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- Peripato, Vinicius, et al.
(författare)
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More than 10,000 pre-Columbian earthworks are still hidden throughout Amazonia
- 2023
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Ingår i: Science (New York, N.Y.). - 1095-9203. ; 382:6666, s. 103-109
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Tidskriftsartikel (refereegranskat)abstract
- Indigenous societies are known to have occupied the Amazon basin for more than 12,000 years, but the scale of their influence on Amazonian forests remains uncertain. We report the discovery, using LIDAR (light detection and ranging) information from across the basin, of 24 previously undetected pre-Columbian earthworks beneath the forest canopy. Modeled distribution and abundance of large-scale archaeological sites across Amazonia suggest that between 10,272 and 23,648 sites remain to be discovered and that most will be found in the southwest. We also identified 53 domesticated tree species significantly associated with earthwork occurrence probability, likely suggesting past management practices. Closed-canopy forests across Amazonia are likely to contain thousands of undiscovered archaeological sites around which pre-Columbian societies actively modified forests, a discovery that opens opportunities for better understanding the magnitude of ancient human influence on Amazonia and its current state.
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| 2. |
- Pértille, Fábio, et al.
(författare)
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High-throughput and Cost-effective Chicken Genotyping Using Next-Generation Sequencing
- 2016
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Ingår i: Scientific Reports. - : Nature Publishing Group. - 2045-2322. ; 6
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Tidskriftsartikel (refereegranskat)abstract
- Chicken genotyping is becoming common practice in conventional animal breeding improvement.Despite the power of high-throughput methods for genotyping, their high cost limits large scale use inanimal breeding and selection. In the present paper we optimized the CornellGBS, an efficient and costeffectivegenotyping by sequence approach developed in plants, for its application in chickens. Herewe describe the successful genotyping of a large number of chickens (462) using CornellGBS approach.Genomic DNA was cleaved with the PstI enzyme, ligated to adapters with barcodes identifyingindividual animals, and then sequenced on Illumina platform. After filtering parameters were applied,134,528 SNPs were identified in our experimental population of chickens. Of these SNPs, 67,096 hada minimum taxon call rate of 90% and were considered ‘unique tags’. Interestingly, 20.7% of theseunique tags have not been previously reported in the dbSNP. Moreover, 92.6% of these SNPs wereconcordant with a previous Whole Chicken-genome re-sequencing dataset used for validation purposes.The application of CornellGBS in chickens showed high performance to infer SNPs, particularly inexonic regions and microchromosomes. This approach represents a cost-effective (~US$50/sample)and powerful alternative to current genotyping methods, which has the potential to improve wholegenomeselection (WGS), and genome-wide association studies (GWAS) in chicken production.
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| 3. |
- da Silva, Vinicius Henrique
(författare)
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Structural variants in the great tit genome and their effect on seasonal timing
- 2020
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- The biodiversity of our planet has been increasingly endangered by human actions. This nature biodiversity is strictly correlated with genomic diversity of all the species in the ecosystem. Thus, a broader understanding on the genome of wild species may be extremely useful to understand selection and plasticity in the natural species of our changing world. The great tit (Parus major ) is a songbird that has been extensively explored in ecological and evolutionary studies, shedding light on the effects of the global warming on nature. The seasonal timing of the great tit has been shifting under the global warming, but the knowledge on particular genes associated with timing is still limited. Although the effect of single nucleotide changes on the breeding timing of great tits has been investigated, the effect of more complex structural variants is largely unknown. In fact, the genomic structural variability was never explored in detail in these species. The aim of this thesis was to detect, map, characterize and associate, with seasonal timing, structural variants that are present in the great tit genome such as copy number variations (CNVs) and inversions. First, this thesis presents a genome-wide map of CNV regions in the great tit genome, showing how these variants are associated with genomic architecture that underlies their molecular formation. Great tit CNVs, in accordance to reported in several mammalian species, are enriched at evolutionary breakpoints. Although it supports the importance of CNVs during speciation like is described in mammals, a remarkable difference is that neuronal related genes may play a central role on the great tit speciation. Second, CNVs were associated with breeding timing. Although no strong association was found, suggestive associations such as a copy number gain in a gene related to circadian clock deserves further investigation. Finally, this thesis investigate in detail the genomic complexity of a large (≈64 Mb) and widespread (≈5%) inversion in the Chromosome 1A. Interestingly, this inversion is a recessive lethal selfish structural rearrangement (i.e. breaks the Mendel’s law). The inversion is inherited twice more than expected from male carriers but are normally inherited from female carriers, suggesting that a meiotic drive mechanism during spermatogenesis maintains this large inversion in great tit populations.
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