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    Fasteris Life fasteris sa sequencing service
    We collected eight lake sediment cores from seven sites in Siberia and Alaska. DNA was extracted from subsamples taken at different depths, corresponding to various sediment age layers. After amplifying the tnr L P6loop region, amplicon sequence variants (ASVs) were identified and assigned to taxa using the SibAla_2023 database, with confidence levels ranging from 90% to 100%. To discern true taxonomic signals from potential chimeric sequences caused by PCR or <t>sequencing</t> errors, we developed a co-occurrence-based community detection approach. This analysis identified 359 taxa, with 216 taxa matching the SibAla_2023 database at 100% confidence (dbtaxa) and 143 taxa matching at 90–99% confidence (non-dbtaxa). From these 359 Taxa, 242 taxa are also present in the modern time-slices and are thus identified as neither extirpated nor extinct. Of these 359 taxa, 242 are also present in modern time-slices, indicating they are neither extirpated nor extinct. Among the remaining 117 taxa, 67 are considered extirpated, while 60 are absent from the region-specific SibAla_2023 database. These 60 taxa could be missing from the database, extirpated from Siberia and Alaska, or potentially globally extinct. After evaluating database coverage with a synthetic dataset simulated using data from GBIF, we found that 42 taxa could be missing due to insufficient coverage in the SibAla_2023 reference database. This suggests that 18 (60 minus 42) non-dbtaxa might be globally extinct. Further checks with global databases showed that 54 of the 60 taxa (88%) could not be assigned. Among the six taxa matching global databases, there is an 18% likelihood of having refugia outside Siberia and Alaska, suggesting that one taxon (1 out of 18–60) might only be extirpated. In conclusion, 17 taxa found in sediments from the last 28,000 years are potentially globally extinct. Modified DNA strand Vectorportal.com ( https://vectorportal.com/ ) by CC BY ( https://creativecommons.org/licenses/by/4.0/ ).
    Fasteris Sa Sequencing Service, supplied by Fasteris Life, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/fasteris+sequencing/pmc11733255-331-6-6?v=Fasteris+Life
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    fasteris sa sequencing service - by Bioz Stars, 2026-07
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    1) Product Images from "Potential plant extinctions with the loss of the Pleistocene mammoth steppe"

    Article Title: Potential plant extinctions with the loss of the Pleistocene mammoth steppe

    Journal: Nature Communications

    doi: 10.1038/s41467-024-55542-x

    We collected eight lake sediment cores from seven sites in Siberia and Alaska. DNA was extracted from subsamples taken at different depths, corresponding to various sediment age layers. After amplifying the tnr L P6loop region, amplicon sequence variants (ASVs) were identified and assigned to taxa using the SibAla_2023 database, with confidence levels ranging from 90% to 100%. To discern true taxonomic signals from potential chimeric sequences caused by PCR or sequencing errors, we developed a co-occurrence-based community detection approach. This analysis identified 359 taxa, with 216 taxa matching the SibAla_2023 database at 100% confidence (dbtaxa) and 143 taxa matching at 90–99% confidence (non-dbtaxa). From these 359 Taxa, 242 taxa are also present in the modern time-slices and are thus identified as neither extirpated nor extinct. Of these 359 taxa, 242 are also present in modern time-slices, indicating they are neither extirpated nor extinct. Among the remaining 117 taxa, 67 are considered extirpated, while 60 are absent from the region-specific SibAla_2023 database. These 60 taxa could be missing from the database, extirpated from Siberia and Alaska, or potentially globally extinct. After evaluating database coverage with a synthetic dataset simulated using data from GBIF, we found that 42 taxa could be missing due to insufficient coverage in the SibAla_2023 reference database. This suggests that 18 (60 minus 42) non-dbtaxa might be globally extinct. Further checks with global databases showed that 54 of the 60 taxa (88%) could not be assigned. Among the six taxa matching global databases, there is an 18% likelihood of having refugia outside Siberia and Alaska, suggesting that one taxon (1 out of 18–60) might only be extirpated. In conclusion, 17 taxa found in sediments from the last 28,000 years are potentially globally extinct. Modified DNA strand Vectorportal.com ( https://vectorportal.com/ ) by CC BY ( https://creativecommons.org/licenses/by/4.0/ ).
    Figure Legend Snippet: We collected eight lake sediment cores from seven sites in Siberia and Alaska. DNA was extracted from subsamples taken at different depths, corresponding to various sediment age layers. After amplifying the tnr L P6loop region, amplicon sequence variants (ASVs) were identified and assigned to taxa using the SibAla_2023 database, with confidence levels ranging from 90% to 100%. To discern true taxonomic signals from potential chimeric sequences caused by PCR or sequencing errors, we developed a co-occurrence-based community detection approach. This analysis identified 359 taxa, with 216 taxa matching the SibAla_2023 database at 100% confidence (dbtaxa) and 143 taxa matching at 90–99% confidence (non-dbtaxa). From these 359 Taxa, 242 taxa are also present in the modern time-slices and are thus identified as neither extirpated nor extinct. Of these 359 taxa, 242 are also present in modern time-slices, indicating they are neither extirpated nor extinct. Among the remaining 117 taxa, 67 are considered extirpated, while 60 are absent from the region-specific SibAla_2023 database. These 60 taxa could be missing from the database, extirpated from Siberia and Alaska, or potentially globally extinct. After evaluating database coverage with a synthetic dataset simulated using data from GBIF, we found that 42 taxa could be missing due to insufficient coverage in the SibAla_2023 reference database. This suggests that 18 (60 minus 42) non-dbtaxa might be globally extinct. Further checks with global databases showed that 54 of the 60 taxa (88%) could not be assigned. Among the six taxa matching global databases, there is an 18% likelihood of having refugia outside Siberia and Alaska, suggesting that one taxon (1 out of 18–60) might only be extirpated. In conclusion, 17 taxa found in sediments from the last 28,000 years are potentially globally extinct. Modified DNA strand Vectorportal.com ( https://vectorportal.com/ ) by CC BY ( https://creativecommons.org/licenses/by/4.0/ ).

    Techniques Used: Amplification, Sequencing, Modification



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    We collected eight lake sediment cores from seven sites in Siberia and Alaska. DNA was extracted from subsamples taken at different depths, corresponding to various sediment age layers. After amplifying the tnr L P6loop region, amplicon sequence variants (ASVs) were identified and assigned to taxa using the SibAla_2023 database, with confidence levels ranging from 90% to 100%. To discern true taxonomic signals from potential chimeric sequences caused by PCR or <t>sequencing</t> errors, we developed a co-occurrence-based community detection approach. This analysis identified 359 taxa, with 216 taxa matching the SibAla_2023 database at 100% confidence (dbtaxa) and 143 taxa matching at 90–99% confidence (non-dbtaxa). From these 359 Taxa, 242 taxa are also present in the modern time-slices and are thus identified as neither extirpated nor extinct. Of these 359 taxa, 242 are also present in modern time-slices, indicating they are neither extirpated nor extinct. Among the remaining 117 taxa, 67 are considered extirpated, while 60 are absent from the region-specific SibAla_2023 database. These 60 taxa could be missing from the database, extirpated from Siberia and Alaska, or potentially globally extinct. After evaluating database coverage with a synthetic dataset simulated using data from GBIF, we found that 42 taxa could be missing due to insufficient coverage in the SibAla_2023 reference database. This suggests that 18 (60 minus 42) non-dbtaxa might be globally extinct. Further checks with global databases showed that 54 of the 60 taxa (88%) could not be assigned. Among the six taxa matching global databases, there is an 18% likelihood of having refugia outside Siberia and Alaska, suggesting that one taxon (1 out of 18–60) might only be extirpated. In conclusion, 17 taxa found in sediments from the last 28,000 years are potentially globally extinct. Modified DNA strand Vectorportal.com ( https://vectorportal.com/ ) by CC BY ( https://creativecommons.org/licenses/by/4.0/ ).
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    We collected eight lake sediment cores from seven sites in Siberia and Alaska. DNA was extracted from subsamples taken at different depths, corresponding to various sediment age layers. After amplifying the tnr L P6loop region, amplicon sequence variants (ASVs) were identified and assigned to taxa using the SibAla_2023 database, with confidence levels ranging from 90% to 100%. To discern true taxonomic signals from potential chimeric sequences caused by PCR or <t>sequencing</t> errors, we developed a co-occurrence-based community detection approach. This analysis identified 359 taxa, with 216 taxa matching the SibAla_2023 database at 100% confidence (dbtaxa) and 143 taxa matching at 90–99% confidence (non-dbtaxa). From these 359 Taxa, 242 taxa are also present in the modern time-slices and are thus identified as neither extirpated nor extinct. Of these 359 taxa, 242 are also present in modern time-slices, indicating they are neither extirpated nor extinct. Among the remaining 117 taxa, 67 are considered extirpated, while 60 are absent from the region-specific SibAla_2023 database. These 60 taxa could be missing from the database, extirpated from Siberia and Alaska, or potentially globally extinct. After evaluating database coverage with a synthetic dataset simulated using data from GBIF, we found that 42 taxa could be missing due to insufficient coverage in the SibAla_2023 reference database. This suggests that 18 (60 minus 42) non-dbtaxa might be globally extinct. Further checks with global databases showed that 54 of the 60 taxa (88%) could not be assigned. Among the six taxa matching global databases, there is an 18% likelihood of having refugia outside Siberia and Alaska, suggesting that one taxon (1 out of 18–60) might only be extirpated. In conclusion, 17 taxa found in sediments from the last 28,000 years are potentially globally extinct. Modified DNA strand Vectorportal.com ( https://vectorportal.com/ ) by CC BY ( https://creativecommons.org/licenses/by/4.0/ ).
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    We collected eight lake sediment cores from seven sites in Siberia and Alaska. DNA was extracted from subsamples taken at different depths, corresponding to various sediment age layers. After amplifying the tnr L P6loop region, amplicon sequence variants (ASVs) were identified and assigned to taxa using the SibAla_2023 database, with confidence levels ranging from 90% to 100%. To discern true taxonomic signals from potential chimeric sequences caused by PCR or <t>sequencing</t> errors, we developed a co-occurrence-based community detection approach. This analysis identified 359 taxa, with 216 taxa matching the SibAla_2023 database at 100% confidence (dbtaxa) and 143 taxa matching at 90–99% confidence (non-dbtaxa). From these 359 Taxa, 242 taxa are also present in the modern time-slices and are thus identified as neither extirpated nor extinct. Of these 359 taxa, 242 are also present in modern time-slices, indicating they are neither extirpated nor extinct. Among the remaining 117 taxa, 67 are considered extirpated, while 60 are absent from the region-specific SibAla_2023 database. These 60 taxa could be missing from the database, extirpated from Siberia and Alaska, or potentially globally extinct. After evaluating database coverage with a synthetic dataset simulated using data from GBIF, we found that 42 taxa could be missing due to insufficient coverage in the SibAla_2023 reference database. This suggests that 18 (60 minus 42) non-dbtaxa might be globally extinct. Further checks with global databases showed that 54 of the 60 taxa (88%) could not be assigned. Among the six taxa matching global databases, there is an 18% likelihood of having refugia outside Siberia and Alaska, suggesting that one taxon (1 out of 18–60) might only be extirpated. In conclusion, 17 taxa found in sediments from the last 28,000 years are potentially globally extinct. Modified DNA strand Vectorportal.com ( https://vectorportal.com/ ) by CC BY ( https://creativecommons.org/licenses/by/4.0/ ).
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    We collected eight lake sediment cores from seven sites in Siberia and Alaska. DNA was extracted from subsamples taken at different depths, corresponding to various sediment age layers. After amplifying the tnr L P6loop region, amplicon sequence variants (ASVs) were identified and assigned to taxa using the SibAla_2023 database, with confidence levels ranging from 90% to 100%. To discern true taxonomic signals from potential chimeric sequences caused by PCR or <t>sequencing</t> errors, we developed a co-occurrence-based community detection approach. This analysis identified 359 taxa, with 216 taxa matching the SibAla_2023 database at 100% confidence (dbtaxa) and 143 taxa matching at 90–99% confidence (non-dbtaxa). From these 359 Taxa, 242 taxa are also present in the modern time-slices and are thus identified as neither extirpated nor extinct. Of these 359 taxa, 242 are also present in modern time-slices, indicating they are neither extirpated nor extinct. Among the remaining 117 taxa, 67 are considered extirpated, while 60 are absent from the region-specific SibAla_2023 database. These 60 taxa could be missing from the database, extirpated from Siberia and Alaska, or potentially globally extinct. After evaluating database coverage with a synthetic dataset simulated using data from GBIF, we found that 42 taxa could be missing due to insufficient coverage in the SibAla_2023 reference database. This suggests that 18 (60 minus 42) non-dbtaxa might be globally extinct. Further checks with global databases showed that 54 of the 60 taxa (88%) could not be assigned. Among the six taxa matching global databases, there is an 18% likelihood of having refugia outside Siberia and Alaska, suggesting that one taxon (1 out of 18–60) might only be extirpated. In conclusion, 17 taxa found in sediments from the last 28,000 years are potentially globally extinct. Modified DNA strand Vectorportal.com ( https://vectorportal.com/ ) by CC BY ( https://creativecommons.org/licenses/by/4.0/ ).
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    We collected eight lake sediment cores from seven sites in Siberia and Alaska. DNA was extracted from subsamples taken at different depths, corresponding to various sediment age layers. After amplifying the tnr L P6loop region, amplicon sequence variants (ASVs) were identified and assigned to taxa using the SibAla_2023 database, with confidence levels ranging from 90% to 100%. To discern true taxonomic signals from potential chimeric sequences caused by PCR or sequencing errors, we developed a co-occurrence-based community detection approach. This analysis identified 359 taxa, with 216 taxa matching the SibAla_2023 database at 100% confidence (dbtaxa) and 143 taxa matching at 90–99% confidence (non-dbtaxa). From these 359 Taxa, 242 taxa are also present in the modern time-slices and are thus identified as neither extirpated nor extinct. Of these 359 taxa, 242 are also present in modern time-slices, indicating they are neither extirpated nor extinct. Among the remaining 117 taxa, 67 are considered extirpated, while 60 are absent from the region-specific SibAla_2023 database. These 60 taxa could be missing from the database, extirpated from Siberia and Alaska, or potentially globally extinct. After evaluating database coverage with a synthetic dataset simulated using data from GBIF, we found that 42 taxa could be missing due to insufficient coverage in the SibAla_2023 reference database. This suggests that 18 (60 minus 42) non-dbtaxa might be globally extinct. Further checks with global databases showed that 54 of the 60 taxa (88%) could not be assigned. Among the six taxa matching global databases, there is an 18% likelihood of having refugia outside Siberia and Alaska, suggesting that one taxon (1 out of 18–60) might only be extirpated. In conclusion, 17 taxa found in sediments from the last 28,000 years are potentially globally extinct. Modified DNA strand Vectorportal.com ( https://vectorportal.com/ ) by CC BY ( https://creativecommons.org/licenses/by/4.0/ ).

    Journal: Nature Communications

    Article Title: Potential plant extinctions with the loss of the Pleistocene mammoth steppe

    doi: 10.1038/s41467-024-55542-x

    Figure Lengend Snippet: We collected eight lake sediment cores from seven sites in Siberia and Alaska. DNA was extracted from subsamples taken at different depths, corresponding to various sediment age layers. After amplifying the tnr L P6loop region, amplicon sequence variants (ASVs) were identified and assigned to taxa using the SibAla_2023 database, with confidence levels ranging from 90% to 100%. To discern true taxonomic signals from potential chimeric sequences caused by PCR or sequencing errors, we developed a co-occurrence-based community detection approach. This analysis identified 359 taxa, with 216 taxa matching the SibAla_2023 database at 100% confidence (dbtaxa) and 143 taxa matching at 90–99% confidence (non-dbtaxa). From these 359 Taxa, 242 taxa are also present in the modern time-slices and are thus identified as neither extirpated nor extinct. Of these 359 taxa, 242 are also present in modern time-slices, indicating they are neither extirpated nor extinct. Among the remaining 117 taxa, 67 are considered extirpated, while 60 are absent from the region-specific SibAla_2023 database. These 60 taxa could be missing from the database, extirpated from Siberia and Alaska, or potentially globally extinct. After evaluating database coverage with a synthetic dataset simulated using data from GBIF, we found that 42 taxa could be missing due to insufficient coverage in the SibAla_2023 reference database. This suggests that 18 (60 minus 42) non-dbtaxa might be globally extinct. Further checks with global databases showed that 54 of the 60 taxa (88%) could not be assigned. Among the six taxa matching global databases, there is an 18% likelihood of having refugia outside Siberia and Alaska, suggesting that one taxon (1 out of 18–60) might only be extirpated. In conclusion, 17 taxa found in sediments from the last 28,000 years are potentially globally extinct. Modified DNA strand Vectorportal.com ( https://vectorportal.com/ ) by CC BY ( https://creativecommons.org/licenses/by/4.0/ ).

    Article Snippet: Each sequencing run was performed by Fasteris SA sequencing service (Switzerland) with the paired-end sequencing on a HiSeq or NextSeq Illumina platform (Supplementary Table ).

    Techniques: Amplification, Sequencing, Modification