest the recent Forbes-Pateman et al. (2022) analysis of Bahamas' Lucayan mitochondrial DNA (mtDNA) lineages based on previously generated data by Schroeder et al. (2018), Nägele et al. (2020) and Fernandes et al. (2021. We disagree, however, with their haplogroup assignation for some of the lineages, as well as with their inference of phyletic affinities of others.The authors posit that five haplogroup C1 lineages in their Table 1 belongs into a new, previously unnamed C1d clade and thus adopt the same interpretation than Fernandes and colleagues for four out of those five and further eight samples (see Supplementary Information 10 in Fernandes et al., 2021), all of which share a pronounced, derived motif of 11 polymorphisms. We agree with both set of authors that these 13 sequences represent a new branch of Native American C1 haplogroup, but it is our opinion that assignation to C1dis due to faulty representation of variation at revised Cambridge Reference Sequence (rCRS) positions 493-498, and to the concomitant presence of a recurrent transition at C1d-defining position 16051. Fernandes and co-authors provide their interpretation of each individual mtDNA sequence variation in three columns in the Supplementary Data 9 table as Mutations Missing, Mutations Present, and Mutations Remaining. From the analysis of the first column, it is clear that authors did not bother to take into account indel variation known or suspected to occur in the sequences under analysis during alignment and variant calling. For example, deletions at positions 249 and 290-291, expected in any C1 sequence, are listed as missing. At the same time, unusual variation is offered for neighboring positions as 248G (13 cases), 247T-248G (38 cases), 247N-248G (26 cases), 287C (26 cases), 287T (one case), 287N (two cases), and 286N-287N (eight cases), most likely derived from alignment and variant calling by bioinformatic means without subsequent visual verification.Fernandes and colleagues also failed to detect presence of both 493G and the one nucleotide expansion of the polyC stretch at 494-498, and instead reported the presence of transversion 493C. Failure to detect C1b-defining 493G and the fortuitous presence of C1d-defining 16051G led both Fernandes et al. and Forbes-Pateman et al. to conclude that these lineages represent a new, undescribed branch of C1d. It is noteworthy to recall that recurrence of 16051G has

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Genomic insights into the early peopling of the Caribbean

Cited by 49 publications

References 73 publications

Archaeogenomic Distinctiveness of the Isthmo-Colombian Area

Archaeogenomic Distinctiveness of the Isthmo-Colombian Area

A population history of indigenous Bahamian islanders: Insights from ancient DNA

The devil is in the details

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