Topological Approaches in Animal Comparative Genomics
Open accessAbstract
The surge in chromosome-scale genome sequences from across the tree of life, as well as new comparative methods, has made it possible to study the impact of genomic changes on macroevolution. In this review, we discuss the state of animal comparative genomics. We outline developments in genomic taxonomic sampling and technological advancements in sequencing as well as emerging 3D genomics and provide a perspective on outstanding problems in biodiversity-driven comparative genomics. We discuss the importance of studying genomes holistically and propose the recently introduced evolutionary genome topology framework for topological, multi-scale comparisons across distantly related clades. We highlight how this approach is crucial to understanding the interlinked evolution of subchromosomal and chromosomal changes and their functional implications (e.g., via regulatory entanglement). Lastly, we provide a vision for future areas of research in these approaches and make predictions about the future potential of animal genome evolution.
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Written from the paper’s full text.
TL;DR
This review surveys the state of animal comparative genomics, arguing that the surge in chromosome-scale assemblies and emerging 3D genomics now permits macroevolutionary inference, but that existing tools analyze genomic scales in isolation. The authors propose an "evolutionary genome topology" framework with two methods—multi-locus topology (MLT) and multi-genome topology (MGT)—for multi-scale comparison across distantly related clades.
Key findings
- Chromosome-scale genome sampling rose from 45 animal species in 2015 to 2,287 species by the end of 2024, though this remains a small fraction of the ~1.5 million described animal species (less than 1% sequenced).
- Comparative analyses identified 29 ancestral linkage groups (ALGs) representing whole or partial chromosomes of the last common ancestor of Myriazoa/Benthozoa (>600 million years ago); some ALGs predate animals, extending to a unicellular ancestor more than one billion years ago, with the largest (e.g., A1a) matching whole chromosomes or arms in *Salpingoeca rosetta* and *Capsaspora owczarzaki*.
- Fusion-with-mixing (FWM) is a multistep, largely irreversible process producing mosaic chromosomes; small translocations ("dispersal") erode ALG identity at roughly one event per million years, and fixed inversion rates are reported at 0.4–7 per million years across animal clades.
- Topological analyses are reported to distinguish major animal clades and to reveal hundreds of synapomorphic subchromosomal co-localizations between anciently separated clades (e.g., deuterostomes vs. spiralians, diverged ~500–600 million years ago), including lineage-wide signatures shared across coleoid cephalopods despite rearrangements since the octopus–squid divergence 241 million years ago.
Methods
- This is a review/perspective article, not a primary study; it synthesizes literature on genome sequencing technology, karyotype and synteny evolution, and 3D genomics, and presents the authors' conceptual framework.
- The proposed framework comprises MLT (each data point is a locus; features are distances to all other loci, visualized by dimensionality reduction such as UMAP) and MGT (each data point is a genome; features are inter-locus distances across all locus pairs), with matrices comparable via dimensionality reduction and distance-matrix comparisons.
- Illustrative analyses cited include a UMAP of 3,631 chromosome-scale genomes spanning animal diversity and pan-metazoan topological analyses; the paper also outlines proposed future predictive modeling (phylogenetic frequentist models and convolutional neural networks) rather than reporting new results.
Limitations
- Stated: phylogenetic and geographic sampling biases persist, with deuterostomes and vertebrates overrepresented and arthropods and mollusks underrepresented; many genomes contain errors, unplaced scaffolds, structural uncertainties, or gaps, and few reach telomere-to-telomere completeness; reference genomes rarely capture intraspecific or intraindividual structural variation; 3D genomic comparisons remain nascent and transitioning to 3D genomics is a significant technological challenge given tissue- and cell-type-specific structures; few methods integrate genome organization across multiple scales.
- Stated: whether selection drives conservation of certain ALGs remains unclear; the macroevolutionary explanation for Hox gene order diversity remains to be explained; questions about cross-scale coevolution and topological trajectory transitions remain largely unresolved.
- Evident from the text: the MLT/MGT framework is presented largely as a proposal, with predictive modeling, 3D integration, and noncoding-element extension described as future work rather than demonstrated; several cited topological results are attributed to prior studies (e.g., reference 101) rather than to new analyses in this review.
Model-written summary. Check it against the paper before relying on it.
Integrity signals
Registry
Cites
Statistics
Claims the paper makes
108 of 136 cited sources checked · 43 supported · 2 flagged · accuracy not yet measured
- Findingcitation§ acknowledgments
Thousands of newly sequenced chromosome-scale genomes are rapidly filling phylogenetic gaps of animal diversity.
“thousands of newly sequenced chromosome-scale genomes are rapidly filling phylogenetic gaps of animal diversity”
Quote in the paperNot a substantial claim4 of 4 sources checked- cites [1] 2021, Towards complete and error-free genome assemblies of all vertebrate species, Nature source
The Vertebrate Genomes Project section describes a plan to sequence representatives across vertebrate orders, families and genera, supporting the idea of filling phylogenetic gaps. But the Abstract reports assemblies for 16 species, while the thousands of additional genomes are future goals—not newly sequenced genomes already filling gaps across animal diversity. Page numbers are unavailable in our copy. (LLM, conf=0.85)
Experimental — accuracy not yet measured - cites [2] 2022, Sequence locally, think globally: the Darwin Tree of Life Project, PNAS source
The ‘Open Data, Current Progress, and Future Prospects’ section (page not provided) reports sequencing across hundreds of taxonomic families and plans to release at least 2,000 high-quality genomes. But it reports only 200 chromosomally complete assemblies submitted by September 2021, not thousands already filling gaps in animal diversity; the project covers eukaryotes more broadly. (LLM, conf=0.88)
Experimental — accuracy not yet measured - cites [3] 2021, The Aquatic Symbiosis Genomics Project: probing the evolution of symbiosis across the tree of life, Wellcome Open Res source
The Abstract (page not specified) describes a plan to assemble genomes of 500 symbiotic organisms, including eukaryotic hosts and microbial symbionts. The section “Sequencing symbionts: from sample to openly accessible genome assembly” says Hi-C data will scaffold assemblies into near-chromosomal pseudomolecules. The paper does not establish that thousands of animal genomes have already been sequenced or are rapidly filling phylogenetic gaps. (LLM, conf=0.86)
Experimental — accuracy not yet measured - cites [4] 2018, Earth BioGenome Project: sequencing life for the future of life, PNAS source
In Project Goals and Anticipated Outcomes (page not available), the paper says that as of October 2017 only 2,534 eukaryotic species had sequenced genomes, only 25 met its reference-genome standard, and reference-quality assemblies were phylogenetically skewed. The 10-Year Road Map (page not available) proposes chromosome-scale assemblies across approximately 9,000 eukaryotic families as a future goal, rather than reporting thousands of newly sequenced animal genomes already filling phylogenetic gaps. (LLM, conf=0.87)
Checked by a reasoning model — may be wrong.
Experimental — accuracy not yet measured
- Premisecitation§ acknowledgments
Genome sequences of sponges, placozoans, and cnidarians suggested that many genes thought to define vertebrates were present even in earlier ancestral animals.
“Genome sequences of some animal clades very distantly related to humans, including sponges (37), placozoans (flat animals) (38), and cnidarians (i.e., true jellyfish, corals) (39, 40), suggested that many genes thought to define vertebrates were, in fact, present even in earlier ancestral animals”
Quote in the paperNot a substantial claim4 of 4 sources checked- cites [37] 2010, The Amphimedon queenslandica genome and the evolution of animal complexity, Nature source
- cites [38] 2008, The Trichoplax genome and the nature of placozoans, Nature source
The paper’s Trichoplax gene-complement section reports that many gene families shared by sea anemones and bilaterians also have homologues in this placozoan; its Conclusions say Trichoplax retains ancestral genomic features. This supports the placozoan contribution to the inference about early animals, but the paper does not establish that these genes had been thought to define vertebrates. The other cited clades are not attributed to this source specifically. (LLM, conf=0.78)
Experimental — accuracy not yet measured - cites [39] 2010, The dynamic genome of Hydra, Nature source
- cites [40] 2007, Sea anemone genome reveals ancestral eumetazoan gene repertoire and genomic organization, Science source
- Premisecitation§ acknowledgments
Scaffold-level genome assemblies revealed surprising syntenic conservation over hundreds of millions of years of evolution, spanning divergence between cnidarians, chordates, sponges, and placozoans.
“scaffold-level genome assemblies revealed surprising syntenic conservation over hundreds of millions of years of evolution, spanning the divergence between cnidarians, chordates, sponges, and placozoans”
Quote in the paperNot a substantial claim3 of 3 sources checked- cites [37] 2010, The Amphimedon queenslandica genome and the evolution of animal complexity, Nature source
- cites [38] 2008, The Trichoplax genome and the nature of placozoans, Nature source
The ‘Conserved synteny with other eumetazoans’ section (page unavailable) reports conserved linkage in Trichoplax scaffolds relative to sea anemone and vertebrate genomes, despite divergence in the Precambrian. It does not show conserved synteny spanning the divergence of sponges; sponges appear in the paper’s phylogenetic discussion, not its synteny comparison. (LLM, conf=0.88)
Experimental — accuracy not yet measured - cites [40] 2007, Sea anemone genome reveals ancestral eumetazoan gene repertoire and genomic organization, Science source
The “Conservation of ancient eumetazoan linkage groups” section reports surprising conserved synteny between Nematostella (a cnidarian) and vertebrate genomes, and the methods compare anemone scaffolds with human genome segments. The paper estimates the cnidarian–bilaterian split at roughly 670–820 million years ago. It does not establish conserved synteny spanning divergence with sponges or placozoans; the sponge appears in a phylogenetic comparison, not the synteny analysis. Page numbers are unavailable in our copy. (LLM, conf=0.90)
Experimental — accuracy not yet measured
- Premisecitation§ acknowledgments
Some chromosomes in these lineages appear to have not undergone major fusions or translocations since their ancestor existed more than 600 million years ago, such as those of the myriazoan ALGs G, H, and P.
“Some chromosomes in these lineages appear to have not undergone major fusions or translocations since their ancestor existed more than 600 million years ago (99), such as those of the myriazoan ALGs G, H, and P (69).”
Quote in the paperNot a substantial claim2 of 2 sources checked- cites [99] 2021, A molecular timescale for eukaryote evolution with implications for the origin of red algal-derived plastids, Nat. Commun. source
In Results, ‘Timescale for eukaryote evolution’ (Table 1; page unavailable), the paper uses a 635-million-year minimum age for Metazoa, supporting an animal ancestry older than 600 million years. It does not date the specific myriazoan ancestor or assess chromosome fusions and translocations; the citing sentence attaches a different reference to the chromosome examples. (LLM, conf=0.78)
Experimental — accuracy not yet measured - cites [69] 2022, Deeply conserved synteny and the evolution of metazoan chromosomes, Sci. Adv. source
The Discussion (page unavailable) reports that only a handful of chromosome-scale fusions typically occurred on each lineage since the Cambrian, and the Results section on syntenic equivalence identifies chromosomes descended from ancestral linkage groups with only internal rearrangement. This supports the claim that some chromosomes retained their ancestral linkage, but our copy does not establish the specific ‘more than 600 million years’ date. The G, H, and P examples are attached to a different citation and are not judged here. (LLM, conf=0.82)
Experimental — accuracy not yet measured
- Premisecitation§ acknowledgments
Comparative analyses of chromosome-scale assemblies from across animal diversity revealed that deeply conserved synteny extends beyond vertebrates to encompass most animal lineages.
“comparative analyses of chromosome-scale assemblies from across animal diversity revealed that deeply conserved synteny extends beyond vertebrates to encompass most animal lineages (69).”
Quote in the paperSubstantial claim1 of 1 sources checked- cites [69] 2022, Deeply conserved synteny and the evolution of metazoan chromosomes, Sci. Adv. source
The Introduction and Results (page numbers unavailable) report chromosome-scale conserved synteny across diverse animals, including bilaterians, cnidarians, and sponges, well beyond vertebrates. But the study focuses on five species and notes lineages in which cross-lineage synteny is absent or weak, so it does not establish the claim for most animal lineages. (LLM, conf=0.84)
Experimental — accuracy not yet measured
- Premisecitation§ acknowledgments
These comparisons identified 29 sets of genes that represent whole or partial chromosomes present in the last common ancestor of bilaterians, cnidarians, and sponges-a clade referred to as Myriazoa or Benthozoa.
“These comparisons identified 29 sets of genes that represent whole or partial chromosomes present in the last common ancestor of bilaterians, cnidarians, and sponges—a clade referred to as Myriazoa (97) or Benthozoa (98)”
Quote in the paperSubstantial claim2 of 2 sources checked - Premisecitation§ acknowledgments
High-throughput, inexpensive proximity sequencing methods emerged as powerful tools to scaffold subchromosomal genomic contigs into chromosome-scale sequences.
“High-throughput, inexpensive proximity sequencing methods (reviewed in 83) emerged as powerful tools to scaffold subchromosomal genomic contigs into sequences reconstructing whole chromosomes (i.e., chromosome-scale) (54, 55)”
Quote in the paperNot a substantial claim2 of 3 sources checked- cites [54] 2013, Chromosome-scale scaffolding of de novo genome assemblies based on chromatin interactions, Nat. Biotechnol. source
- cites [55] 2016, Chromosome-scale shotgun assembly using an in vitro method for long-range linkage, Genome Res source
- cites [83] 2019, New approaches for genome assembly and scaffolding, Annu. Rev. Anim. Biosci. source
- Premisecitation§ acknowledgments
Linear reference genomes collapse population diversity into a single path, which biases alignment and variant discovery from different individuals of the same species.
“Linear reference genomes collapse population diversity into a single path, which biases alignment and variant discovery from different individuals of the same species.”
Quote in the paperSubstantial claim1 of 1 sources checked- cites [95] 2020, Pangenome graphs, Annu. Rev. Genom. Hum. Genet. source
- Premisecitation§ acknowledgments
Some ALGs are found on separate chromosomes in choanoflagellates and filastereans and also on separate comb jelly chromosomes but are fused and mixed on single chromosomes in all other animal lineages.
“Some of these ALGs are found on separate chromosomes in choanoflagellates and filastereans and also on separate comb jelly (Ctenophora) chromosomes but are fused and mixed on single chromosomes in all other animal lineages (97).”
Quote in the paperSubstantial claim1 of 1 sources checked- cites [97] 2023, Ancient gene linkages support ctenophores as sister to other animals, Nature source
The Main section (page unavailable) reports ancestral linkages shared by ctenophores and one or both unicellular outgroups, and four fusion-with-mixing events shared by the studied sponges, cnidarians and bilaterians. The claim overstates this as established for both choanoflagellates and filastereans and for all other animal lineages: the Conclusions (page unavailable) say chromosome-scale confirmation in placozoans remains a prediction and note uncertainty for some sponge classes. (LLM, conf=0.85)
Experimental — accuracy not yet measured
- Premisecitation§ acknowledgments
ALG G has survived with rare translocations in several vertebrate lineages after the two rounds of vertebrate WGD in the lineages leading to jawed vertebrates (Gnathostoma).
“This particular chromosome ALG G has survived even with rare translocations in several vertebrate lineages after the two rounds of vertebrate WGD in the lineages leading to jawed vertebrates (Gnathostoma).”
Quote in the paperNot a substantial claim1 of 1 sources checked- cites [67] 2020, Deeply conserved synteny resolves early events in vertebrate evolution, Nat. Ecol. Evol. source
The Results and discussion sections on early vertebrate evolution say that CLGG has evidently not fused and that ancestral linkage-group descendants persist in bony vertebrates after two genome duplications. The section on deep ancestry says translocations or fissions are rare, but does not specifically report rare translocations of CLGG across several vertebrate lineages. It also places the first duplication before the lamprey–jawed vertebrate split, rather than both duplications in the jawed-vertebrate lineage. (LLM, conf=0.82)
Experimental — accuracy not yet measured
- Premisecitation§ acknowledgments
Chromosome-scale assemblies of Amphioxus enabled further comparison and polarization of karyotype changes relative to pre-2R metazoan ancestors.
“Chromosome-scale assemblies of the chordate Amphioxus, a lancelet in the lineage sister to all other chordates, enabled further comparison and polarization of karyotype changes relative to the pre-2R metazoan ancestors (67).”
Quote in the paperSubstantial claim1 of 1 sources checked- cites [67] 2020, Deeply conserved synteny resolves early events in vertebrate evolution, Nat. Ecol. Evol. source
- Premisecitation§ acknowledgments
Graph-based pangenomes replace that single path with a network of alternative haplotypes, explicitly modeling variation from single-nucleotide polymorphisms to megabase-scale structural changes.
“Graph-based pangenomes replace that single path with a network of alternative haplotypes, explicitly modeling variation from single-nucleotide polymorphisms to megabase-scale structural changes ( 95 ).”
Quote in the paperSubstantial claim1 of 1 sources checked- cites [95] 2020, Pangenome graphs, Annu. Rev. Genom. Hum. Genet. source
The Introduction describes replacing a linear reference with a graphical pangenome, and Graphical models explains that alternative paths represent variation. The Adding variation and Variant calling and genotyping sections cover small variants and structural variants, but the passages found do not establish the claim’s specific megabase scale. (LLM, conf=0.82)
Experimental — accuracy not yet measured
- Findingcitation§ acknowledgments
By 2020 and 2021, technological and algorithmic advances culminated in publication of the first complete, chromosome-scale genomes of non-bilaterian animals, including jellyfish Rhopilema esculentum, sponge Ephydatia muelleri, and ctenophore Hormiphora californiensis.
“By 2020 and 2021, these technological and algorithmic advances culminated in the publication of the first complete, chromosome-scale genomes of non-bilaterian animals, including the jellyfish Rhopilema esculentum (92), the sponge Ephydatia muelleri (93), and the ctenophore Hormiphora californiensis (57).”
Quote in the paperNot a substantial claim3 of 3 sources checked- cites [92] 2020, Chromosome-level reference genome of the jellyfish Rhopilema esculentum, Gigascience source
- cites [93] 2020, Tracing animal genomic evolution with the chromosomal-level assembly of the freshwater sponge Ephydatia muelleri, Nat. Commun. source
The Introduction identifies this paper as presenting a chromosome-level assembly of the sponge Ephydatia muelleri. But the Results and discussion section reports that only 83.7% of the genome lies in the largest 24 scaffolds, with the remainder in smaller scaffolds; it therefore does not support calling the assembly complete. The citation is attached to the sponge, not the other two animals. (LLM, conf=0.86)
Experimental — accuracy not yet measured - cites [57] 2021, A chromosome-scale genome assembly and karyotype of the ctenophore Hormiphora californensis, G3 source
- Premisecitation§ acknowledgments
Building assembly graphs rather than using single reference genomes is now routine with mature tools and advancements in genome assembly.
“Building assembly graphs rather than using single reference genomes is now routine with mature tools and advancements in genome assembly ( 207 )”
Quote in the paperSubstantial claim1 of 1 sources checked- cites [207] 2024, Pangenome graph construction from genome alignments with Minigraph-Cactus, Nat. Biotechnol. source
The Abstract says advances in long-read sequencing are making high-quality assemblies widely available, and the paper presents a tool for constructing pangenome graphs from them. But the Discussion says graph construction remains an active research area and predicts that producing large numbers of high-quality genomes will soon be routine; it does not say that building assembly graphs is already routine. The supplied passages have section labels but no page numbers. (LLM, conf=0.86)
Experimental — accuracy not yet measured
- Premisecitation§ acknowledgments
Many higher-order chromosomal features, including TADs, lamina-associated domains, chromatin loops, and nuclear compartments, are conserved across distantly related species.
“Many such features are conserved across distantly related species.”
Quote in the paperSubstantial claim3 of 3 sources checked- cites [124] 2018, Epigenetic maintenance of topological domains in the highly rearranged gibbon genome, Genome Res source
The Abstract passage says TADs are largely conserved across species, and the Discussion reports conservation of large TADs across six mammals. The cited passages do not establish comparable conservation of lamina-associated domains, chromatin loops, or nuclear compartments, so the broader list is not fully supported. (LLM, conf=0.84)
Experimental — accuracy not yet measured - cites [125] 2023, A chromosome-level reference genome for the common octopus, Octopus vulgaris (Cuvier, 1797), G3 source
In Results and discussion, ‘The octopus karyotype’ (page unavailable), the paper reports homologous chromosomes among compared octopus species, not conservation of TADs, lamina-associated domains, chromatin loops, or nuclear compartments across distantly related species. It says a more-distant species’ genome would be needed even to claim karyotype stasis in octopuses. Searches for the named higher-order features found no passage addressing the claim. (LLM, conf=0.76)
Experimental — accuracy not yet measured - cites [126] 2023, TAD evolutionary and functional characterization reveals diversity in mammalian TAD boundary properties and function, Nat. Commun. source
The Discussion reports that 14% of human and 15% of mouse TAD boundaries were conserved across the eight primate and rodent species studied. It also says these proportions challenge the notion that TAD organization is highly conserved across species. Our copy does not establish cross-species conservation of lamina-associated domains, chromatin loops, or nuclear compartments. (LLM, conf=0.88)
Experimental — accuracy not yet measured
- Premisecitation§ acknowledgments
At the chromosomal level, mixing through Robertsonian fusions and centric insertions opens up new topological landscapes via the process of FWM, typically unfolding over tens of millions of years.
“At the chromosomal level, mixing through Robertsonian fusions and centric insertions opens up new topological landscapes via the process of FWM (69), typically unfolding over tens of millions of years (101).”
Quote in the paperNot a substantial claim1 of 2 sources checked- cites [69] 2022, Deeply conserved synteny and the evolution of metazoan chromosomes, Sci. Adv. source
- cites [101] 2024, Topological mixing and irreversibility in animal chromosome evolution
Not checked in the free run.
- Premisecitation§ acknowledgments
These patterns of conservation hold largely for smaller chromosomes across vertebrates, including mammals.
“These patterns of conservation hold largely for smaller chromosomes across vertebrates, including mammals (65, 67, 100)”
Quote in the paperNot a substantial claim3 of 3 sources checked- cites [65] 2021, Reconstruction of proto-vertebrate, proto-cyclostome and proto-gnathostome genomes provides new insights into early vertebrate evolution, Nat. Commun. source
The Results section on the origin of microchromosomes reports that smaller ancestral chromosomes tend to have higher gene densities across the species studied, including human-derived segments (Fig. 5). But it says intact microchromosomes persist in some gnathostomes, such as chicken, spotted gar and elephant shark, and explicitly states that humans have no microchromosomes. It therefore supports conservation of some features in mammalian chromosomal regions, not conservation of the small chromosomes themselves in mammals; page numbers were not available in our copy. (LLM, conf=0.87)
Experimental — accuracy not yet measured - cites [67] 2020, Deeply conserved synteny resolves early events in vertebrate evolution, Nat. Ecol. Evol. source
The Results and discussion section, “Deep ancestry of vertebrate chromosomes” (page not available), reports that micro-chromosomes in chicken, gar and lamprey typically descend from single ancestral linkage groups, and that chicken and gar micro-chromosomes are often orthologous. It does not establish that this pattern holds for smaller mammalian chromosomes; it instead notes that human chromosomes have undergone more rearrangements than those of chicken, gar and lamprey. (LLM, conf=0.85)
Experimental — accuracy not yet measured - cites [100] 2021, Microchromosomes are building blocks of bird, reptile, and mammal chromosomes, PNAS source
The Abstract describes microchromosomes as highly conserved among birds and reptiles. But the Results (‘The Fate of Microchromosomes in Mammals’) find no intact microchromosomes in the human or koala genomes and no enrichment of ancestral microchromosomes in small platypus chromosomes. The extension of this conservation pattern to smaller mammalian chromosomes is therefore not supported. (LLM, conf=0.88)
Experimental — accuracy not yet measured
- Premisecitation§ acknowledgments
Chromosome-scale genome assemblies of choanoflagellates, filastereans, and ichthyosporeans revealed that the largest animal ALGs, e.g., A1a, correspond to entire chromosome arms or whole chromosomes in Salpingoeca rosetta and Capsaspora owczarzaki.
“Chromosome-scale genome assemblies of these species revealed that the largest animal ALGs, e.g., A1a, correspond to entire chromosome arms or whole chromosomes in the choanoflagellate Salpingoeca rosetta and the amoeboid filasterean Capsaspora owczarzaki (97).”
Quote in the paperSubstantial claim1 of 1 sources checked- cites [97] 2023, Ancient gene linkages support ctenophores as sister to other animals, Nature source
The Main section reports chromosome-scale assemblies of Salpingoeca rosetta, Capsaspora owczarzaki, and an ichthyosporean, and finds conserved animal synteny groups in both Salpingoeca and Capsaspora. It says 11 of 29 such groups in Capsaspora are concentrated on single chromosome arms. The passages do not establish that the largest ALGs—specifically A1a—correspond to entire arms or whole chromosomes in both named species; no page numbers are provided in our copy. (LLM, conf=0.84)
Experimental — accuracy not yet measured
- Premisecitation§ acknowledgments
In several jawed vertebrate lineages, three of the four ALG G homeologous chromosomes derived from two rounds of WGD remain largely intact and lack major translocations or fusions with other chromosomes.
“In several jawed vertebrate lineages, three of the four ALG G homeologous chromosomes derived from two rounds of WGD remain largely intact and lack major translocations or fusions with other chromosomes (67).”
Quote in the paperNot a substantial claim1 of 1 sources checked- cites [67] 2020, Deeply conserved synteny resolves early events in vertebrate evolution, Nat. Ecol. Evol. source
- Premisecitation§ acknowledgments
Inversions bringing two pairs of loci into proximity occur at inversion rates ranging between 0.4 and 7 fixed inversions per million years in animal clades.
“These changes are limited by other rearrangement mechanisms, like inversions bringing two pairs of loci into proximity to one another, occurring at inversion rates ranging between 0.4 and 7 fixed inversions per million years in animal clades (176–179).”
Quote in the paperNot a substantial claim2 of 3 sources checked- cites [176] 2020, Recurrent inversion toggling and great ape genome evolution, Nat. Genet. source
The Results section (‘Phylogenetic reconstruction’; page unavailable) estimates approximately 7 fixed autosomal inversions per million years in great apes. It does not establish a range beginning at 0.4 across animal clades or say that these inversions bring two pairs of loci into proximity. (LLM, conf=0.86)
Experimental — accuracy not yet measured - cites [177] 1997, Chromosomal evolution and comparative gene mapping in the Drosophila repleta species group, Rev. Bras. Genet.
Not checked in the free run.
- cites [178] 2015, Rates of karyotypic evolution in Estrildid finches differ between island and continental clades, Evolution source
The Results (section 319; page unavailable) report an average of one fixed pericentric inversion every 2.26 million years, about 0.44 per million years, and an example reaching 5.72 per million years in Australian grassfinches. The paper does not establish the stated 0.4–7 range across animal clades or show that these inversions brought two pairs of loci into proximity. (LLM, conf=0.85)
Experimental — accuracy not yet measured
- Premisecitation§ acknowledgments
At the locus level, protein domains often fuse, resulting in novel domains.
“Even at the locus level, protein domains often fuse, resulting in novel domains (175).”
Quote in the paperNot a substantial claim1 of 1 sources checked- cites [175] 2010, Quantifying the mechanisms of domain gain in animal proteins, Genome Biol source
The Discussion (page not provided) says that joining exons from adjacent genes creates novel domain combinations in animal proteins. It does not say that protein domains themselves fuse to create new domains; the novelty described is in the combination, not necessarily in the individual domains. (LLM, conf=0.88)
Experimental — accuracy not yet measured
- Premisecitation§ acknowledgments
Many conserved local (subchromosomal) linkages of genes exist across many clades despite hundreds of millions of years of divergence.
“many conserved local (subchromosomal) linkages of genes across many clades despite hundreds of millions of years of divergence”
Quote in the paperNot a substantial claim2 of 2 sources checked - Premisecitation§ acknowledgments
Many conserved noncoding elements are consistently located near the same developmental and transcription factor genes in cnidarians and bilaterians, indicating that such regulatory associations predate the origin of their common ancestor.
“many conserved noncoding elements are consistently located near the same developmental and transcription factor genes in cnidarians and bilaterians, indicating that such regulatory associations predate the origin of their common ancestor”
Quote in the paperNot a substantial claim1 of 1 sources checked- cites [51] 2024, Conserved noncoding elements evolve around the same genes throughout metazoan evolution, Genome Biol. Evol. source
The Significance section (page unavailable) says CNEs cluster around the same developmental and transcription-factor genes across metazoan groups, supporting the location pattern. It describes CNEs as evolving repeatedly around those genes, however, and does not establish that the associations predate the cnidarian–bilaterian common ancestor. (LLM, conf=0.88)
Experimental — accuracy not yet measured
- Premisecitation§ acknowledgments
Chromosomal rearrangements often occur at TAD boundaries, preserving internal topological structures.
“Notably, chromosomal rearrangements often occur at TAD boundaries, preserving internal topological structures (125).”
Quote in the paperSubstantial claim1 of 1 sources checked- cites [125] 2023, A chromosome-level reference genome for the common octopus, Octopus vulgaris (Cuvier, 1797), G3 source
The Results and discussion section (‘The octopus karyotype’; page unavailable) describes intrachromosomal rearrangements and conservation of individual chromosomes, but does not address where rearrangements occur relative to TAD boundaries or whether they preserve internal topological structures. Searches for ‘TAD boundaries’ and ‘topologically associating domains’ found no passage addressing that claim. (LLM, conf=0.76)
Experimental — accuracy not yet measured
- Premisecitation§ acknowledgments
Genome sequencing and assembly have become increasingly affordable and computationally tractable thanks to long-read sequencing technologies, DNA proximity ligation sequencing techniques, and genome sequencing consortia.
“Genome sequencing and assembly have become increasingly affordable and computationally tractable thanks to the development of long-read sequencing technologies like the Pacific Biosciences and Oxford Nanopore platforms (52); the development of DNA proximity ligation sequencing techniques, like Hi-C, for genome scaffolding (53–55); and the efforts of genome sequencing consortia (1, 2, 4, 56)”
Quote in the paperNot a substantial claim8 of 8 sources checked- cites [52] 2016, The Oxford Nanopore MinION: delivery of nanopore sequencing to the genomics community, Genome Biol source
The Outlook’s “Read length” section identifies PacBio and MinION as long-read technologies, and “De novo assembly” describes a bacterial genome assembled using MinION data. The paper also cites MinION’s cost as an advantage, but these passages do not establish the broader claim that long-read technologies have made genome sequencing and assembly increasingly affordable and computationally tractable. Hi-C and consortium efforts are attached to other citations in the citing sentence and are not assessed here. (LLM, conf=0.82)
Experimental — accuracy not yet measured - cites [53] 2023, YaHS: yet another Hi-C scaffolding tool, Bioinformatics source
- cites [54] 2013, Chromosome-scale scaffolding of de novo genome assemblies based on chromatin interactions, Nat. Biotechnol. source
- cites [55] 2016, Chromosome-scale shotgun assembly using an in vitro method for long-range linkage, Genome Res source
- cites [1] 2021, Towards complete and error-free genome assemblies of all vertebrate species, Nature source
The Main section identifies the G10K consortium and describes its work evaluating sequencing and assembly approaches; the Vertebrate Genomes Project section describes plans to scale genome production using improved technology and computational infrastructure. The paper also says sequencing became more affordable, but it does not establish that consortium efforts themselves made sequencing and assembly more affordable or computationally tractable. The citations for long-read platforms and Hi-C are attached to other parts of the citing sentence. (LLM, conf=0.78)
Experimental — accuracy not yet measured - cites [2] 2022, Sequence locally, think globally: the Darwin Tree of Life Project, PNAS source
- cites [4] 2018, Earth BioGenome Project: sequencing life for the future of life, PNAS source
- cites [56] 2015, The Genome 10K Project: a way forward, Annu. Rev. Anim. Biosci. source
The citation is attached to the consortium-efforts clause, not the separately cited claims about long-read sequencing or Hi-C. In GENOME 10K RESPONSIBILITIES (page unavailable), the paper describes G10K’s collaborations with sequencing centers and declining sequencing costs. It does not say those consortium efforts made genome assembly computationally tractable; it says data processing and bioinformatic analysis remain substantial costs. (LLM, conf=0.82)
Experimental — accuracy not yet measured
- Premisecitation§ acknowledgments
Some ALGs predate animals, extending back to a unicellular ancestor more than one billion years ago.
“Some ALGs even predate animals, extending back to a unicellular ancestor more than one billion years ago.”
Quote in the paperNot a substantial claim1 of 1 sources checked- cites [69] 2022, Deeply conserved synteny and the evolution of metazoan chromosomes, Sci. Adv. source
The Results section (“Conserved synteny between animals and their unicellular relatives”; page unavailable) reports that 16 ALGs share conserved synteny with unicellular relatives, supporting a pre-animal origin for some linkages. It dates their persistence to more than 800 million years of independent evolution, however, and does not establish the claim’s more-than-one-billion-year date. (LLM, conf=0.87)
Experimental — accuracy not yet measured
- Premisecitation§ acknowledgments
Comparable lineage-wide signatures are also shared across coleoid cephalopods, despite the dramatic chromosomal rearrangements that occurred since the octopus-squid divergence 241 million years ago.
“Comparable lineage-wide signatures are also shared across coleoid cephalopods (octopuses and squids) (170), despite the dramatic chromosomal rearrangements that occurred (170) since the octopus–squid divergence 241 million years ago (171).”
Quote in the paperNot a substantial claim1 of 2 sources checked- cites [170] 2022, Emergence of novel cephalopod gene regulation and expression through large-scale genome reorganization, Nat. Commun. source
The Results and discussion section reports cephalopod-specific microsyntenic blocks shared by squid and octopus and evidence of large-scale chromosomal reorganization. It suggests that many translocations or chromosomal fusions occurred in the coleoid ancestor, however, rather than establishing that they occurred since the octopus–squid divergence. The 241-million-year date is attributed to a different citation in the citing sentence. (LLM, conf=0.84)
Experimental — accuracy not yet measured - cites [171] 2022, Mesozoic origin of coleoid cephalopods and their abrupt shifts of diversification patterns, Mol. Phylogenet. Evol. source
- Interpretationreasoning§ acknowledgments
Locus entanglement, and more broadly genomic topology, can be viewed as a multi-scale unification of existing techniques that infer phylogenies from single genomic scales.
“In this sense, locus entanglement, and more broadly genomic topology, can be viewed as a multi-scale unification of existing techniques that infer phylogenies from single genomic scales, like locus adjacencies (202), microsyntenic clusters (203), macrosyntenic similarity (202), or irreversible FWM events (97).”
Quote in the paperNot a substantial claim3 of 3 sources checked - Premisecitation§ acknowledgments
SVs can now be detected alongside SNVs using cost-effective methods such as single-enzyme Hi-C with short-read sequencing.
“Importantly, SVs can now be detected alongside SNVs using cost-effective methods such as single-enzyme Hi-C with short-read sequencing, making their integration into conservation genomics protocols both feasible and scalable (196, 197).”
Quote in the paperSubstantial claim2 of 2 sources checked- cites [196] 2020, HiNT: a computational method for detecting copy number variations and translocations from Hi-C data, Genome Biol source
The Conclusion (page not specified) says HiNT detects copy-number variations and interchromosomal translocations from Hi-C data, supporting the SV-detection portion of the claim. It does not establish detection alongside SNVs or describe single-enzyme Hi-C with short-read sequencing as a cost-effective method; the Methods passage examined describes Hi-C read processing, not those claims. (LLM, conf=0.87)
Experimental — accuracy not yet measured - cites [197] 2017, Hi-C as a tool for precise detection and characterisation of chromosomal rearrangements and copy number variation in human tumours, Genome Biol source
The Conclusions report that Hi-C detects chromosomal rearrangements without deep sequencing, and the Discussion says it costs significantly less than deep whole-genome sequencing. Methods describe short paired-end reads and corrections for HindIII sites. Our copy does not show SNVs being detected alongside SVs from the same Hi-C data; the cited evidence therefore supports only part of the attributed claim. (LLM, conf=0.87)
Experimental — accuracy not yet measured
- Interpretationcitation§ acknowledgments
Topological evolutionary genomics approaches can be used in chromosomal instabilities in cancer, through mechanisms like chromothripsis.
“Finally, topological evolutionary genomics approaches can also be used in much faster but configurationally important processes, such as chromosomal instabilities in cancer, through mechanisms like chromothripsis (204) ( Figure 6 ).”
Quote in the paperNot a substantial claim1 of 1 sources checked- cites [204] 2011, Chromothripsis is a common mechanism driving genomic rearrangements in primary and metastatic colorectal cancer, Genome Biol source
- Findingnone given§ acknowledgments
In 2015, only 45 animal species had publicly available chromosome-scale genome assemblies.
“In 2015, only 45 animal species had publicly available chromosome-scale genome assemblies”
Quote in the paperSubstantial claim - Findingown data§ acknowledgments
By the end of 2024, 2,287 animal species had chromosome-scale genome assemblies.
“By the end of 2024, that number had risen to 2,287 species”
- Also stated in: § acknowledgments · plain
“As of late 2024, these large initiatives and individual contributing universities have produced chromosome-scale genome assemblies from 2,287 species”
Quote in the paperSubstantial claim - Also stated in: § acknowledgments · plain
- Findingnone given§ acknowledgments
Current reference genomes rarely capture intraspecific, or even intraindividual, structural variation, which is especially pronounced in species with high genetic diversity, such as many marine broadcast spawners.
“current reference genomes rarely capture intraspecific, or even intraindividual, structural variation, which is especially pronounced in species with high genetic diversity, such as many marine broadcast spawners.”
Quote in the paperSubstantial claim - Findingreasoning§ acknowledgments
By the end of 2017, only 30 chromosome-scale genome assemblies came from Protostomia.
“only 30 such assemblies came from the clade Protostomia”
Quote in the paperSubstantial claim - Findingreasoning§ acknowledgments
Deuterostomes, and vertebrates in particular, continue to be heavily overrepresented among chromosome-scale genomes.
“Deutero-stomes, and vertebrates in particular, continue to be heavily overrepresented among chromosome-scale genomes”
Quote in the paperNot a substantial claim - Findingnone given§ acknowledgments
By the end of 2017, there were no chromosome-scale assemblies from Cnidaria, Placozoa, Porifera, or Ctenophora.
“There were no chromosome-scale assemblies from the more distantly related animal phyla Cnidaria (anemones, jellyfish), Placozoa (flat animals), Porifera (sponges), or Ctenophora (comb jellies).”
Quote in the paperSubstantial claim - Findingcitation§ acknowledgments
Initial analyses based on coding genes and their orthology have demonstrated that topological methods distinguish phylogenetic relationships among major animal clades.
“Initial analyses based on coding genes and their orthology have already demonstrated that topological methods distinguish phylogenetic relationships among major animal clades (101).”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites [101] 2024, Topological mixing and irreversibility in animal chromosome evolution
Not checked in the free run.
- Interpretationreasoning§ Abstract
The surge in chromosome-scale genome sequences from across the tree of life, as well as new comparative methods, has made it possible to study the impact of genomic changes on macroevolution.
“The surge in chromosome-scale genome sequences from across the tree of life, as well as new comparative methods, has made it possible to study the impact of genomic changes on macroevolution.”
Quote in the paperSubstantial claim - Premisereasoning§ acknowledgments
Early comparative genomics work broadly sampling animal diversity revealed large-scale evolutionary patterns through synteny conservation and genome architecture.
“early comparative genomics work broadly sampling animal diversity revealed large-scale evolutionary patterns through synteny conservation and genome architecture.”
Quote in the paperNot a substantial claim - Interpretationreasoning§ acknowledgments
These resources make it possible, for the first time, to compare genome structure, rearrangements, regulatory organization, and key evolutionary genomic changes across the full breadth of animal diversity.
“These resources make it possible, for the first time, to compare genome structure, rearrangements, regulatory organization, and key evolutionary genomic changes that mark evolution across the full breadth of animal diversity.”
Quote in the paperNot a substantial claim - Premisecitation§ acknowledgments
Initial findings suggest that even genomes with similar gene content can have strikingly different topologies.
“Initial findings suggest that even genomes with similar gene content can have strikingly different topologies.”
Quote in the paperSubstantial claim0 of 1 sources checked- cites [101] 2024, Topological mixing and irreversibility in animal chromosome evolution
Not checked in the free run.
- Interpretationreasoning§ acknowledgments
This lack of taxonomic breadth severely limited comparative analyses of whole-chromosome evolution, in most cases restricting studies to closely related species.
“This lack of taxonomic breadth severely limited comparative analyses of whole-chromosome evolution, in most cases restricting studies to closely related species.”
Quote in the paperSubstantial claim - Interpretationreasoning§ acknowledgments
Timescales of mixing differ markedly across genomic scales.
“The timescales of mixing differ markedly across genomic scales ( Figure 3a ).”
Quote in the paperSubstantial claim - Premisecitation§ acknowledgments
Comparative analyses of molluscan genomes show that species with superficially similar karyotypes, like anemones versus other hexacorals, are in fact distinguished by unique patterns of locus mixing, fusion history, and internal reordering.
“For instance, comparative analyses of molluscan genomes show that species with superficially similar karyotypes, like anemones versus other hexacorals, are in fact distinguished by unique patterns of locus mixing, fusion history, and internal reordering (101) ( Figure 5a , b ).”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites [101] 2024, Topological mixing and irreversibility in animal chromosome evolution
Not checked in the free run.
- Premisereasoning§ acknowledgments
Current homology tools, designed for linear comparisons, often analyze genomes at only one of multiple scales, despite genome evolution operating across interconnected structural and functional levels.
“Current homology tools, designed for linear comparisons, often analyze genomes at only one of these scales, despite the fact that genome evolution operates across interconnected structural and functional levels ( Figure 3a ).”
Quote in the paperSubstantial claim - Premisecitation§ acknowledgments
Clades with stable, conserved karyotypes, including spiralians, invertebrate chordates, sponges, and cnidarians, have conserved karyotypes composed of minimally changed chromosomes.
“This is in strong contrast to clades with stable, conserved karyotypes, including spiralians (mostly marine invertebrates that include annelids and mollusks), invertebrate chordates (lancelets, sea squirts), sponges, and cnidarians (true jellyfish, corals), which have conserved karyotypes composed of minimally changed chromosomes, akin to the previous examples of ALGs G and D.”
Quote in the paperNot a substantial claim - Interpretationreasoning§ acknowledgments
Irreversible genomic changes at different scales are largely independent of one another.
“These differences imply that irreversible genomic changes at different scales are largely independent of one another.”
Quote in the paperSubstantial claim - Premisecitation§ acknowledgments
MLT analyses have revealed dozens of clade-specific pairs and clusters of loci, often in cases where traditional sequence-based approaches found few synapomorphies.
“MLT analyses have revealed dozens of clade-specific pairs and clusters of loci, often in cases where traditional sequence-based approaches found few synapomorphies (101).”
Quote in the paperSubstantial claim0 of 1 sources checked- cites [101] 2024, Topological mixing and irreversibility in animal chromosome evolution
Not checked in the free run.
- Interpretationreasoning§ acknowledgments
Only with chromosome-scale assemblies has it become possible to broadly and clearly link sequence- and regulatory-level conservation to whole-chromosome changes, and thereby connect genome architecture to deep evolutionary history of animals and their close relatives.
“only with chromosome-scale assemblies has it become possible to broadly and clearly link this sequence- and regulatory-level conservation to whole-chromosome changes, and thereby connect the genome architecture to the deep evolutionary history of animals and their close relatives.”
Quote in the paperSubstantial claim - Premisecitation§ acknowledgments
Exploration of the full chromosomal configuration space may take hundreds of millions of years.
“Yet, exploration of the full chromosomal configuration space may take hundreds of millions of years (101).”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites [101] 2024, Topological mixing and irreversibility in animal chromosome evolution
Not checked in the free run.
- Interpretationnone given§ acknowledgments
The first prediction of evolutionary topology is that species evolve on different evolutionary trajectories.
“The first prediction of evolutionary topology is that species evolve on different evolutionary trajectories ( Figure 5a , b ).”
Quote in the paperSubstantial claim - Premisenone given§ acknowledgments
We developed a multi-genomic-scale topological framework that captures how loci move and reconfigure over macroevolutionary time.
“To address the challenge of comparing genome evolution across multiple levels of organization, we developed a multi-genomic-scale topological framework that captures how loci move and reconfigure over macroevolutionary time ( Figure 4a ).”
Quote in the paperSubstantial claim- The authors state this as an assumption: The genome can be modeled as a structured system in which orthologous loci have spatial relationships that shift, persist, or recur across lineages.
- Interpretationreasoning§ acknowledgments
These findings suggest that the spatial genome organization itself can carry phylogenetic signals, especially when structural rearrangements are irreversible.
“These findings suggest that the spatial genome organization itself can carry phylogenetic signals, especially when structural rearrangements are irreversible, which we discuss below.”
Quote in the paperSubstantial claim - Interpretationown data§ acknowledgments
This order-of-magnitude acceleration in number of species sequenced in one decade has led to a dramatic shift in phylogenetic sampling-from biomedically and commercially important species to sampling that covers much of animal diversity.
“This order-of-magnitude acceleration in the number of species sequenced in one decade has finally led to a dramatic shift in phylogenetic sampling—from biomedically and commercially important species to a sampling that covers much of animal diversity”
Quote in the paperNot a substantial claim - Interpretationreasoning§ acknowledgments
These methods enable measurement of the degree of mixing within each FWM event, integrating over the pairwise distances of participating loci at the subchromosomal level.
“Going beyond a qualitative description, these methods enable measurement of the degree of mixing within each FWM event, i.e., integrating over the pairwise distances of participating loci at the subchromosomal level.”
Quote in the paperSubstantial claim- The authors state this as an assumption: The genome can be modeled as a structured system in which orthologous loci have spatial relationships that shift, persist, or recur across lineages.
- Interpretationreasoning§ acknowledgments
Capturing genomic distances enables identification of FWM events that have been described at the chromosomal level.
“Capturing genomic distances enables identification of FWM events that have been described at the chromosomal level.”
Quote in the paperSubstantial claim- The authors state this as an assumption: The genome can be modeled as a structured system in which orthologous loci have spatial relationships that shift, persist, or recur across lineages.
- Premisecitation§ acknowledgments
3D genome architecture can be preserved in ancient specimens, as shown by Hi-C data recovered from a 52,000-year-old mammoth skin sample.
“Notably, 3D genome architecture can be preserved in ancient specimens, with Hi-C data successfully recovered from a 52,000-year-old mammoth skin sample (201), making it increasingly feasible to study topological features directly from well-preserved samples of extinct species.”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites [201] 2023, Three-dimensional genome architecture persists in a 52,000-year-old woolly mammoth skin sample, Cell
Not checked in the free run.
- Interpretationreasoning§ acknowledgments
Accumulation of irreversible states proceeds asynchronously across different organizational levels of the genome.
“Thus, accumulation of irreversible states proceeds asynchronously across different organizational levels of the genome.”
Quote in the paperSubstantial claim - Interpretationreasoning§ acknowledgments
Topological evolutionary genomics can help identify species on endangered genomic trajectories, those with few neighbors in configuration space.
“Topological evolutionary genomics can help identify species on endangered genomic trajectories, those with few neighbors in configuration space ( Figure 5d ).”
Quote in the paperSubstantial claim - Interpretationcitation§ acknowledgments
Experimental validation methods such as optical mapping, in situ hybridization, and expansion microscopy could provide diagnostic access to disease-indicative rearranged configurations.
“Experimental validation, such as optical mapping (205), in situ hybridization for specific mixing markers, and expansion microscopy, could provide diagnostic access to these disease-indicative rearranged configurations.”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites [205] 2018, Structural variation detection and analysis using bionano optical mapping, Methods Mol. Biol. source
- Premisecitation§ acknowledgments
A lineage with a high rate of genome inversions does not necessarily exhibit a correspondingly high rate of protein domain evolution, as seen in clitellate annelids.
“For example, a lineage with a high rate of genome inversions does not necessarily exhibit a correspondingly high rate of protein domain evolution, as seen in clitellate annelids (162).”
Quote in the paperSubstantial claim0 of 1 sources checked- cites [162] 2024, Acceleration of genome rearrangement in clitellate annelids
Not checked in the free run.
- Interpretationreasoning§ acknowledgments
The entangled conserved state of stable associations, and the low probability of reversal, may be sufficient to conduct phylogenetic inferences.
“Although not all such stable associations will be functionally linked, their entangled conserved state, and the low probability of reversal, may be sufficient to conduct phylogenetic inferences.”
Quote in the paperSubstantial claim - Interpretationreasoning§ acknowledgments
Topological evolutionary genomics can aid de-extinction by providing complementary information on genome structure beyond protein-coding sequence.
“Topological evolutionary genomics can also aid de-extinction, which aims to reintroduce extinct species by editing the genomes of closely related extant organisms.”
- Also stated in: § acknowledgments · plain
“Although protein-coding sequence is central to de-extinction, topological approaches offer complementary information by accounting for genome structure.”
Quote in the paperNot a substantial claim - Also stated in: § acknowledgments · plain
- Interpretationnone given§ acknowledgments
The accumulation of translocations, deletions, or rearrangements can lead to effectively irreversible genomic states in cancer cells.
“The accumulation of translocations, deletions, or rearrangements can lead to effectively irreversible genomic states in cancer cells, providing a new lens through which to interpret how mutational load influences somatic evolution during development and disease progression.”
Quote in the paperSubstantial claim - Interpretationreasoning§ acknowledgments
Species further along endangered genomic trajectories may have accumulated irreversible synapomorphic features, making ancestral states increasingly difficult to infer.
“Species further along these trajectories may have accumulated irreversible synapomorphic features, making ancestral states increasingly difficult to infer.”
Quote in the paperNot a substantial claim - Premisecitation§ acknowledgments
Intrachromosomal mixing across animals has generated hundreds of new, conserved genomic co-localizations over evolutionary timescales spanning tens to hundreds of millions of years.
“For example, intrachromosomal mixing across animals has generated hundreds of new, conserved genomic co-localizations over evolutionary timescales spanning tens to hundreds of millions of years (101) ( Figure 5c ).”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites [101] 2024, Topological mixing and irreversibility in animal chromosome evolution
Not checked in the free run.
- Premisecitation§ acknowledgments
Subchromosomal mixing or entanglement forms stable associations.
“Similar to FWM of chromosomal characters, subchromosomal mixing or entanglement (101) forms stable associations ( Figure 4c ).”
Quote in the paperSubstantial claim0 of 1 sources checked- cites [101] 2024, Topological mixing and irreversibility in animal chromosome evolution
Not checked in the free run.
- May combine two claims. 48
- Classified as probably not a substantial claim. 49
May combine two claims.
Premisecitation§ acknowledgmentsScallop chromosome 10 (ALG G) has 1:1 homology with lancelet chromosome 1, freshwater sponge chromosome 15, and flame jellyfish chromosome 1.
“scallop chromosome 10 (ALG G) has 1:1 homology with lancelet (Amphioxus floridae) chromosome 1, freshwater sponge (E. muelleri) chromosome 15, and flame jellyfish (R. esculentum) chromosome 1 (69).”
Quote in the paperSubstantial claim1 of 1 sources checked- cites [69] 2022, Deeply conserved synteny and the evolution of metazoan chromosomes, Sci. Adv. source
In Materials and Methods, under “ALG and BLG nomenclature,” the paper identifies amphioxus chromosome BFL1 as a fusion of BLG_A1 and BLG_A2, not a one-to-one counterpart of ALG_G. The “Identification of ALGs” section does say ALG_G corresponds uniquely to single chromosomes across species, but it does not identify those chromosomes as the four numbered in the claim; the stated lancelet chromosome 1 correspondence conflicts with the paper’s account. (LLM, conf=0.84)
Checked by a reasoning model — may be wrong.
Experimental — accuracy not yet measured
May combine two claims.
Premisecitation§ acknowledgmentsThe variation graph toolkit (vg) showed that read mapping to graphs reduces reference bias and better recovers complex variants.
“The variation graph toolkit (vg) showed that read mapping to graphs reduces reference bias and better recovers complex variants”
Quote in the paperNot a substantial claim1 of 1 sources checked- cites [206] 2018, Variation graph toolkit improves read mapping by representing genetic variation in the reference, Nat. Biotechnol. source
The paper reports that vg mapping to a population graph nearly balances reference- and alternate-allele coverage, while linear-reference mapping increasingly misses reads containing longer insertions (Abstract; no page given). It also reports better mapping of reads containing non-reference variants. These results support reduced reference bias, but do not demonstrate better recovery or calling of complex variants themselves. (LLM, conf=0.84)
Experimental — accuracy not yet measured
May combine two claims.
Premisecitation§ acknowledgmentsIn non-bilaterian lineages such as cnidarians, available data suggest that topological domains are smaller, if they exist at all, and potentially less insulated.
“By contrast, in non-bilaterian lineages such as cnidarians, available data suggest that topological domains are smaller, if they exist at all (134), and potentially less insulated (135).”
Quote in the paperNot a substantial claim2 of 2 sources checked- cites [134] 2023, Topological structures and syntenic conservation in sea anemone genomes, Nat. Commun. source
- cites [135] 2023, A chromosome-scale epigenetic map of the Hydra genome reveals conserved regulators of cell state, Genome Res source
The Results section, “Hydra chromatin is organized into localized contact domains” (page unavailable), reports putative Hydra contact domains with a median size of about 176 kb and says some resemble TADs. It does not establish that domains in cnidarians generally are smaller than those in bilaterians. The separate claim about insulation is attached to citation 135, not this source. (LLM, conf=0.78)
Experimental — accuracy not yet measured
May combine two claims.
Interpretationcitation§ acknowledgmentsThese irreversible FWM events provided powerful phylogenomic markers, offering strong evidence for resolving the long-debated relationships between ctenophores, sponges, and the rest of Metazoa.
“These irreversible FWM events provided powerful phylogenomic markers (97), offering strong evidence for resolving the long-debated relationships (104, 105) between ctenophores, sponges, and the rest of Metazoa.”
Quote in the paperSubstantial claim3 of 3 sources checked- cites [97] 2023, Ancient gene linkages support ctenophores as sister to other animals, Nature source
- cites [104] 2021, Rooting the animal tree of life, Mol. Biol. Evol. source
- cites [105] 2017, Contentious relationships in phylogenomic studies can be driven by a handful of genes, Nat. Ecol. Evol. source
Probably not a substantial claim: may not pass S3 (load-bearing).
Premisecitation§ acknowledgmentsRobertsonian fusions can result in the recruitment of autosomes into becoming sex chromosomes, as has been seen in fishes.
“On the scale of whole chromosomes, dramatic changes like Robertsonian fusions can result in the recruitment of autosomes into becoming sex chromosomes, as has been seen in fishes (155)”
Quote in the paperNot a substantial claim1 of 1 sources checked- cites [155] 2012, Turnover of sex chromosomes and speciation in fishes, Environ. Biol. Fishes source
Probably not a substantial claim: may not pass S3 (load-bearing).
Premisecitation§ acknowledgmentsA single inversion in the mole genome has resulted in a high testosterone level in females, thought to aide in digging.
“several recent studies demonstrated that a single inversion in the mole genome has resulted in a high testosterone level in females, thought to aide in digging (153)”
Quote in the paperNot a substantial claim1 of 1 sources checked- cites [153] 2020, The mole genome reveals regulatory rearrangements associated with adaptive intersexuality, Science source
The CYP17A1 triplication section reports high circulating androgens in female moles and links increased testosterone to the triplication’s regulatory effects, not to a single inversion. The Discussion suggests that androgen-related muscle strength may aid a burrowing lifestyle. The paper instead associates an FGF9 inversion with delayed meiosis and gonadal masculinization. (LLM, conf=0.90)
Experimental — accuracy not yet measured
May combine two claims.
Premisecitation§ acknowledgmentsOikopleura dioica has a highly compacted genome and extensive rearrangements that led to a loss of macrosynteny relative to other chordates.
“the free-swimming marine invertebrate chordate Oikopleura dioica has a highly compacted genome and extensive rearrangements that led to a loss of macrosynteny relative to other chordates (163, 164).”
Quote in the paperNot a substantial claim1 of 2 sources checkedMay combine two claims.
Interpretationcitation§ acknowledgmentsTAD and lamina-associated domain boundaries are often conserved between species and correspond with breaks of synteny between species, implying that chromosomal inversions that break TADs are selected against.
“For example, TAD and lamina-associated domain (120) boundaries are often conserved between species and correspond with breaks of synteny between species (124–126), implying that chromosomal inversions that break TADs are selected against.”
Quote in the paperNot a substantial claim3 of 3 sources checked- cites [124] 2018, Epigenetic maintenance of topological domains in the highly rearranged gibbon genome, Genome Res source
- cites [125] 2023, A chromosome-level reference genome for the common octopus, Octopus vulgaris (Cuvier, 1797), G3 source
The Results and discussion section on the octopus karyotype reports chromosomal collinearity and inversions among octopus species, but does not discuss TAD or lamina-associated domain boundaries, their correspondence with synteny breaks, or selection against inversions that disrupt TADs. Searches for those domain and selection terms found no passage addressing the attributed claim. (LLM, conf=0.76)
Experimental — accuracy not yet measured - cites [126] 2023, TAD evolutionary and functional characterization reveals diversity in mammalian TAD boundary properties and function, Nat. Commun. source
The Introduction reports shared TAD boundaries between species, and the Results report that evolutionary breaks of synteny are enriched at TAD boundaries. The paper says selection to preserve TAD integrity is an interpretation of that pattern, but its Discussion also finds species-specific boundaries at breaks and proposes that some rearrangements may help establish new boundaries. It does not establish that inversions breaking TADs are selected against; the lamina-associated-domain point has a separate citation in the citing sentence. (LLM, conf=0.84)
Experimental — accuracy not yet measured
Probably not a substantial claim: may not pass S3 (load-bearing).
Premisecitation§ acknowledgmentsThese technological advancements led to a new generation of genome alignment and assembly algorithms leveraging new data types.
“These technological advancements also led to a new generation of genome alignment and assembly algorithms leveraging the new data types (84–89).”
Quote in the paperNot a substantial claim6 of 6 sources checked- cites [84] 2021, Haplotype-resolved de novo assembly using phased assembly graphs with hifiasm, Nat. Methods source
- cites [85] 2024, Scalable telomere-to-telomere assembly for diploid and polyploid genomes with double graph, Nat. Methods source
- cites [86] 2020, Nanopore sequencing and the Shasta toolkit enable efficient de novo assembly of eleven human genomes, Nat. Biotechnol. source
- cites [87] 2020, Progressive Cactus is a multiple-genome aligner for the thousand-genome era, Nature source
- cites [88] 2020, Telomere-to-telomere assembly of a complete human X chromosome, Nature source
The ‘Highly continuous whole-genome assembly’ section (page not provided) describes assembling nanopore and PacBio reads with Canu, and ‘Methods > Manual gap closure’ describes using Minimap2 for read mapping. This supports the paper as an example of alignment and assembly algorithms applied to new sequencing data, but it does not establish that the technological advances led to a new generation of those algorithms. (LLM, conf=0.78)
Experimental — accuracy not yet measured - cites [89] 2022, The complete sequence of a human genome, Science source
Probably not a substantial claim: may not pass S3 (load-bearing).
Premisecitation§ acknowledgmentsA single inversion in the genome of skates and rays contributes to large fin sizes during development.
“whereas a single inversion in the genome of skates and rays contributes to large fin sizes during development (154).”
Quote in the paperNot a substantial claim1 of 1 sources checked- cites [154] 2023, The little skate genome and the evolutionary emergence of wing-like fins, Nature source
The ‘PCP pathway as a driver of fin expansion’ section links skate-specific genomic rearrangements to genes potentially involved in pectoral fin expansion, and reports reduced anterior fin expansion after PCP-pathway inhibition (page unavailable). It does not identify a single inversion as the contributor; the paper describes multiple rearrangements and candidate genes instead. (LLM, conf=0.88)
Experimental — accuracy not yet measured
May combine two claims.
Premisecitation§ acknowledgmentsOverall genome topology, including TAD organization, shows conservation across distant lineages but does degrade over macroevolutionary time.
“Preliminary studies suggest that overall genome topology, including TAD organization, shows conservation across distant lineages (124–126) but does degrade over macroevolutionary time (121, 132, 133).”
Quote in the paperNot a substantial claim3 of 3 sources checked- cites [124] 2018, Epigenetic maintenance of topological domains in the highly rearranged gibbon genome, Genome Res source
- cites [125] 2023, A chromosome-level reference genome for the common octopus, Octopus vulgaris (Cuvier, 1797), G3 source
This source is cited for the claim that genome organization degrades over evolutionary time, not for the preceding conservation claim. In Results and discussion, “The octopus karyotype” (page unavailable), the paper reports more chromosomal rearrangements and less collinearity between more distantly related octopus species. That supports a loss of chromosome-scale similarity over time, but the paper does not assess TAD organization or establish that overall genome topology degrades. (LLM, conf=0.86)
Experimental — accuracy not yet measured - cites [126] 2023, TAD evolutionary and functional characterization reveals diversity in mammalian TAD boundary properties and function, Nat. Commun. source
The Results section reports that TAD boundaries were shared more often among closely related species and that evolutionary distance shaped cross-species TAD organization. The Discussion reports that only 14% of human and 15% of mouse TAD boundaries were conserved across all eight species. These findings support evolutionary divergence in TAD organization, but the paper does not establish that overall genome topology degrades over macroevolutionary time. (LLM, conf=0.83)
Experimental — accuracy not yet measured
Probably not a substantial claim: may not pass S3 (load-bearing).
Premisecitation§ acknowledgmentsThe ancestor of Myriazoa/Benthozoa likely existed more than 600 million years ago.
“Notably, the ancestor of this clade likely existed more than 600 million years ago (99).”
Quote in the paperNot a substantial claim1 of 1 sources checked- cites [99] 2021, A molecular timescale for eukaryote evolution with implications for the origin of red algal-derived plastids, Nat. Commun. source
The Results (Timescale for eukaryote evolution; page unavailable) describe a dated eukaryote phylogeny, but the text in our copy does not identify Myriazoa/Benthozoa or give an age for its ancestor. Searches for both clade names and a common-ancestor estimate around 600 Ma found no passage establishing the claimed date. (LLM, conf=0.75)
Experimental — accuracy not yet measured
May combine two claims.
Premisecitation§ acknowledgmentsWeaker signals are also detectable in the ichthyosporean Creolimax fragrantissima, though no homologies have been reported with fungi.
“Weaker signals are also detectable in the ichthyosporean Creolimax fragrantissima (97), though no homologies have been reported with fungi, the next most distant lineage.”
Quote in the paperNot a substantial claim1 of 1 sources checked- cites [97] 2023, Ancient gene linkages support ctenophores as sister to other animals, Nature source
The Main section reports that Creolimax fragrantissima retains eight conserved synteny groups with metazoans, fewer than the other unicellular outgroups, supporting the weaker-signal claim. Our copy does not report a comparison of those syntenies with fungi or state that no fungal homologies have been reported. (LLM, conf=0.88)
Experimental — accuracy not yet measured
May combine two claims.
Premisecitation§ acknowledgmentsAcross lancelets, mollusks, cnidarians, and demosponges, entire chromosomes retain 1:1 correspondences, indicating few chromosome-scale rearrangements since their common ancestor over 600 million years ago and making the ancestral karyotype readily reconstructable.
“Across lancelets, mollusks, cnidarians, and demosponges, entire chromosomes retain 1:1 correspondences, indicating few chromosome-scale rearrangements since their common ancestor over 600 million years ago and making the ancestral karyotype readily reconstructable (69)”
Quote in the paperNot a substantial claim1 of 1 sources checked- cites [69] 2022, Deeply conserved synteny and the evolution of metazoan chromosomes, Sci. Adv. source
Split into 2 atoms — 1 confirmed, 1 partially supported, 0 disputed, 0 misattributed, 0 unverifiable. Expand the claim to see per-atom verdicts.
Experimental — accuracy not yet measured
May combine two claims.
Premisecitation§ acknowledgmentsALG identities erode slowly over time due to small translocations (dispersal) that can result in several genes migrating from one chromosome to another at a slow rate, estimated at approximately one event per million years.
“Despite these detectable patterns of conservation, these ALG identities erode slowly over time due to small translocations (dispersal) that can result in several genes migrating from one chromosome to another at a slow rate, estimated at approximately one event per million years (69, 97, 101).”
Quote in the paperNot a substantial claim2 of 3 sources checked- cites [69] 2022, Deeply conserved synteny and the evolution of metazoan chromosomes, Sci. Adv. source
The Results section, “Finding ancestral metazoan linkage groups” (page unavailable), attributes gene dispersal to numerous small-scale interchromosomal translocations over time. It estimates a handful of genes translocated per million years, not approximately one translocation event per million years. (LLM, conf=0.89)
Experimental — accuracy not yet measured - cites [97] 2023, Ancient gene linkages support ctenophores as sister to other animals, Nature source
The Main section says that small-scale translocations slowly erode conserved gene linkages and estimates that they move 1% of genes to a different chromosome every approximately 40 million years. It does not estimate approximately one translocation event per million years; a rate of genes transferred is not an event rate. No page number is available in our copy. (LLM, conf=0.88)
Experimental — accuracy not yet measured - cites [101] 2024, Topological mixing and irreversibility in animal chromosome evolution
Not checked in the free run.
May combine two claims.
Premisecitation§ acknowledgmentsDespite not undergoing major fusions or fissions with other chromosomes, chromosome ALG G's gene orders between these species are not conserved due to 600 million years of intrachromosomal inversions that shuffled gene order independently in each lineage.
“Despite not undergoing major fusions or fissions with other chromosomes, chromosome ALG G's gene orders between these species are not conserved due to the 600 million years of intrachromosomal inversions that shuffled the gene order independently in each lineage.”
Quote in the paperNot a substantial claim1 of 1 sources checked- cites [69] 2022, Deeply conserved synteny and the evolution of metazoan chromosomes, Sci. Adv. source
Split into 2 atoms — 1 confirmed, 1 partially supported, 0 disputed, 0 misattributed, 0 unverifiable. Expand the claim to see per-atom verdicts.
Experimental — accuracy not yet measured
Probably not a substantial claim: may not pass S3 (load-bearing).
Premisecitation§ acknowledgmentsFWM can be seen to a lesser extent over more recently diverged genomes if they evolve relatively slowly, such as the similar-yet-rearranged karyotypes of human and mouse.
“FWM can be seen to a lesser extent over more recently diverged genomes if they evolve relatively slowly, such as the similar-yet-rearranged karyotypes of human and mouse (70).”
Quote in the paperNot a substantial claim1 of 1 sources checked- cites [70] 2003, Genome rearrangements in mammalian evolution: lessons from human and mouse genomes, Genome Res source
The Synteny Blocks section reports that human and mouse share 281 synteny blocks but have undergone at least 245 rearrangements, supporting the similar-yet-rearranged comparison. Our copy does not discuss FWM or show that it is visible in these genomes; the Genome Rearrangements section also cautions that rodents may have unusually rapid chromosome alterations, rather than establishing the claimed slow evolution. (LLM, conf=0.86)
Experimental — accuracy not yet measured
May combine two claims.
Interpretationcitation§ acknowledgmentsThe multistep dynamic of FWM helps explain the mosaic origins of extant chromosomes and can be thought of as contributing to diversification through population-level, speciation, and macroevolutionary processes.
“The multistep dynamic of FWM helps explain the mosaic origins of extant chromosomes and can be thought of as contributing to diversification through population-level, speciation, and macroevolutionary processes (67, 69).”
Quote in the paperNot a substantial claim2 of 2 sources checked- cites [67] 2020, Deeply conserved synteny resolves early events in vertebrate evolution, Nat. Ecol. Evol. source
The Results and discussion sections describe a multistep history of chromosome duplication, fusion and mixing that explains mixed ancestry in extant vertebrate chromosomes. The Conclusion links post-duplication fusions and rearrangements to early vertebrate diversification, but the paper does not frame this as a general contribution through population-level, speciation and macroevolutionary processes. Page numbers are not available in our copy. (LLM, conf=0.84)
Experimental — accuracy not yet measured - cites [69] 2022, Deeply conserved synteny and the evolution of metazoan chromosomes, Sci. Adv. source
The Results section (“Fusion-with-mixing”; page unavailable) describes a multistep process in which ancestral chromosomes fuse and their genes become interspersed, supporting the explanation of mosaic chromosome origins. The Discussion (page unavailable) discusses population constraints on chromosomal change and the use of fusion-with-mixing to trace evolutionary lineages, but does not establish that the process contributes to diversification through speciation or across all three stated levels. (LLM, conf=0.84)
Experimental — accuracy not yet measured
May combine two claims.
Premisecitation§ acknowledgmentsComparison of chromosome-scale genomes across vertebrates has clarified the timing and consequences of ancient whole-genome duplications that led to extant vertebrate genomes, supporting Ohno's hypothesis.
“Comparison of chromosome-scale genomes across vertebrates has clarified the timing and consequences of the ancient whole-genome duplications (WGDs) that led to extant vertebrate genomes (59–65), supporting Ohno's (66) hypothesis.”
Quote in the paperNot a substantial claim6 of 8 sources checked- cites [59] 2015, The sea lamprey meiotic map improves resolution of ancient vertebrate genome duplications, Genome Res source
The Abstract reports that comparative mapping clarified vertebrate genome-duplication history, and the Conclusions discuss its evolutionary consequences. But the Abstract finds strong support for one ancestral whole-genome duplication, not strong support for a second; the citing sentence presents ancient WGDs in the plural without that qualification. The paper discusses Ohno's proposal of at least one duplication. (LLM, conf=0.86)
Experimental — accuracy not yet measured - cites [60] 2018, The sea lamprey germline genome provides insights into programmed genome rearrangement and vertebrate evolution, Nat. Genet. source
The Results (Vertebrate Genome Evolution; page unavailable) use lamprey, chicken, and gar genome comparisons to infer the timing and pattern of ancestral vertebrate duplications. But the paper favors one whole-genome duplication preceded by three chromosome-scale duplications over an explanation involving two whole-genome duplications. It therefore does not fully support the citing sentence’s plural characterization of the ancient whole-genome duplications. (LLM, conf=0.87)
Experimental — accuracy not yet measured - cites [61] 2006, Reconstruction of a 450-My-old ancestral vertebrate protokaryotype, Trends Genet source
- cites [62] 2007, Reconstruction of the vertebrate ancestral genome reveals dynamic genome reorganization in early vertebrates, Genome Res source
- cites [63] 2018, Chromosome evolution at the origin of the ancestral vertebrate genome, Genome Biol source
- cites [64] 2017, Genomes as documents of evolutionary history: a probabilistic macrosynteny model for the reconstruction of ancestral genomes, Bioinformatics source
The Introduction describes ancient WGDs and their proposed effects on present-day genomes, while Results §4.2 compares vertebrate genomes and refines the reconstruction of chromosome changes around the teleost WGD. The cited paper therefore supports the comparison and evolutionary-consequences portions of the claim, but it does not itself clarify the timing of the ancient vertebrate WGDs. The separate citation (66), not this paper, is attached to Ohno’s hypothesis. (LLM, conf=0.82)
Experimental — accuracy not yet measured - cites [65] 2021, Reconstruction of proto-vertebrate, proto-cyclostome and proto-gnathostome genomes provides new insights into early vertebrate evolution, Nat. Commun. source
- cites [66] 1970
Not checked in the free run.
Probably not a substantial claim: may not pass S3 (load-bearing).
Findingcitation§ acknowledgmentsParticularly large or complex genomes, such as that of the lungfish, remain difficult to assemble to chromosomal completeness.
“Particularly large or complex genomes, such as that of the lungfish, remain difficult to assemble to chromosomal completeness (94).”
Quote in the paperNot a substantial claim1 of 1 sources checked- cites [94] 2021, Giant lungfish genome elucidates the conquest of land by vertebrates, Nature source
May combine two claims.
Premisecitation§ acknowledgmentsThe most highly conserved of the three ALG G ohnologs among diverse vertebrates are microchromosomes 15 and 19 in chicken, the two small chromosomes 20 and 22 in spotted gar, and independently integrated into larger chromosomes in frog and human.
“The most highly conserved of the three ALG G ohnologs among diverse vertebrates are microchromosomes 15 and 19 in chicken (Gallus gallus), the two small chromosomes 20 and 22 in the spotted gar (Lepisosteus oculatus), and independently integrated into larger chromosomes in frog (Xenopus tropicalis) and human (Homo sapiens) (67).”
Quote in the paperNot a substantial claim1 of 1 sources checked- cites [67] 2020, Deeply conserved synteny resolves early events in vertebrate evolution, Nat. Ecol. Evol. source
The Results and discussion section, under “Deep ancestry of vertebrate chromosomes” (page unavailable), says chicken and spotted-gar microchromosomes are often orthologous and lists CLGG among ancestral linkage groups found unfused in a bony vertebrate. The Fig. 3 caption describes paralogous chromosome segments in chicken, gar and frog, but the available passages do not identify chicken chromosomes 15 and 19 or gar chromosomes 20 and 22 as the most conserved CLGG copies, or establish their independent integration into larger frog and human chromosomes. (LLM, conf=0.78)
Experimental — accuracy not yet measured
May combine two claims.
Premisecitation§ acknowledgmentsProtein folding exhibits irreversible fates and fitness landscapes, whereas irreversibility is rarely quantified in population genetics, where traditional models are fundamentally time reversible.
“Like development, protein folding exhibits irreversible fates (184, 185) and fitness landscapes (186–189), whereas irreversibility is rarely quantified in population genetics, where traditional models are fundamentally time reversible (190).”
Quote in the paperNot a substantial claim2 of 3 sources checked- cites [184] 2007, Reversible and irreversible unfolding of multi-domain proteins, Biochim. Biophys. Acta. source
- cites [185] 2016, Energy landscape in protein folding and unfolding, PNAS source
In “Energy landscape in protein folding and unfolding” (page unavailable), the paper describes a free-energy landscape for protein folding and an irreversible denatured state. It does not describe that landscape as a fitness landscape; the citing sentence assigns the population-genetics comparison to a different citation. (LLM, conf=0.86)
Experimental — accuracy not yet measured - cites [186] 1997, Folding funnels and energy landscapes of larger proteins within the capillarity approximation, PNAS source
The introduction (p. 1) describes an energy landscape and folding funnel for proteins, and the discussion (p. 5) describes molecules taking different folding paths or becoming trapped. These passages do not establish irreversible fates or call the protein-folding landscape a fitness landscape. The population-genetics comparison is attached to a different citation, not this source. (LLM, conf=0.84)
Experimental — accuracy not yet measured
Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.
Premisecitation§ acknowledgmentsDevelopment is fundamentally irreversible, providing a strong analogy for the irreversible changes that churn during chromosome and genome evolution.
“Interestingly, development is fundamentally irreversible (181–183), providing a strong analogy for the irreversible changes that churn during chromosome and genome evolution.”
Quote in the paperNot a substantial claim1 of 3 sources checked- cites [181] 1978, Irreversible gene repression model for control of development: Lessening of developmental potential may result from progressive repression of previously active genes, Science source
- cites [182] 2021, Chromatin-state barriers enforce an irreversible mammalian cell fate decision, Cell Rep source
- cites [183] 2006, G9a-mediated irreversible epigenetic inactivation of Oct-3/4 during early embryogenesis, Nat. Cell Biol. source
Probably not a substantial claim: may not pass S3 (load-bearing).
Premisecitation§ acknowledgmentsOur previous studies estimated the probabilities of chromosomal fusion convergence across major metazoan lineages.
“Our previous studies (69, 97) estimated the probabilities of chromosomal fusion convergence across major metazoan lineages.”
Quote in the paperNot a substantial claim2 of 2 sources checked- cites [69] 2022, Deeply conserved synteny and the evolution of metazoan chromosomes, Sci. Adv. source
The Results section on spiralian karyotypes considers convergent fusion-with-mixing in bivalves and gastropods as an alternative explanation, but gives no probability estimate for it. Searches for convergent fusions and their probabilities found no estimate across major metazoan lineages in our copy. (LLM, conf=0.73)
Experimental — accuracy not yet measured - cites [97] 2023, Ancient gene linkages support ctenophores as sister to other animals, Nature source
The Main section says the alternative sponge-sister hypothesis would require multiple convergent chromosomal fusions across animal lineages, and reports genome-shuffling simulations showing that comparable syntenic patterns were extremely unlikely to arise by chance. It does not report estimates of the probabilities of fusion convergence itself; the simulations assess chance recovery of the observed syntenic signal. (LLM, conf=0.82)
Experimental — accuracy not yet measured
May combine two claims.
Interpretationcitation§ acknowledgmentsMost possible fusions between ALGs occur in at least one extant clade, suggesting that genome evolution samples an immense configuration space.
“Notably, our findings indicate that most possible fusions between ALGs occur in at least one extant clade, suggesting that genome evolution samples an immense configuration space.”
Quote in the paperNot a substantial claim2 of 2 sources checked- cites [69] 2022, Deeply conserved synteny and the evolution of metazoan chromosomes, Sci. Adv. source
The Results (Fusion-with-mixing and the evolution of spiralian karyotypes; page unavailable) identify several ALG fusions shared by extant mollusks, supporting the occurrence of particular fusions in extant clades. The Discussion (page unavailable) says that typically only a handful of chromosome-scale fusions have occurred per lineage; it does not establish that most possible ALG pairs have fused in at least one extant clade. The configuration-space interpretation is framed in the citing sentence as the citing authors’ own inference. (LLM, conf=0.82)
Experimental — accuracy not yet measured - cites [97] 2023, Ancient gene linkages support ctenophores as sister to other animals, Nature source
The Main section reports that ALG fusions occur in animal lineages and identifies seven derived fusions shared by bilaterians, cnidarians and sponges. It does not say that most possible ALG fusions occur in extant clades or draw the claimed conclusion about an immense configuration space; the citing sentence presents those as its authors’ own findings. (LLM, conf=0.85)
Experimental — accuracy not yet measured
Probably not a substantial claim: may not pass S3 (load-bearing).
Interpretationcitation§ acknowledgmentsIntroducing SVs into small populations may carry evolutionary risks, particularly if they alter regulatory architecture.
“However, introducing SVs into small populations may carry evolutionary risks, particularly if they alter regulatory architecture, which underscores the importance of weighing potential benefits against the disruption of locally adapted genomic configurations (198).”
Quote in the paperNot a substantial claim1 of 1 sources checked- cites [198] 2011, Assessing the benefits and risks of translocations in changing environments: a genetic perspective: translocations in changing environments, Evol. Appl. source
The “Weighing the risks” section says translocations can cause outbreeding depression, particularly when populations have fixed chromosomal differences or are adapted to different environments. The Rutidosis leptorrhynchoides case study also warns that mixing chromosome races could harm fitness in small populations. Our copy does not attribute that risk specifically to introduced structural variants altering regulatory architecture. (LLM, conf=0.87)
Experimental — accuracy not yet measured
Probably not a substantial claim: may not pass S3 (load-bearing).
Premisecitation§ acknowledgmentsA widely used intervention strategy involves identifying genetically diverse populations of the same species to serve as donor populations, whose individuals can be translocated to increase genetic variation in the at-risk group.
“A widely used intervention strategy involves identifying genetically diverse populations of the same species to serve as donor populations, whose individuals can be translocated to increase genetic variation in the at-risk group (194, 195).”
Quote in the paperNot a substantial claim1 of 2 sources checked- cites [194] 2010, Genetic rescue guidelines with examples from Mexican wolves and Florida panthers, Conserv. Genet. source
- cites [195] 2010, Genetic restoration of the Florida panther, Science source
The Abstract reports that managers translocated eight Texas pumas to increase the Florida panther population’s depleted genetic diversity, directly illustrating the intervention described. Our copy does not establish that this strategy is widely used or describe a general process for identifying donor populations. (LLM, conf=0.82)
Experimental — accuracy not yet measured
Probably not a substantial claim: may not pass S3 (load-bearing), S4 (based).
Findingnone given§ acknowledgmentsSampling gaps in high-quality genomes remain for much of animal diversity.
“Sampling gaps in high-quality genomes remain for much of animal diversity”
Quote in the paperNot a substantial claimProbably not a substantial claim: may not pass S3 (load-bearing).
Findingreasoning§ acknowledgmentsChordates and arthropods are the best-represented clades in terms of total proportion of chromosome-scale species relative to known species.
“Thanks to community focus, the chordates and arthropods are the best-represented clades in terms of total proportion of chromosome-scale species relative to the known number of species”
Quote in the paperNot a substantial claimProbably not a substantial claim: may not pass S3 (load-bearing).
Findingnone given§ acknowledgmentsOnly a chromosome-scale genome of a placozoan remains to be published.
“Only a chromosome-scale genome of a placozoan remains to be published.”
Quote in the paperNot a substantial claimProbably not a substantial claim: may not pass S3 (load-bearing), S4 (based).
Findingnone given§ acknowledgments3D genomic comparisons remain nascent.
“3D genomic comparisons remain nascent”
Quote in the paperNot a substantial claimProbably not a substantial claim: may not pass S4 (based).
Findingnone given§ acknowledgmentsFew methods integrate genome organization across multiple scales, despite being linked through function and selection.
“few methods integrate genome organization across multiple scales, despite being linked through function and selection”
Quote in the paperNot a substantial claimProbably not a substantial claim: may not pass S3 (load-bearing).
Findingnone given§ acknowledgmentsThe progress of taxonomic sampling in chromosome-scale genome sequencing was concentrated initially in vertebrate genomes and later expanded to other animal clades.
“The progress of taxonomic sampling in chromosome-scale genome sequencing was concentrated initially in vertebrate genomes and later expanded to other animal clades”
Quote in the paperNot a substantial claimProbably not a substantial claim: may not pass S3 (load-bearing).
Findingnone given§ acknowledgmentsBy the end of 2017, 77% of the 136 published chromosome-scale genome assemblies were from vertebrates.
“By the end of 2017, 77% of the 136 published chromosome-scale genome assemblies were from vertebrates.”
Quote in the paperNot a substantial claimMay combine two claims.
Findingreasoning§ acknowledgmentsAlthough the original goal of closing major phylogenetic gaps has largely been achieved, substantial underrepresentation persists in several clades, including arthropods and mollusks.
“Although the original goal of closing major phylogenetic gaps has largely been achieved, substantial underrepresentation persists in several clades, including arthropods and mollusks.”
Quote in the paperNot a substantial claimMay combine two claims.
Findingown data§ acknowledgmentsDespite progress, important phylogenetic gaps and biases remain.
“Despite this progress, important phylogenetic gaps and biases remain”
Quote in the paperNot a substantial claimClassified as probably not a substantial claim.
Findingnone given§ acknowledgmentsThe timing of the first of the two rounds of vertebrate WGDs (the 2R events) remained unresolved.
“the timing of the first of the two rounds of vertebrate WGDs (the 2R events) remained unresolved.”
Quote in the paperSubstantial claimMay combine two claims.
Findingown data§ acknowledgmentsHexacoral and anemone genomes are distinct and each clade is defined by unique clade-specific chromosomal fusions, as revealed by MGT topological view.
“a MGT (one-dot-one-genome) topological view of cnidarian genomes reveals that hexacoral and anemone genomes are distinct and that each clade is defined by unique clade-specific chromosomal fusions”
Quote in the paperSubstantial claimProbably not a substantial claim: may not pass S3 (load-bearing), S4 (based).
Findingnone given§ acknowledgmentsAs of writing, the only remaining non-bilaterian animal phylum without a chromosome-scale genome is Placozoa.
“As of writing, the only remaining non-bilaterian animal phylum without a chromosome-scale genome is Placozoa”
Quote in the paperNot a substantial claimProbably not a substantial claim: may not pass S3 (load-bearing).
Findingnone given§ acknowledgmentsWithin these clades, some families remain poorly sampled, often due to challenges related to availability, culturing, or genome size.
“Within these clades, some families remain poorly sampled, often due to challenges related to availability, culturing, or genome size.”
Quote in the paperNot a substantial claimProbably not a substantial claim: may not pass S3 (load-bearing), S4 (based). May combine two claims.
Findingnone given§ acknowledgmentsAlthough more than 2,000 species now have chromosome-scale genome assemblies, this number still represents only a small fraction of the approximately 1.5 million described animal species.
“although more than 2,000 species now have chromosome-scale genome assemblies, this number still represents only a small fraction of the approximately 1.5 million described animal species.”
Quote in the paperNot a substantial claim- Rests on an assumption: Approximately 1.5 million animal species have been described.
May combine two claims.
Findingnone given§ acknowledgmentsEven among species with chromosome-scale assemblies, many genomes still contain errors, unplaced scaffolds, structural uncertainties, or gaps, and few reach telomere-to-telomere completeness.
“Even among species with chromosome-scale assemblies, many genomes still contain errors, unplaced scaffolds, structural uncertainties, or gaps, and few reach telomere-to-telomere completeness.”
Quote in the paperNot a substantial claimProbably not a substantial claim: may not pass S3 (load-bearing), S4 (based). May combine two claims.
Findingnone given§ acknowledgmentsDeeply conserved ancestral linkage groups show that many chromosomes remained intact for more than 600 million years, and some predate animals, whereas other lineages exhibit extensive fusions, fissions, and translocations.
“Deeply conserved ancestral linkage groups show that many chromosomes remained intact for more than 600 million years, and some predate animals, whereas other lineages exhibit extensive fusions, fissions, and translocations.”
Quote in the paperNot a substantial claimProbably not a substantial claim: may not pass S3 (load-bearing), S4 (based). May combine two claims.
Findingnone given§ acknowledgmentsFusion-with-mixing is a common, multistep process that creates irreversible chromosomal mosaics, providing informative markers for phylogenetic inference and distinguishing major evolutionary transitions.
“Fusion-with-mixing is a common, multistep process that creates irreversible chromosomal mosaics, providing informative markers for phylogenetic inference and distinguishing major evolutionary transitions.”
Quote in the paperNot a substantial claimProbably not a substantial claim: may not pass S3 (load-bearing), S4 (based). May combine two claims.
Findingnone given§ acknowledgmentsMany 3D genomic features align with synteny breaks and show cross-clade conservation, although domain architecture can differ outside Bilateria.
“Many 3D genomic features align with synteny breaks and show cross-clade conservation, although domain architecture can differ outside Bilateria.”
Quote in the paperNot a substantial claimProbably not a substantial claim: may not pass S3 (load-bearing), S4 (based). May combine two claims.
Findingnone given§ acknowledgmentsLarge biodiversity initiatives and many individual labs have broadened taxonomic coverage immensely, yet substantial phylogenetic and geographic sampling biases persist.
“Large biodiversity initiatives and many individual labs have broadened taxonomic coverage immensely, yet substantial phylogenetic and geographic sampling biases persist.”
Quote in the paperNot a substantial claimProbably not a substantial claim: may not pass S3 (load-bearing).
Interpretationnone given§ acknowledgmentsThe sequencing of whole genomes opened the door to sequence-driven comparative genomics.
“The sequencing of whole genomes opened the door to sequence-driven comparative genomics”
Quote in the paperNot a substantial claimProbably not a substantial claim: may not pass S3 (load-bearing).
Interpretationreasoning§ acknowledgmentsWithout whole-genome sequences, comparative genomics was limited to laborious methods that did not scale well outside of a small number of species.
“without whole-genome sequences, comparative genomics was limited to laborious methods that did not scale well outside of a small number of species.”
Quote in the paperNot a substantial claimProbably not a substantial claim: may not pass S3 (load-bearing), S4 (based). May combine two claims.
Premisenone given§ acknowledgmentsGenome sequencing remained expensive and time-consuming, limiting studies to a small number of well-established model organisms.
“genome sequencing remained expensive and time-consuming, limiting studies to a small number of well-established model organisms.”
Quote in the paperNot a substantial claimProbably not a substantial claim: may not pass S3 (load-bearing), S4 (based).
Interpretationreasoning§ acknowledgmentsGenomic neighborhoods evolve and persist over far longer timescales than those of population-level dynamics.
“Given the structural basis of these trajectories, this framework emphasizes that genomic neighborhoods evolve and persist over far longer timescales than those of population-level dynamics.”
Quote in the paperNot a substantial claimMay combine two claims.
Interpretationreasoning§ acknowledgmentsThese findings suggest that the transition to animal multicellularity was not a complete genomic scrambling but rather a slower process of chromosome structure evolution combined with the emergence of novel genome regulatory mechanisms.
“These findings suggest that the transition to animal multicellularity was not a complete genomic scrambling but rather a slower process of chromosome structure evolution combined with the emergence of novel genome regulatory mechanisms.”
Quote in the paperSubstantial claimMay combine two claims.
Interpretationreasoning§ acknowledgmentsThese patterns suggest that structural, sequence-level, and regulatory changes may proceed independently, or at least the interplay between these organizational scales may manifest in specific loci and interactions, rather than fit broad-strokes trends.
“These patterns suggest that structural, sequence-level, and regulatory changes may proceed independently, or at least the interplay between these organizational scales may manifest in specific loci and interactions, rather than fit broad-strokes trends.”
Quote in the paperSubstantial claimMay combine two claims.
Premisenone given§ acknowledgmentsAt the subchromosomal level, translocations of enhancer and promoter contacts can either create novel regulatory configurations or produce mixed or entangled states without immediate functional consequences.
“At the subchromosomal level ( Figures 3b and 5c ), translocations of enhancer and promoter contacts can either create novel regulatory configurations or produce mixed or entangled states without immediate functional consequences.”
Quote in the paperNot a substantial claimClassified as probably not a substantial claim.
Premisenone given§ acknowledgmentsThis framework includes two complementary methods: multi-locus topology (MLT) and multi-genome topology (MGT).
“This framework includes two complementary methods: multi-locus topology (MLT) and multi-genome topology (MGT).”
Quote in the paperSubstantial claim- The authors state this as an assumption: The genome can be modeled as a structured system in which orthologous loci have spatial relationships that shift, persist, or recur across lineages.
Probably not a substantial claim: may not pass S3 (load-bearing).
Premisecitation§ acknowledgmentsPan-metazoan topological analyses predict that subchromosomal constraints and mixed states are a major factor in shaping macroevolutionary genomic trajectories.
“Pan-metazoan topological analyses (101) predict that such subchromosomal constraints and mixed states are a major factor in shaping macroevolutionary genomic trajectories ( Figure 4c,f )”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites [101] 2024, Topological mixing and irreversibility in animal chromosome evolution
Not checked in the free run.
Probably not a substantial claim: may not pass S2 (checkable), S3 (load-bearing).
Interpretationreasoning§ acknowledgmentsFor evolutionary topology, assembly graph references are a natural substrate.
“For evolutionary topology, assembly graph references are a natural substrate.”
Quote in the paperNot a substantial claimProbably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.
Premisecitation§ acknowledgmentsHox genes in bilaterian animals often occur in a cluster, the order of which is generally conserved across animal groups that diverged hundreds of millions of years ago.
“In perhaps the most famous case, Hox genes in bilaterian animals often occurs in a cluster, the order of which is generally conserved across animal groups that diverged hundreds of millions of years ago (147).”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites [147] 2007, The rise and fall of Hox gene clusters, Development source
May combine two claims.
Premisenone given§ acknowledgmentsChromosomes of many clades of extant organisms can often be described by algebraic operations of the 29 ancestral animal linkage groups; however, not all chromosomal identities have persisted since the early animal ancestors.
“Chromosomes of many clades of extant organisms can often be described by algebraic operations of the 29 ancestral animal linkage groups; however, not all chromosomal identities have persisted since the early animal ancestors ( Figure 3c ).”
Quote in the paperSubstantial claimMay combine two claims.
Premisecitation§ acknowledgmentsHundreds of synapomorphic, subchromosomal gene co-localizations differ between anciently separated animal clades, including deuterostomes and spiralians, whose ancestors diverged between ∼500 and 600 million years ago.
“Hundreds of synapomorphic, subchromosomal gene co-localizations differ between anciently separated animal clades (101), including deuterostomes and spiralians, whose ancestors diverged between ∼500 and 600 million years ago.”
Quote in the paperSubstantial claim0 of 1 sources checked- cites [101] 2024, Topological mixing and irreversibility in animal chromosome evolution
Not checked in the free run.
Probably not a substantial claim: may not pass S3 (load-bearing).
Premisenone given§ acknowledgmentsThe development of highly accurate long-reads (HiFi) and ultralong-reads (Oxford Nanopore) and decreasing sequencing costs fueled a new wave of high-quality genome assemblies.
“The development of highly accurate long-reads (HiFi) from Pacific Biosciences, the accessibility of ultralong-reads from Oxford Nanopore, and steadily decreasing sequencing costs further fueled a new wave of high-quality genome assemblies.”
Quote in the paperNot a substantial claimMay combine two claims.
Interpretationreasoning§ acknowledgmentsTransitions between trajectories are unlikely because they require breakages of existing chromosomal or subchromosomal linkages, resulting in deleterious genotypes in a population, and the establishment of a new genomic configuration resembling another trajectory, an event implying extraordinary convergence.
“Transitions between trajectories are unlikely because they require (a) breakages of existing chromosomal or subchromosomal linkages, like breakages of cis-regulatory elements from their downstream loci, resulting in deleterious genotypes in a population, and (b) the establishment of a new genomic configuration resembling another trajectory, an event implying extraordinary convergence.”
Quote in the paperNot a substantial claimMay combine two claims.
Premisecitation§ acknowledgmentsClitellate annelid genomes are not exceptionally smaller than those of closely related polychaete annelids, but they have extensive chromosomal rearrangements, and those rearrangements do not correlate with equally extensive amino acid changes.
“for instance, clitellate annelid genomes are not exceptionally smaller than those of closely related polychaete annelids (i.e., Figure 3c ), but they have extensive chromosomal rearrangements, and those rearrangements do not correlate with equally extensive amino acid changes (162).”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites [162] 2024, Acceleration of genome rearrangement in clitellate annelids
Not checked in the free run.
Probably not a substantial claim: may not pass S4 (based).
Interpretationnone given§ acknowledgmentsTopological approaches can be used for conservation genomics in that they provide complementary information on genome diversity, resilience, and uniqueness relative to standard SNP/structural variant approaches.
“Topological approaches can be used for conservation genomics in that they provide complementary information on genome diversity, resilience, and uniqueness relative to standard single-nucleotide polymorphism/structural variant approaches.”
Quote in the paperNot a substantial claimMay combine two claims.
Interpretationreasoning§ acknowledgmentsGenome evolution is shaped not only by coding sequence but also by structural and regulatory constraints that persist over deep evolutionary time.
“These findings, even from subchromosome-level genome assemblies, highlighted that genome evolution is shaped not only by coding sequence but also by structural and regulatory constraints that persist over deep evolutionary time.”
Quote in the paperSubstantial claimProbably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.
Premisenone given§ acknowledgmentsSingle-nucleotide variations can influence protein function, regulatory element activity, and RNA structure.
“At the finest scale, single-nucleotide variations (SNVs) can influence protein function, regulatory element activity, and RNA structure ( Figure 3a , step 1).”
Quote in the paperNot a substantial claimMay combine two claims.
Interpretationreasoning§ acknowledgmentsThese lineage-specific configurations indicate that chromosomal evolution is not constrained to a single path but instead explores a broad topological space, with clade-defining features emerging through structural divergence.
“These lineage-specific configurations indicate that chromosomal evolution is not constrained to a single path but instead explores a broad topological space, with clade-defining features emerging through structural divergence.”
Quote in the paperSubstantial claimClassified as probably not a substantial claim. May combine two claims.
Interpretationreasoning§ acknowledgmentsThe MGT approach could reveal species with unique genome conformations not found elsewhere in the tree of life, offering a complementary layer of evidence to prioritize species for conservation.
“In other words, the MGT approach could reveal species with unique genome conformations not found elsewhere in the tree of life, offering a complementary layer of evidence to prioritize species for conservation.”
Quote in the paperSubstantial claimMay combine two claims.
Interpretationnone given§ acknowledgmentsSVs can impact genome function at a larger scale than SNVs, affecting gene order, dosage, and regulatory context, and may be especially relevant in the context of adaptive potential and evolutionary resilience.
“Because SVs can impact genome function at a larger scale than SNVs, affecting gene order, dosage, and regulatory context, they may be especially relevant in the context of adaptive potential and evolutionary resilience.”
Quote in the paperSubstantial claimProbably not a substantial claim: may not pass S3 (load-bearing), S4 (based). May combine two claims.
Interpretationreasoning§ acknowledgmentsEvolutionary topological genomics has actionable applications in conservation and medicine by prioritizing unique genomic trajectories and diagnosing cancers via irreversible structural configurations.
“Evolutionary topological genomics has actionable applications in conservation and medicine by prioritizing unique genomic trajectories and diagnosing cancers via irreversible structural configurations.”
Quote in the paperNot a substantial claimMay combine two claims.
Premisecitation§ acknowledgmentsExisting topological simulations in populations generally assume a static space; they do not easily accommodate dynamic changes in topology itself.
“However, existing topological simulations in populations (e.g., fitness landscapes) generally assume a static space; they do not easily accommodate dynamic changes in topology itself, a major challenge for modeling genome evolution (191).”
Quote in the paperSubstantial claim0 of 1 sources checked- cites [191] 2004
Not checked in the free run.
Probably not a substantial claim: may not pass S4 (based). May combine two claims.
Interpretationnone given§ acknowledgmentsThe evolutionary genome topology framework, MGT and MLT, is a tool for detecting irreversible FWM events and reconstructing genome configuration trajectories over macroevolutionary timescales.
“We outline our evolutionary genome topology framework, MGT and MLT, as a tool for detecting irreversible FWM events and reconstructing genome configuration trajectories over macroevolutionary timescales.”
Quote in the paperNot a substantial claimProbably not a substantial claim: may not pass S3 (load-bearing), S4 (based).
Interpretationnone given§ acknowledgmentsMLT applied to closely related species can identify conserved co-localizations or synapomorphic features that may represent key functional linkages in a clade.
“Even absent direct Hi-C data, MLT applied to closely related species can identify conserved co-localizations or synapomorphic features that may represent key functional linkages in this clade.”
Quote in the paperNot a substantial claimProbably not a substantial claim: may not pass S3 (load-bearing), S4 (based).
Interpretationnone given§ acknowledgmentsRecent advances in chromosome-scale genome assemblies and 3D genomics enable comparative studies to connect sequence, structure, and regulation across the full breadth of animal evolution.
“Recent advances in chromosome-scale genome assemblies and 3D genomics enable comparative studies to connect sequence, structure, and regulation across the full breadth of animal evolution.”
Quote in the paperNot a substantial claimProbably not a substantial claim: may not pass S4 (based).
Interpretationnone given§ acknowledgmentsTopological modeling provides a way to link molecular rates of genome evolution to chromosomal rearrangement dynamics.
“Topological modeling provides a way to link these molecular rates to chromosomal rearrangement dynamics and may eventually help predict whether particular modes or speeds of genome evolution are associated with greater adaptive or speciation potential over macroevolutionary time.”
Quote in the paperNot a substantial claimProbably not a substantial claim: may not pass S4 (based).
Interpretationnone given§ acknowledgmentsThe MLT framework can add resolution by pinpointing specific genomic configurations, such as conserved co-localizations or rearrangement breakpoints, that define a clade's genomic uniqueness and may not be recoverable once extinct.
“The MLT framework can add resolution by pinpointing the specific genomic configurations, such as conserved co-localizations or rearrangement breakpoints, that define a clade's genomic uniqueness and may not be recoverable once extinct.”
Quote in the paperNot a substantial claimProbably not a substantial claim: may not pass S3 (load-bearing), S4 (based). May combine two claims.
Interpretationnone given§ acknowledgmentsEvolutionary genome topology introduces two complementary methods: multi-locus topology identifies conserved co-localizations and clade-specific entanglements of loci, and multi-genome topology compares whole-genome configurations across species.
“Evolutionary genome topology introduces two complementary methods: Multi-locus topology identifies conserved co-localizations and clade-specific entanglements of loci, and multi-genome topology compares whole-genome configurations across species.”
Quote in the paperNot a substantial claimProbably not a substantial claim: may not pass S2 (checkable), S3 (load-bearing). May combine two claims.
Interpretationreasoning§ acknowledgmentsMGT approaches could be used with single-cell Hi-C or other SV detection methods to cluster cells based on genome configuration and possibly identify highly metastatic populations.
“In such cases, MGT approaches could be used in conjunction with single-cell Hi-C or other SV detection methods to cluster cells based on genome configuration, and possibly to identify highly metastatic populations.”
Quote in the paperNot a substantial claimProbably not a substantial claim: may not pass S2 (checkable), S4 (based). May combine two claims.
Interpretationnone given§ acknowledgmentsTreating nucleotide changes, microsynteny, macrosynteny, and topology separately obscures cross-scale dynamics, whereas integrated multi-scale analyses clarify both constraint and changes linked with clade-specific traits or innovations.
“Treating nucleotide changes, microsynteny, macrosynteny, and topology separately obscures cross-scale dynamics; integrated multi-scale analyses clarify both constraint and changes linked with clade-specific traits or innovations.”
Quote in the paperNot a substantial claimMay combine two claims.
Premisecitation§ acknowledgmentsEndangered populations that have experienced severe demographic bottlenecks often exhibit reduced genetic diversity and an accumulation of deleterious alleles, making them more vulnerable to extinction.
“These populations often exhibit reduced genetic diversity and an accumulation of deleterious alleles, making them more vulnerable to extinction.”
Quote in the paperSubstantial claim0 of 1 sources checked- cites [193] 2010, Conservation genetics of population bottlenecks: the role of chance, selection, and history, Conserv. Genet. source
Probably not a substantial claim: may not pass S2 (checkable), S3 (load-bearing), S4 (based).
Interpretationnone given§ acknowledgmentsTransitioning toward 3D genomics remains a significant technological challenge, especially given the tissue- and cell-type-specific utility of many genomic structures.
“However, transitioning toward 3D genomics remains a significant technological challenge, especially given the tissue- and cell-type-specific utility of many genomic structures.”
Quote in the paperNot a substantial claimProbably not a substantial claim: may not pass S2 (checkable), S3 (load-bearing), S4 (based). May combine two claims.
Interpretationnone given§ acknowledgmentsMLT approaches could complement single-cell clustering and provide key rearrangement targets for personalized DNA- and RNA-based therapies.
“MLT approaches could complement this approach and provide key rearrangement targets for personalized DNA- and RNA-based therapies.”
Quote in the paperNot a substantial claim
The paper relies on this without support.
Approximately 1.5 million animal species have been described.
“only a small fraction of the approximately 1.5 million described animal species”
The authors state this as an assumption.
The genome can be modeled as a structured system in which orthologous loci have spatial relationships that shift, persist, or recur across lineages.
“Rather than treating changes in nucleotide sequences, microsynteny, and macrosynteny as separate domains as other tools do, this approach models the genome as a structured system in which orthologous loci have spatial relationships that shift, persist, or recur across lineages.”
The paper relies on this without support.
Topological persistence is a reliable indicator of meaningful evolutionary patterns.
“It does not require prior assumptions about what size of change matters but instead detects meaningful patterns through their topological persistence.”
The paper relies on this without support.
Less than 1% of all species have been sequenced and many lineages remain underrepresented.
“Despite this progress, less than 1% of all species have been sequenced, and many lineages remain underrepresented.”
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
Each contradiction between two passages listed here was confirmed by an independent check.
Anemone comparison is assigned to molluscan genomes
MinorThe text presents anemones and other hexacorals as an example from comparative analyses of molluscan genomes, but the paper's Figure 5 caption identifies the comparison as one of cnidarian genomes.
“comparative analyses of molluscan genomes show that species with superficially similar karyotypes, like anemones versus other hexacorals, are in fact distinguished by unique patterns of locus mixing, fusion history, and internal reordering (101) ( Figure 5a , b ).”
“a MGT (one-dot-one-genome) topological view of cnidarian genomes reveals that hexacoral and anemone genomes are distinct”
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Mesozoic origin of coleoid cephalopods and their abrupt shifts of diversification patterns
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Cited by
Sorted by citations
Tally, D. G., Pittman, C., & Bracewell, R. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.05.15.725483 · Cited by 2 · see citing works
- Authors
- Schultz, D. T., & Simakov, O.
- Affiliations
- University of Vienna (AT)
- Venue
- Annual Review of Animal Biosciences
- Publisher
- Annual Reviews
- Published
- 2026-02-18
- Volume
- 14
- Issue
- 1
- Pages
- 17-48
- ISSN
- 2165-8102 (ISSN-L)
- 2165-8110
- OpenAlex
- W7130544806
- Cited by
- 1
- References
- 184
- Citations by year
- 2026: 1
- FWCI
- 0.66
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Locations
- Annual Review of Animal Biosciences (publishedVersion, cc-by)
- PubMed (publishedVersion)
- Topics
- Life Sciences › Agricultural and Biological Sciences › Plant Science › Chromosomal and Genetic Variations
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genome Rearrangement Algorithms
- Keywords
- genome topology, 3D genomics, macroevolution, genomic changes, karyotype evolution
- MeSH terms
- Animals, Biological Evolution, Phylogeny, Genome, Evolution, Molecular, Genomics
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Claims read by deepseek-v4.1-flash under definition version 3 (extract-v3) on 2026-11-03.
Classified by jev-1.13-20260917 (gold-guideline-v0.2) on 2026-11-03.
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