Blazer, V. S., Shaw, C. H., Smith, C. R., Emerson, P. & Jones, T. Malignant melanoma of brown bullhead (Ameiurus nebulosus) in Lake Memphremagog, Vermont/Quebec. J. Fish Dis. 43, 91–100 (2020).
Google Scholar
Metzger, M. J. & Goff, S. P. A sixth modality of infectious disease: contagious cancer from devils to clams and beyond. PLoS Pathog. 12, e1005904 (2016).
Google Scholar
The Cancer Genome Atlas Research Network. The Cancer Genome Atlas Pan-Cancer analysis project. Nat. Genet. 45, 1113–1120 (2013).
Murgia, C., Pritchard, J. K., Kim, S. Y., Fassati, A. & Weiss, R. A. Clonal origin and evolution of a transmissible cancer. Cell 126, 477–487 (2006).
Google Scholar
Pearse, A.-M. & Swift, K. Transmission of devil facial-tumour disease. Nature 439, 549 (2006).
Google Scholar
Metzger, M. J., Reinisch, C., Sherry, J. & Goff, S. P. Horizontal transmission of clonal cancer cells causes leukemia in soft-shell clams. Cell 161, 255–263 (2015).
Google Scholar
Metzger, M. J. et al. Widespread transmission of independent cancer lineages within multiple bivalve species. Nature 534, 705–709 (2016).
Google Scholar
Yonemitsu, M. A. et al. A single clonal lineage of transmissible cancer identified in two marine mussel species in South America and Europe. eLife 8, e47788 (2019).
Skazina, M. et al. First description of a widespread Mytilus trossulus-derived bivalve transmissible cancer lineage in M. trossulus itself. Sci Rep. 11, 5809 (2021).
Google Scholar
Hammel, M. et al. Prevalence and polymorphism of a mussel transmissible cancer in Europe. Mol. Ecol. 31, 736–751 (2022).
Google Scholar
Michnowska, A., Hart, S. F. M., Smolarz, K., Hallmann, A. & Metzger, M. J. Horizontal transmission of disseminated neoplasia in the widespread clam Macoma balthica from the Southern Baltic Sea. Mol. Ecol. 31, 3128–3136 (2022).
Google Scholar
Garcia-Souto, D. et al. Mitochondrial genome sequencing of marine leukaemias reveals cancer contagion between clam species in the Seas of Southern Europe. eLife 11, e66946 (2022).
Google Scholar
Yonemitsu, M. A. et al. Multiple lineages of transmissible neoplasia in the basket cockle (C. nuttallii) with repeated horizontal transfer of mitochondrial DNA. Mol. Ecol. 34, e17682 (2025).
Google Scholar
Sakaris, Jesien, P. C., Roman, V. & & Pinkney, A. E. Brown bullhead as an indicator species: seasonal movement patterns and home ranges within the Anacostia River, Washington, D.C. Trans. Am. Fish. Soc. 134, 1262–1270 (2005).
Google Scholar
Agency of Natural Resources, Department of Environmental Conservation. Lake Memphremagog. (2026).
Ní Leathlobhair, M. & Lenski, R. E. Population genetics of clonally transmissible cancers. Nat. Ecol. Evol. 6, 1077–1089 (2022).
Google Scholar
Baez-Ortega, A. et al. Somatic evolution and global expansion of an ancient transmissible cancer lineage. Science 365, eaau9923 (2019).
Google Scholar
Pye, R. J. et al. A second transmissible cancer in Tasmanian devils. Proc. Natl Acad. Sci. USA 113, 374–379 (2016).
Google Scholar
Stammnitz, M. R. et al. The evolution of two transmissible cancers in Tasmanian devils. Science 380, 283–293 (2023).
Google Scholar
Osburn, R. C. Black tumor of the catfish. Bull. Bur. Fish. 41, 9–13 (1925).
Riquet, F., Simon, A. & Bierne, N. Weird genotypes? Don’t discard them, transmissible cancer could be an explanation. Evol. Appl. 10, 140–145 (2017).
Google Scholar
Martincorena, I. et al. Universal patterns of selection in cancer and somatic tissues. Cell 171, 1029–1041 (2017).
Google Scholar
Alexandrov, L. B. et al. Signatures of mutational processes in human cancer. Nature 500, 415–421 (2013).
Google Scholar
Ellrott, K. et al. Scalable open science approach for mutation calling of tumor exomes using multiple genomic pipelines. Cell Syst. 6, 271–281 (2018).
Google Scholar
Burioli, E. A. V. et al. Traits of a mussel transmissible cancer are reminiscent of a parasitic life style. Sci Rep. 11, 24110 (2021).
Google Scholar
Giersch, R. M. et al. Survival and detection of bivalve transmissible neoplasia from the soft-shell clam Mya arenaria (MarBTN) in seawater. Pathogens 11, 283 (2022).
Google Scholar
Hart, S. F. M., Garrett, F. E. S., Kerr, J. S. & Metzger, M. J. Gene expression in soft-shell clam (Mya arenaria) transmissible cancer reveals survival mechanisms during host infection and seawater transfer. PLoS Genet. 21, e1011629 (2025).
Google Scholar
Blumer, L. S. Reproductive natural history of the brown bullhead Ictalurus nebulosus in Michigan. Am. Midl. Nat. 114, 318–330 (1985).
Google Scholar
Harris, J. & Bird, D. J. Modulation of the fish immune system by hormones. Vet. Immunol. Immunopathol. 77, 163–176 (2000).
Google Scholar
McCallum, H. et al. Distribution and impacts of Tasmanian devil facial tumor disease. EcoHealth 4, 318–325 (2007).
Google Scholar
Frampton, D. et al. Molecular signatures of regression of the canine transmissible venereal tumor. Cancer Cell 33, 620–633 (2018).
Google Scholar
Farley, C. A., Plutschak, D. L. & Scott, R. F. Epizootiology and distribution of transmissible sarcoma in Maryland softshell clams, Mya arenaria, 1984-1988. Environ. Health Perspect. 90, 35–41 (1991).
Google Scholar
Muttray, A. et al. Haemocytic leukemia in Prince Edward Island (PEI) soft shell clam (Mya arenaria): spatial distribution in agriculturally impacted estuaries. Sci. Total Environ. 424, 130–142 (2012).
Google Scholar
Hart, S. F. M. et al. Centuries of genome instability and evolution in soft-shell clam, Mya arenaria, bivalve transmissible neoplasia. Nat. Cancer (2023).
Weinandt, S.A. et al. Atlantic to Pacific: outbreak of bivalve transmissible neoplasia detected in hybridizing soft-shell clams and eDNA in Puget Sound. Proc. Natl Acad. Sci. USA 123, e2611852123 (2026).
Siciliano, M. J., Perlmutter, A. & Clark, E. Effect of sex on the development of melanoma in hybrid fish of the genus Xiphophorus. Cancer Res. 31, 725–729 (1971).
Google Scholar
Sweet, M. et al. Evidence of melanoma in wild marine fish populations. PLoS ONE 7, e41989 (2012).
Google Scholar
Schall, M. K., Smith, G. D., Blazer, V. S., Walsh, H. L. & Wagner, T. Factors influencing the prevalence of hyperpigmented melanistic lesions in smallmouth bass Micropterus dolomieu in the Susquehanna River Basin, Pennsylvania. J. Fish. Dis. 48, e14033 (2025).
Google Scholar
Blazer, V. S. et al. Melanoma and other melanistic lesions in brown bullhead Ameiurus nebulosus from waterbodies in the northeastern United States and Canada: identification of risk factors. J. Fish Dis. (2026).
Jin, J.-J. et al. GetOrganelle: a fast and versatile toolkit for accurate de novo assembly of organelle genomes. Genome Biol. 21, 241 (2020).
Google Scholar
Chen, S., Zhou, Y., Chen, Y. & Gu, J. fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics 34, i884–i890 (2018).
Google Scholar
Lopez, M. L. D. et al. mtGrasp: streamlined reference-grade mitochondrial genome assembly and standardization to enhance metazoan mitogenome resources. Methods Ecol. Evol. 16, 668–677 (2025).
Google Scholar
Li, H. Minimap2: pairwise alignment for nucleotide sequences. Bioinformatics 34, 3094–3100 (2018).
Google Scholar
Danecek, P. et al. Twelve years of SAMtools and BCFtools. GigaScience 10, giab008 (2021).
Google Scholar
Lubkowitz, J., Curd, E., Dragon, J. & Harcourt, E. PEGASUS: a comprehensive hybrid genome assembly pipeline. Zenodo (2024).
De Coster, W. & Rademakers, R. NanoPack2: population-scale evaluation of long-read sequencing data. Bioinformatics 39, btad311 (2023).
Google Scholar
Andrews, S. FastQC: a quality control tool for high throughput sequence data. Babraham Bioinformatics (2010).
Kim, D., Song, L., Breitwieser, F. P. & Salzberg, S. L. Centrifuge: rapid and sensitive classification of metagenomic sequences. Genome Res. 26, 1721–1729 (2016).
Google Scholar
Lin, Y. et al. Assembly of long error-prone reads using de Bruijn graphs. Proc. Natl Acad. Sci. USA 113, E8396–E8405 (2016).
Google Scholar
Aury, J.-M. & Istace, B. Hapo-G, haplotype-aware polishing of genome assemblies with accurate reads. NAR Genom. Bioinform. 3, lqab034 (2021).
Google Scholar
Vaser, R., Sović, I., Nagarajan, N. & Šikić, M. Fast and accurate de novo genome assembly from long uncorrected reads. Genome Res. 27, 737–746 (2017).
Google Scholar
Coombe, L. et al. LongStitch: high-quality genome assembly correction and scaffolding using long reads. BMC Bioinform. 22, 534 (2021).
Google Scholar
Manni, M., Berkeley, M. R., Seppey, M. & Zdobnov, E. M. BUSCO: assessing genomic data quality and beyond. Curr. Protoc. 1, e323 (2021).
Google Scholar
Gurevich, A., Saveliev, V., Vyahhi, N. & Tesler, G. QUAST: quality assessment tool for genome assemblies. Bioinformatics 29, 1072–1075 (2013).
Google Scholar
Pedersen, B. S. & Quinlan, A. R. Mosdepth: quick coverage calculation for genomes and exomes. Bioinformatics 34, 867–868 (2018).
Google Scholar
Cantalapiedra, C. P., Hernández-Plaza, A., Letunic, I., Bork, P. & Huerta-Cepas, J. eggNOG-mapper v2: functional annotation, orthology assignments, and domain prediction at the metagenomic scale. Mol. Biol. Evol. 38, 5825–5829 (2021).
Google Scholar
Seemann, T. Barrnap. GitHub (2025).
Auwera, G. van der. Genomics in the Cloud: Using Docker, GATK, and WDL in Terra (O’Reilly Media, 2020).
Robinson, J. T. et al. Integrative Genomics Viewer. Nat. Biotechnol. 29, 24–26 (2011).
Google Scholar
R Core Team. R: a language and environment for statistical computing. R (2025).
Benjamin, D. et al. Calling somatic SNVs and indels with Mutect2. Preprint at bioRxiv (2019).
Rausch, T. et al. DELLY: structural variant discovery by integrated paired-end and split-read analysis. Bioinformatics 28, i333–i339 (2012).
Google Scholar
Smolka, M. et al. Detection of mosaic and population-level structural variants with Sniffles2. Nat. Biotechnol. 42, 1571–1580 (2024).
Google Scholar
Gkanogiannis, A. & Bruls, T. A scalable assembly-free variable selection algorithm for biomarker discovery from metagenomes. BMC Bioinformatics 17, 311 (2016).
Paradis, E. & Schliep, K. ape 5.0: an environment for modern phylogenetics and evolutionary analyses in R. Bioinformatics 35, 526–528 (2019).
Google Scholar
Katoh, K., Misawa, K., Kuma, K. & Miyata, T. MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Res. 30, 3059–3066 (2002).
Google Scholar
Minh, B. Q. et al. IQ-TREE 2: new models and efficient methods for phylogenetic inference in the genomic era. Mol. Biol. Evol. 37, 1530–1534 (2020).
Google Scholar
Page, A. J. et al. SNP-sites: rapid efficient extraction of SNPs from multi-FASTA alignments. Microb. Genom. 2, e000056 (2016).
Google Scholar
Yu, G. Data Integration, Manipulation and Visualization of Phylogenetic Trees (Chapman and Hall/CRC, 2022); https://doi.org/10.1201/9781003279242.
Wang, L.-G. et al. Treeio: an R package for phylogenetic tree input and output with richly annotated and associated data. Mol. Biol. Evol. 37, 599–603 (2020).
Google Scholar
Ewels, P. A. et al. The nf-core framework for community-curated bioinformatics pipelines. Nat. Biotechnol. 38, 276–278 (2020).
Google Scholar
Krakau, S., Straub, D., Gourlé, H., Gabernet, G. & Nahnsen, S. nf-core/mag: a best-practice pipeline for metagenome hybrid assembly and binning. NAR Genom. Bioinform. 4, lqac007 (2022).
Google Scholar
Nurk, S., Meleshko, D., Korobeynikov, A. & Pevzner, P. A. metaSPAdes: a new versatile metagenomic assembler. Genome Res. 27, 824–834 (2017).
Google Scholar
Camargo, A. P. et al. Identification of mobile genetic elements with geNomad. Nat. Biotechnol. 42, 1303–1312 (2024).
Google Scholar
Wood, D. E., Lu, J. & Langmead, B. Improved metagenomic analysis with Kraken 2. Genome Biol. 20, 257 (2019).
Google Scholar
McMurdie, P. J. & Holmes, S. Phyloseq: an R package for reproducible interactive analysis and graphics of microbiome census data. PLoS ONE 8, e61217 (2013).
Google Scholar
Love, M. I., Huber, W. & Anders, S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 15, 550 (2014).
Google Scholar