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hg38 syntenic ages
<p>### METHOD ###</p> <p>Sequence ages were estimated from hg38 100-way multiZ vertebrate sequence alignments from the UCSC genome browser. Briefly, sequence ages were estimated as the branch length between humans (hg38) and the oldest most recent common ancestor (MRCA) from the 100-way neutral tree. </p> <p> </p> <p>MRCA to taxon mappings are available in the hg38_syn_taxon.bed file. </p> <p> </p> <p># Hg38 100-way vertebrate tree syntenic block age files. </p> <p>Information for hg38 100-way vertebrate multiple sequence alignment can be found here - http://hgdownload.cse.ucsc.edu/goldenPath/hg38/multiz100way/README.txt</p> <p># Scripts generating these files</p> <p>(1) Creating syntenic block .bed files</p> <p>https://github.com/slifong08/enh_ages/blob/54084ff12e521c20cc5288d6cb3590fac93c11ed/age_arch/manuscript_scripts/get_spec_count_msa-hg19.py</p> <p>(2) Assigning most recent common ancestor (MRCA) and patristic distances to syntenic blocks</p> <p>https://github.com/slifong08/enh_ages/blob/54084ff12e521c20cc5288d6cb3590fac93c11ed/age_arch/manuscript_scripts/get_synteny_age_hg19.py</p>
HepG2 and K562 cCRE syntenic ages
<p>### DESCRIPTION ###</p> <p>HepG2 and K562 ENCODE 3 cCRE pELS, dELS, pELS + CTCF, dELS +CTCF.</p> <p>### METHOD ###</p> <p>To assign sequence ages enhancer cCRE .bed coordinates were intersected with hg38 100-way multiZ alignment syntenic blocks from UCSC genome browser.</p> <p> </p> <p>### Column names ###</p> <p>[#chr start_syn end_syn enh_id #chr_enh start_enh end_enh segment_number simple_0_complex_1 core_0_derived_1 mrca_age]</p> <p>### explanation of column names ###</p> <p>[#chr start_syn end_syn]: syntenic block .bed coordinates in hg38</p> <p>[ enh_id #chr_enh start_enh end_enh]: cCRE .bed coordinates in hg38</p> <p>[segment_number]: We count the number of syntenic block segments overlapping a single enhancer. </p> <p>[simple_0_complex_1]: Some syntenic blocks overlap multiple syntenic blocks, which we term "complex". Others overlap a single syntenic block, which we term "simple". Complex elements are annotated with 1 and simple elements are annotated with 0. </p> <p>[core_0_derived_1]: In complex enhancer sequences (i.e. enhancer sequences with multiple sequence ages). We refer to the oldest sequence in an enhancer is the "core" (annotated as 1) and the younger sequence age(s) as "derived" (annotated as 0). </p> <p>[mrca_age]: For each syntenic segment, we annotate the most recent common ancestor (MRCA) age. This corresponds to the estimated branch length between humans and the related MRCA. </p> <p>Taxon and summarized taxon ("Taxon2") for each MRCA age is annotated in the hg38_syn_taxon.bed file. </p>
Supplementary material 7 from: Li X-R (2022) Phylogeny and age of cockroaches: a reanalysis of mitogenomes with selective fossil calibrations. Deutsche Entomologische Zeitschrift 69(1): 1-18. https://doi.org/10.3897/dez.69.68373
Figue S4
Supplementary material 6 from: Li X-R (2022) Phylogeny and age of cockroaches: a reanalysis of mitogenomes with selective fossil calibrations. Deutsche Entomologische Zeitschrift 69(1): 1-18. https://doi.org/10.3897/dez.69.68373
Figure S3
Supplementary material 12 from: Li X-R (2022) Phylogeny and age of cockroaches: a reanalysis of mitogenomes with selective fossil calibrations. Deutsche Entomologische Zeitschrift 69(1): 1-18. https://doi.org/10.3897/dez.69.68373
Figure S9
Supplementary material 13 from: Li X-R (2022) Phylogeny and age of cockroaches: a reanalysis of mitogenomes with selective fossil calibrations. Deutsche Entomologische Zeitschrift 69(1): 1-18. https://doi.org/10.3897/dez.69.68373
Figure S10
Supplementary material 11 from: Li X-R (2022) Phylogeny and age of cockroaches: a reanalysis of mitogenomes with selective fossil calibrations. Deutsche Entomologische Zeitschrift 69(1): 1-18. https://doi.org/10.3897/dez.69.68373
Figure S8
Supplementary material 10 from: Li X-R (2022) Phylogeny and age of cockroaches: a reanalysis of mitogenomes with selective fossil calibrations. Deutsche Entomologische Zeitschrift 69(1): 1-18. https://doi.org/10.3897/dez.69.68373
Figure S7
Supplementary material 1 from: Li X-R (2022) Phylogeny and age of cockroaches: a reanalysis of mitogenomes with selective fossil calibrations. Deutsche Entomologische Zeitschrift 69(1): 1-18. https://doi.org/10.3897/dez.69.68373
Initial pool of 169 mitochondrial genomes
Figure 1 from: Li X-R (2022) Phylogeny and age of cockroaches: a reanalysis of mitogenomes with selective fossil calibrations. Deutsche Entomologische Zeitschrift 69(1): 1-18. https://doi.org/10.3897/dez.69.68373
Figure 1 Representative phylogenetic inferences of cockroaches based on various data and methods. McKittrick (1964) and McKittrick and Mackerras (1965): female and male genitalia, proventriculus and oviposition behaviour; discussion. Roth (1970): oothecal rotation; discussion. Klass and Meier (2006): male genitalia, accompanied by ethology etc.; parsimony. Wang et al. (2017): gene fragments (three mitochondrial and two nuclear), incorporating the data from Djernæs et al. (2015) and others; maximum likelihood. Bourguignon et al. (2018): mitogenome; maximum likelihood and Bayesian. Evangelista et al. (2019): transcriptome; maximum likelihood. Taxa are shown in currently recognized rank instead of original designation. Branches in orange, Blaberoidea; in green, Corydioidea; in purple, Blattoidea. Asterisk, paraphyly.
Figure 3 from: Li X-R (2022) Phylogeny and age of cockroaches: a reanalysis of mitogenomes with selective fossil calibrations. Deutsche Entomologische Zeitschrift 69(1): 1-18. https://doi.org/10.3897/dez.69.68373
Figure 3 Time trees of Dictyoptera estimated by MCMCTREE. Two-calibration result (middle) is regarded as the formal result of this study. Calibrated nodes are coloured, with vertical bars denoting bounds. Calibrations: Qilianiblatta namurensis (green), Valditermes brenanae (red), Piniblattella yixianensis (blue). Abbreviations: A[naplectidae], Dictyop[tera], L[amproblattidae], T[ryonicidae], Xyloph[agodea]. For detailed phylogenies showing species, see Suppl. material 11–13.
Supplementary material 5 from: Li X-R (2022) Phylogeny and age of cockroaches: a reanalysis of mitogenomes with selective fossil calibrations. Deutsche Entomologische Zeitschrift 69(1): 1-18. https://doi.org/10.3897/dez.69.68373
Figure S2
Figure 2 from: Li X-R (2022) Phylogeny and age of cockroaches: a reanalysis of mitogenomes with selective fossil calibrations. Deutsche Entomologische Zeitschrift 69(1): 1-18. https://doi.org/10.3897/dez.69.68373
Figure 2 Bayesian phylogeny of Dictyoptera inferred from ten protein-coding genes of 85 mitogenomes, excluding the third base of codon. Posterior probabilities are shown in percentage otherwise are 100%. Clades of superfamilies or higher rank are numbered, as indicated by black background in the key. Species of major taxonomic identities (all are clades) are coloured, as indicated in the key. Subfamilies of Blattidae and Blaberidae are labeled; asterisked ones are not monophyletic. For comparison with trial analyses, see Suppl. material 6–10.
Supplementary material 3 from: Li X-R (2022) Phylogeny and age of cockroaches: a reanalysis of mitogenomes with selective fossil calibrations. Deutsche Entomologische Zeitschrift 69(1): 1-18. https://doi.org/10.3897/dez.69.68373
Table S2
Supplementary material 2 from: Li X-R (2022) Phylogeny and age of cockroaches: a reanalysis of mitogenomes with selective fossil calibrations. Deutsche Entomologische Zeitschrift 69(1): 1-18. https://doi.org/10.3897/dez.69.68373
Table S1
Supplementary material 4 from: Li X-R (2022) Phylogeny and age of cockroaches: a reanalysis of mitogenomes with selective fossil calibrations. Deutsche Entomologische Zeitschrift 69(1): 1-18. https://doi.org/10.3897/dez.69.68373
Figure S1
Supplementary material 9 from: Li X-R (2022) Phylogeny and age of cockroaches: a reanalysis of mitogenomes with selective fossil calibrations. Deutsche Entomologische Zeitschrift 69(1): 1-18. https://doi.org/10.3897/dez.69.68373
Figure S6
Figure 4 from: Li X-R (2022) Phylogeny and age of cockroaches: a reanalysis of mitogenomes with selective fossil calibrations. Deutsche Entomologische Zeitschrift 69(1): 1-18. https://doi.org/10.3897/dez.69.68373
Figure 4 Comparison among the ages estimated in various studies. The fossils are: Valditermes brenanae Jarzembowski, 1981; Piniblattella yixianensisGao et al., 2018; Nodosigalea burmanica Li & Huang, 2018; Cretaperiplaneta kaonashi Qiu et al., 2020; Stegoblatta irmgardgroehni Anisyutkin & Gröhn, 2012. Abbreviation: ALTB, Anaplectidae + Lamproblattidae + Tryonicidae + Blattidae.
Supplementary material 8 from: Li X-R (2022) Phylogeny and age of cockroaches: a reanalysis of mitogenomes with selective fossil calibrations. Deutsche Entomologische Zeitschrift 69(1): 1-18. https://doi.org/10.3897/dez.69.68373
Figure S5
The contribution of extra-pair paternity to the variation in lifetime and age-specific male reproductive success in a socially monogamous species
<p>In socially monogamous species, extra-pair paternity (EPP) is predicted to increase variance in male reproductive success beyond that resulting from genetic monogamy, thus increasing the 'opportunity for selection' (maximum strength of selection that can act on a trait). This prediction is challenging to investigate in wild populations because lifetime reproduction data are often incomplete. Moreover, age-specific variances in reproductive success have been rarely quantified. We analysed 21 years of near-complete social and genetic reproduction data from an insular population of Seychelles warblers (<em>Acrocephalus sechellensis</em>). We quantified the contribution of EPP to lifetime and age-specific opportunities for selection in males. We also compared the variance in male genetic reproductive success (RS) vs. social ('apparent') reproductive success (RSap) to assess if EPP increased the opportunity for selection over that resulting from genetic monogamy. EPP contributed substantially to the variance in lifetime RS, despite not causing a statistically significant excess of this over the variance in lifetime RSap. Partitioning the opportunity for selection into age-specific (co)variance components, showed that EPP provided a substantial contribution at most ages, varying with age. Therefore, in Seychelles warblers EPP likely provides an age-dependent contribution to the opportunity for selection, which can influence evolutionary processes in age-structured populations.</p>
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Allen Brain Atlas
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DANDI Archive for NWB datasets
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