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Interestingly, 119 SCPCH out of the 246 of FUNYBASE were systematically retained among 30 of the 40 searches.
To identify those duplicates that were systematically retained in Ostariophysi superorder, D. rerio paralogs with a single best hit against the same G. aculeatus (Gasterosteiformes) ortholog were retrieved.
Similarly, 1.3% (418) of total gene number represented cases where TSGD paralogs pairs were systematically retained in the Acanthopterygian but conserved as a single copy in Ostariophysi genomes.
This study has shown that some TSGD paralogs have been systematically retained in Acanthopterygii but Ostariophysi superorders of teleosts (1.3% and 2.6% of total gene content, respectively).
In case of inversions of two markers between maps, only the marker that was present in the lowest number of maps was manually removed to ensure that the most frequent common markers would be systematically retained.
The method for identifying TSGD paralogs that have been systematically retained as pairs in one superorder but as a single copy in the other is schematically illustrated in supplementary figure S1, Supplementary Material online.
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As described in Material and Methods, for each animal, we retained systematically the most parsimonious haplotype reconstruction (the reconstruction that requires the minimum number of recombination of ancestral haplotypes).
Data were missing on 826 people (out of the 85% sample) for this analysis, but the individuals removed did not differ systematically from the retained cases by age (mean difference = 2 years), gender or population group.
To identify a deep signature of this teleost-specific whole-genome duplication (TSGD), we searched for duplicated genes that were systematically and uniquely retained in one or other of the superorders Ostariophysi and Acanthopterygii.
Seventeen studies were systematically reviewed; eleven were retained for meta-analysis.
We systematically choose to retain variables in the final multivariable model if they were significant for any clinical outcome (AGC/ASCUS, LSIL, ≥ HSIL) in order to allow the direct comparison of risk factors between different stages of cervical neoplasia.
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