Verification record for Shared Genetic Mistakes and Common Ancestry.
How these were checked. Each source PDF was downloaded to disk and the quotation matched against the extracted text with whitespace collapsed, line-break hyphens rejoined, and curly quotes normalised. Nothing on this page was established through a web-fetch summary, a search-engine snippet, or a secondary work quoting a primary one.
Two traps hit during this work, recorded so the next person does not lose time to them.
- Two-column PDFs.
pdftotext -layoutinterleaves the columns, so a sentence that runs across a column break is split by unrelated text and reads as absent. Five quotations failed on the first pass for this reason alone and passed after re-extraction with plainpdftotext. A "not found" result from a two-column PDF means nothing until the second extraction has been tried. - Page footers inside sentences. Drouin et al. 2011's bat-reactivation sentence is interrupted by the running header of the next page, so it reads as
…during evolu374 Current Genomics, 2011…. The quotation is real; the extraction is not continuous.
Verified
| Source | Quotation (opening words) | Locator | Status |
|---|---|---|---|
| Hillis 1999 | "the probability that homoplasy will obscure phylogenetic relationships…" | PNAS 96:9979, quoting Nikaido et al. p. 10264 and Murata et al. p. 923 | PASS |
| Hillis 1999 | "Similar claims have been made for other kinds of data in the past…" | PNAS 96:9980 | PASS |
| Hillis 1999 | "Even simple insertions and deletions within coding regions have been considered to be unlikely to be homoplastic (25), but numerous examples…" | PNAS 96:9980 | PASS — see note below |
| Hillis 1999 | "Therefore, the presence of homoplasy is not, in itself, terribly problematic…" | PNAS 96:9980 | PASS |
| Hillis 1999 | "it is highly inadvisable to dispense with statistical analysis altogether" | PNAS 96:9979-9980 | PASS |
| Han et al. 2011 | "Our results also suggest that TEs should not be viewed as perfect characters exempt from homoplasy…" | Syst Biol 60:384 | PASS |
| Han et al. 2011 | "the retention index (RI) of TE insertions on the Hackett et al. (2008) tree is 0.97" | Syst Biol 60:384 | PASS |
| Han et al. 2011 | "We found six potential hot spots" | Syst Biol 60:380 | PASS |
| Braun et al. 2011 | "microinversions are not perfect characters and should be interpreted with caution…" | BMC Evol Biol 11:141, abstract | PASS |
| Braun et al. 2011 | "Two specific loci were microinversion hotspots" | BMC Evol Biol 11:141, abstract | PASS |
| Ray et al. 2006 | "Very low levels of each potential confounding factor…" | Syst Biol 55:928, abstract | PASS |
| Ray et al. 2006 | "precise parallel insertions are exceedingly rare—occurring at only about 0.0005 events/insertion…" | Syst Biol 55:933 | PASS |
| Cantrell et al. 2001 | "These results have major repercussions for phylogenetic analyses based on SINE insertions…" | Genetics 158:769, abstract | PASS |
| Cantrell et al. 2001 | "We have identified two hot spots for SINE insertion within mys-9…" | Genetics 158:769, abstract | PASS |
| Cantrell et al. 2001 | "This SINE inserted by 3′ nicking at exactly the same nucleotide…" | Genetics 158, results | PASS |
| van de Lagemaat et al. 2005 | "The deleted loci are indistinguishable from pre-integration sites, effectively reversing the insertion." | Genome Res 15:1243, abstract | PASS |
| van de Lagemaat et al. 2005 | "we estimate that 0.5%–1% of apparent retroelement 'insertions'…" | Genome Res 15:1243, abstract | PASS |
| Belshaw et al. 2007 | "The fate of most human endogenous retroviruses (HERVs) has been to undergo recombinational deletion." | J Virol 81:9437, abstract | PASS |
| Churakov et al. 2009 | "The Exafroplacentalia hypothesis … is significantly supported by five retroposon insertions…" | Genome Res 19:868, abstract | PASS |
| Churakov et al. 2009 | "These findings provide significant support for a ''soft'' polytomy of the major mammalian clades." | Genome Res 19:868, abstract | PASS |
| Doronina et al. 2017 | "All possible evolutionary scenarios received considerable retrotransposon support…" | Genome Res 27:997, abstract | PASS |
| Doronina et al. 2017 | "revealed 14 markers supporting Chiroptera as the most basal order, eight for Perissodactyla…" | Genome Res 27:998 | PASS |
| Doronina et al. 2017 | "extracted among 162,000 preselected cases 102 virtually homoplasy-free…" | Genome Res 27:997, abstract | PASS |
| Suh et al. 2015 | "particularly rapid speciation events may neither resemble a fully bifurcating tree nor are they resolvable as such" | PLoS Biol 13:e1002224, abstract | PASS |
| Suh et al. 2015 | "ILS-derived incongruences are spread over the genome and involve 35% and 34%…" | PLoS Biol 13:e1002224, abstract | PASS |
| Suh et al. 2015 | "our 2,118 RE markers contain negligible homoplasy, and conflicts are instead due to ILS-derived hemiplasy" | PLoS Biol 13:e1002224, p. 3 | PASS |
| Guerrero & Hahn 2018 | "We find that hemiplasy is as likely—or more likely—than homoplasy…" | PNAS 115:12787, abstract | PASS |
| Salem et al. 2003 | "We identified one Alu element (Ye5AH137) that was present in the genomes of human and gorilla…" | PNAS 100:12789 | PASS |
| Salem et al. 2003 | "Only a single insertion from the entire data set showed any potential evidence of insertion homoplasy…" | PNAS 100:12791 | PASS |
| Hedges et al. 2004 | "one element, designated CS12, was determined to be exclusive to gorilla and chimpanzee genomes…" | Genome Res 14:1072 | PASS |
| Hedges et al. 2004 | "by conservative estimates, [Alu elements] comprise some 10% of the human genome" | Genome Res 14:1068 | PASS |
| Thalmann et al. 2004 | "gorillas are notable for having such a variety of numt sequences…" | Mol Ecol 13:321, abstract | PASS |
| Song et al. 2008 | "even such rigorous quality control measures fail to identify certain numts" | PNAS 105:13486, abstract | PASS |
| Álvarez & Wendel 2003 | "Homoplasy is shown to be higher in ITS than in other DNA sequence data sets" | Mol Phyl Evol 29:417, abstract | PASS |
| Álvarez & Wendel 2003 | "its complex and unpredictable evolutionary behavior reduce its utility for phylogenetic analysis" | Mol Phyl Evol 29:417, abstract | PASS |
| Thomson et al. 2014 | "highly heterogeneous rates of microRNA gain and loss, pervasive secondary loss, and sampling error…" | PNAS 111:E3659, abstract | PASS |
| Pink et al. 2011 | "Far from being silent relics, many pseudogenes are transcribed into RNA…" | RNA 17:792, abstract | PASS |
| Chuong et al. 2016 | "impaired expression of adjacent IFN-induced genes and revealed their involvement in the regulation of essential immune functions…" | Science 351:1083, abstract | PASS |
| Guiblet et al. 2021 | "Approximately 13% of the human genome can fold into non-canonical (non-B) DNA structures" | NAR 49:1497, abstract | PASS |
| Zhang et al. 2010 | "we identify 11 unitary pseudogenes that are polymorphic" | Genome Biol 11:R26, abstract | PASS |
| Zhang et al. 2010 | "suggesting that they represent cases of a gene being resurrected in the human lineage" | Genome Biol 11:R26, abstract | PASS |
| Brawand et al. 2008 | "revealed multiple independent inactivation events (e.g., the independent inactivation of VIT1 in therians and monotremes)" | PLoS Biol 6:e63 | PASS |
| Drouin et al. 2011 | "Given the currently accepted phylogeny of bats, these results therefore conclusively demonstrate that inactive genes can be reactivated during evolution" | Curr Genomics 12:373-374 | PASS — sentence crosses a page footer |
| Drouin et al. 2011 | "If one assumes that the inability to synthesize vitamin C is ancestral in the Passeriformes…" | Curr Genomics 12 | PASS |
| Cunningham et al. 1997 | "caution against giving undue phylogenetic weight to insertion-deletion events" | MBE 14:113, abstract | PASS — previously verified for the phylogenetic-congruence article |
| Theobald 2012 | "they insert fairly randomly and generally cannot be transmitted except by inheritance" | 29+ Evidences §4, Prediction 4.3 | PASS |
| Theobald 2012 | "A possible exception is if this transposition were removed due to a rare deletion event; however, deletions are never clean…" | 29+ Evidences §4, Prediction 4.3 | PASS |
| Theobald 2012 | "Again, this process is rare and fairly random, so finding retrogenes in identical chromosomal positions…" | 29+ Evidences §4, Prediction 4.5 | PASS |
| Theobald 2012 | "It would make no sense, macroevolutionarily, if certain other mammals…" | 29+ Evidences §4, Prediction 4.5 | PASS |
| Theobald 2012 | "the malfunctioning human and chimpanzee pseudogenes are the most similar…" | 29+ Evidences §2, Prediction 2.3 | PASS |
| Liu & Soper 2009 | "The best alternative explanation is that orthologous ERVs were created to occupy similar genomic loci…" | ARJ 2:97, section "The Problem of ERVs" | PASS (2026-10-27, saved HTML) |
| Liu & Soper 2009 | "Thus we speculate exogenous retroviruses were derived from endogenous retroviruses…" | ARJ 2:97, Abstract | PASS (2026-10-27) |
| Liu & Soper 2009 | "Directed integration may also partially explain the positional “conservation”…" | ARJ 2:97, "Regulation of ERVs by the cell" | PASS (2026-10-27) |
| Liu & Soper 2009 | "The findings of comparative genomics around the syncytin-1 loci is especially challenging to creationists." | ARJ 2:97, "A Tale of Two ERV “Cousins”" | PASS (2026-10-27) |
| Liu & Nguyen 2018 | "Structural and positional homology of HERVs between humans and animals are more likely due to functional necessity rather than common descent." | Proc. ICC 8:198 (PDF p. 9) | PASS (2026-10-27, two-column page, checked by page) |
| Terborg 2013 | "the ‘VIGE-first hypothesis’—which holds that RNA viruses originate in the genomes…" | J. Creation 27(3):105 | PASS (2026-10-27) |
| Terborg 2013 | "they map to different genomic locations" | J. Creation 27(3):108 | PASS (2026-10-27) |
| Wood 2006 | "it is difficult to explain why pseudogenes with the exact same substitutions or deletions would be shared…" | Occ. Pap. BSG 7:9 (PDF p. 11) | PASS (2026-10-27) |
| Tomkins 2014 | "multiple GULO exon losses in human, chimpanzee, and gorilla occurred independently in each taxon" | ARJ 7:91, Abstract | PASS (2026-10-27, journal HTML; the PDF font layer is broken) |
| Wang et al. 2007 | "We found 41 sites that hosted two independent integration events at exactly the same base pair…" | Genome Res 17:1188 | PASS (2026-10-27) |
| Inai, Ohta & Nishikimi 2003 | "A high percentage of the same substitutions in the total substitutions (36%)…" | J Nutr Sci Vitaminol 49:316 | PASS (2026-10-27; the text layer splits "96" as "9 6") |
| Inai, Ohta & Nishikimi 2003 | "the probability … was calculated to be 1.84 × 10⁻¹²" | 49:317, Fig. 2 caption | PASS (2026-10-27; superscript minus lost in the text layer, fixed by the next sentence, "This extremely small probability") |
| Lavialle et al. 2013 | "the primate and muroid syncytins are clearly not orthologous genes—they are not syntenic…" | Phil Trans B 368:20120507, p. 6 | PASS (2026-10-27) |
| Hormozdiari et al. 2013 | "A total of 84% (157/187) of these loci were also flanked by SNPs of a similar phylogeny…" | PNAS 110:13458 | PASS (2026-10-27) |
| Doronina et al. 2017 | "For nine of the 10 possible order combinations…" and "ILS, rather than homoplasy, is the predominant reason…" | Genome Res 27:1000 | PASS (2026-10-27, right-column crop) |
| Oda et al. 2002 | "all the other four CGA codons are converted to the TGA termination codon…" and the Appendix II legend "codon 107 is polymorphic" | MBE 19:643, 648 | PASS (2026-10-27; running heads anchor PDF p. 4 = 643, p. 9 = 648) |
Note on the Hillis indel sentence
The project research notes carry this quotation as:
"Even simple insertions and deletions within coding regions have been considered to be unlikely to be homoplastic, but numerous examples of convergence and parallelism of these events are now known."
The source reads:
"Even simple insertions and deletions within coding regions have been considered to be unlikely to be homoplastic (25), but numerous examples of convergence and parallelism of these events are now known (e.g., ref. 26)."
The notes silently dropped two reference markers. Nothing substantive changed, but the version in the notes is not verbatim and should be corrected there. The article quotes it with the marker retained.
Unverified — must not be published as they stand
| Source | Quotation | Why it is unverified | Priority |
|---|---|---|---|
| Crow 2000, Nature Reviews Genetics 1:40 | "The most striking is achondroplasia, in which 153 of 154 analysed cases are due to a glycine to arginine substitution at codon 1,138 … a nucleotide with the highest known mutation rate (about 10−5 per generation)." | Closed at Nature; no open-access location. Carried from the project research notes. | High. It is the cleanest illustration of recurrent identical mutation available. |
| Shapiro 2011, Evolution: A View from the 21st Century, p. 82 | "It is difficult (if not impossible) to find a genome change operator that is truly random in its action within the DNA of the cell where it works." | Located through Google Books search-inside rather than from a copy on disk. The page is right and the wording matches the Google Books rendering, but the book is not in the source library. | Low. The claim is uncontroversial and better peer-reviewed sources exist (Guiblet et al. 2021). Simplest fix is to drop it. |
Quarantine
Nothing has been quarantined for this article. No quotation gathered during the research turned out to be fabricated or unlocatable — the three above are simply behind paywalls that have not yet been cleared. If any of them fails on inspection, it moves to quarantine.md with its wording and its claimed source intact rather than being deleted.
Second-hand citations, declared
Two claims in the article are quoted through an intermediary, and the article says so at the point of use:
- Rokas & Holland 2000 on rare genomic changes, quoted through Han et al. 2011's summary. The primary is closed at Elsevier with no OA location.
- Nikaido, Rooney & Okada 1999 on homoplasy being "for all practical purposes, zero," quoted through Hillis 1999. This one is comparatively safe: Hillis gives page numbers for both fragments (ref. 3 p. 10264 and ref. 19 p. 923), he is disagreeing with the authors rather than endorsing them, and the commentary was published in the same issue as the paper it quotes.