Origins and genetic legacies of the Caribbean Taino Schroeder, Hannes; Sikora, Martin; Gopalakrishnan, Shyam ...
Proceedings of the National Academy of Sciences - PNAS,
03/2018, Volume:
115, Issue:
10
Journal Article
Peer reviewed
Open access
The Caribbean was one of the last parts of the Americas to be settled by humans, but how and when the islands were first occupied remains a matter of debate. Ancient DNA can help answering these ...questions, but the work has been hampered by poor DNA preservation. We report the genome sequence of a 1,000-year-old Lucayan Taino individual recovered from the site of Preacher’s Cave in the Bahamas. We sequenced her genome to 12.4-fold coverage and show that she is genetically most closely related to present-day Arawakan speakers from northern South America, suggesting that the ancestors of the Lucayans originated there. Further, we find no evidence for recent inbreeding or isolation in the ancient genome, suggesting that the Lucayans had a relatively large effective population size. Finally, we show that the native American components in some present-day Caribbean genomes are closely related to the ancient Taino, demonstrating an element of continuity between precontact populations and present-day Latino populations in the Caribbean.
Patagonia was the last region of the Americas reached by humans who entered the continent from Siberia ∼15,000–20,000 y ago. Despite recent genomic approaches to reconstruct the continental ...evolutionary history, regional characterization of ancient and modern genomes remains understudied. Exploring the genomic diversity within Patagonia is not just a valuable strategy to gain a better understanding of the history and diversification of human populations in the southernmost tip of the Americas, but it would also improve the representation of Native American diversity in global databases of human variation. Here, we present genome data from four modern populations from Central Southern Chile and Patagonia (n = 61) and four ancient maritime individuals from Patagonia (∼1,000 y old). Both the modern and ancient individuals studied in this work have a greater genetic affinity with other modern Native Americans than to any non-American population, showing within South America a clear structure between major geographical regions. Native Patagonian Kawéskar and Yámana showed the highest genetic affinity with the ancient individuals, indicating genetic continuity in the region during the past 1,000 y before present, together with an important agreement between the ethnic affiliation and historical distribution of both groups. Lastly, the ancient maritime individuals were genetically equidistant to a ∼200-y-old terrestrial hunter-gatherer from Tierra del Fuego, which supports a model with an initial separation of a common ancestral group to both maritime populations from a terrestrial population, with a later diversification of the maritime groups.
Evolutionary processes, including selection, can be indirectly inferred based on patterns of genomic variation among contemporary populations or species. However, this often requires unrealistic ...assumptions of ancestral demography and selective regimes. Sequencing ancient DNA from temporally spaced samples can inform about past selection processes, as time series data allow direct quantification of population parameters collected before, during, and after genetic changes driven by selection. In this Comment and Opinion, we advocate for the inclusion of temporal sampling and the generation of paleogenomic datasets in evolutionary biology, and highlight some of the recent advances that have yet to be broadly applied by evolutionary biologists. In doing so, we consider the expected signatures of balancing, purifying, and positive selection in time series data, and detail how this can advance our understanding of the chronology and tempo of genomic change driven by selection. However, we also recognize the limitations of such data, which can suffer from postmortem damage, fragmentation, low coverage, and typically low sample size. We therefore highlight the many assumptions and considerations associated with analyzing paleogenomic data and the assumptions associated with analytical methods.
The total proteomes of
s.s.,
and their hybrid genotype have been compared by quantitative proteomics (iTRAQ approach), which considers the level of expressed proteins. Comparison was made by means of ...two independent experiments considering four biological replicates of
and two each for
and hybrid between both species. A total of 1811 and 1976 proteins have been respectively identified in the experiments using public databases. One hundred ninety-six proteins were found significantly differentially expressed, and their relationships with the nematodes' biological replicates were estimated by a multidimensional statistical approach. Results of pairwise Log
ratio comparisons among them were statistically treated and supported in order to convert them into discrete character states. Principal component analysis (PCA) confirms the validity of the method. This comparison selected thirty seven proteins as discriminant taxonomic biomarkers among
,
and their hybrid genotype; 19 of these biomarkers, encoded by ten loci, are specific allergens of
(Ani s7, Ani s8, Ani s12, and Ani s14) and other (Ancylostoma secreted) is a common nematodes venom allergen. The rest of the markers comprise four unknown or non-characterized proteins; five different proteins (leucine) related to innate immunity, four proteolytic proteins (metalloendopeptidases), a lipase, a mitochondrial translocase protein, a neurotransmitter, a thyroxine transporter, and a structural collagen protein. The proposed methodology (proteomics and statistical) solidly characterize a set of proteins that are susceptible to take advantage of the new targeted proteomics.
In plant and animal nematode parasites, proteins derived from esophageal gland cells have been shown to be important in the host-nematodes relationship but little is known about the allergenic ...potential of these proteins in the genus
. Taking into account the increase of anisakiasis and allergies related to these nematodes, immunoreactive properties of gland cell proteins were investigated. Two hundred ventricles were manually dissected from L3 stage larvae of
. to allow direct protein analysis. Denaturing gel electrophoresis followed by monochromatic silver staining which revealed the presence of differential (enriched) proteins when compared to total nematode extracts. Such comparison was performed by means of 1D and 2D electrophoresis. Pooled antisera from
spp.-allergic patients were used in western blots revealing the presence of 13 immunoreactive bands in the ventricular extracts in 1D, with 82 spots revealed in 2D. The corresponding protein bands and spots were excised from the silver-stained gel and protein assignation was made by MALDI-TOF/TOF. A total of 13 (including proteoforms) were unambiguously identified. The majority of these proteins are known to be secreted by nematodes into the external environment, of which three are described as being major allergens in other organisms with different phylogenetic origin and one is an
allergen.
ABSTRACT
Classical B emission (Be) stars are fast rotating, near-main-sequence B-type stars. The rotation and the presence of circumstellar discs profoundly modify the observables of active Be stars. ...Our goal is to infer stellar and disc parameters, as well as distance and interstellar extinction, using the currently most favoured physical models for these objects. We present BeAtlas, a grid of $61\, 600$ non-local thermodynamic equilibrium radiative transfer models for Be stars, calculated with the hdust code. The grid was coupled with a Monte Carlo Markov chain (MCMC) code to sample the posterior distribution. We test our method on two well-studied Be stars, α Eri and β CMi, using photometric, polarimetric, and spectroscopic data as input to the code. We recover literature determinations for most of the parameters of the targets, in particular the mass and age of α Eri, the disc parameters of β CMi, and their distances and inclinations. The main discrepancy is that we estimate lower rotational rates than previous works. We confirm previously detected signs of disc truncation in β CMi and note that its inner disc seems to have a flatter density slope than its outer disc. The correlations between the parameters are complex, further indicating that exploring the entire parameter space simultaneously is a more robust approach, statistically. The combination of BeAtlas and Bayesian-MCMC techniques proves successful, and a powerful new tool for the field: The fundamental parameters of any Be star can now be estimated in a matter of hours or days.
The characterization of biomolecules from ancient samples can shed otherwise unobtainable insights into the past. Despite the fundamental role of transcriptomal change in evolution, the potential of ...ancient RNA remains unexploited - perhaps due to dogma associated with the fragility of RNA. We hypothesize that seeds offer a plausible refuge for long-term RNA survival, due to the fundamental role of RNA during seed germination. Using RNA-Seq on cDNA synthesized from nucleic acid extracts, we validate this hypothesis through demonstration of partial transcriptomal recovery from two sources of ancient maize kernels. The results suggest that ancient seed transcriptomics may offer a powerful new tool with which to study plant domestication.
The island of St Helena played a crucial role in the suppression of the transatlantic slave trade. Strategically located in the middle of the South Atlantic, it served as a staging post for the Royal ...Navy and reception point for enslaved Africans who had been “liberated” from slave ships intercepted by the British. In total, St Helena received approximately 27,000 liberated Africans between 1840 and 1867. Written sources suggest that the majority of these individuals came from West Central Africa, but their precise origins are unknown. Here, we report the results of ancient DNA analyses that we conducted as part of a wider effort to commemorate St Helena’s liberated Africans and to restore knowledge of their lives and experiences. We generated partial genomes (0.1–0.5×) for 20 individuals whose remains had been recovered during archaeological excavations on the island. We compared their genomes with genotype data for over 3,000 present-day individuals from 90 populations across sub-Saharan Africa and conclude that the individuals most likely originated from different source populations within the general area between northern Angola and Gabon. We also find that the majority (17/20) of the individuals were male, supporting a well-documented sex bias in the latter phase of the transatlantic slave trade. The study expands our understanding of St Helena’s liberated African community and illustrates how ancient DNA analyses can be used to investigate the origins and identities of individuals whose lives were bound up in the story of slavery and its abolition.
During the mid-19th century, around 27,000 “liberated Africans” were brought to St Helena island as part of the Royal Navy’s efforts to suppress the transatlantic trade in enslaved Africans. Ancient DNA analyses, carried out on behalf of the community on St Helena, now shed light on their origins and identities.
The 'red complex' is an aggregate of three oral bacteria (
,
and
) responsible for severe clinical manifestation of periodontal disease. Here, we report the first direct evidence of ancient
DNA in ...dentin and dental calculus samples from archaeological skeletal remains that span from the Pre-Hispanic to the Colonial period in Mexico. We recovered twelve partial ancient
genomes and observed a distinct phylogenetic placement of samples, suggesting that the strains present in Pre-Hispanic individuals likely arrived with the first human migrations to the Americas and that new strains were introduced with the arrival of European and African populations in the sixteenth century. We also identified instances of the differential presence of genes between periods in the
ancient genomes, with certain genes present in Pre-Hispanic individuals and absent in Colonial individuals, and
. This study highlights the potential for studying ancient
genomes to unveil past social interactions through analysis of disease transmission. Our results illustrate the long-standing relationship between this oral pathogen and its human host, while also unveiling key evidence to understand its evolutionary history in Pre-Hispanic and Colonial Mexico. This article is part of the theme issue 'Insights into health and disease from ancient biomolecules'.
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