Weird genotypes? Don't discard them, transmissible cancer could be an explanation

Abstract

Genetic chimerism is rarely considered in the analysis of population genetics data, because assumed to be an exceptionally rare, mostly benign, developmental accident. An unappreciated source of chimerism is transmissible cancer, when malignant cells have become independent parasites and can infect other individuals. Parasitic cancers were thought to be rare exceptions, only reported in dogs (Murgia et al., Cell, 2006, 126, 477; Rebbeck et al., Evolution, 2009, 63, 2340), Tasmanian devils (Pearse and Swift, Nature, 2006, 439, 549; Pye et al., Proceedings of the National Academy of Sciences, 2016, 113, 374), and soft‐shell clams (Metzger et al., Cell, 2015, 161, 255). However, the recent simultaneous report of four new contagious leukemias in marine mollusks (Metzger et al., Nature, 2016, 534, 705) might change the rules. By doubling up the number of naturally occurring transmissible cancers, this discovery suggests they may essentially be missed because not sufficiently searched for, especially outside mammals. We encourage population geneticists to keep in mind infectious cancer when interpreting weird genotypes in their molecular data. It would then contribute in the investigation of how widespread contagious cancer could really be in the wild. We provide an example with our own data in Mytilus mussels, a commercially important shellfish. We identified genetic chimerism in a few mussels that suggests the possible occurrence at low prevalence in European M. edulis populations of a M. trossulus contagious cancer related to the one described by Metzger et al. (Nature, 2016, 534, 705) in populations of British Columbia.

Patterns of cross-contamination in a multispecies population genomic project: detection, quantification, impact, and solutions

“…This might indicate that a fraction of the events of within-species contamination did occur in our laboratory. Alternatively, λ might be inflated by processes different from contamination, such as hotspots of systematic errors [43], mosaicism [48], hidden paralogy, and variable expression level between alleles and individuals [17, 18]. Approaching and quantifying within-species contamination is actually a difficult problem, especially with RNAseq data, because a number of distinct processes can potentially generate asymmetric read counts.…”

Experimental infection of Mytilus edulis by two Vibrio splendidus‐related strains: Determination of pathogenicity level of strains and influence of the origin and annual cycle of mussels on their sensitivity

“…Mytilus edulis and M. galloprovincialis are native species to the French coast, and numerous different natural populations exist and are capable to hybridize with each other. Thus, the Atlantic coast of France is very complex—in terms of genetic structure—with several mosaic hybrid zone between M. edulis and M. galloprovincialis (Bierne et al, ; Riquet, Simon, & Bierne, ). It is therefore possible that some natural French populations could be more resistant than others.…”

Replicated anthropogenic hybridisations reveal parallel patterns of admixture in marine mussels

“…Over 81 markers, the maximum number of mismatches observed between two duplicated individuals was 2 (without considering missing data), showing that the genotyping method is mostly accurate. A few individuals identified as affected by a M. trossulus transmissible cancer were removed from the dataset (Metzger et al, 2016;Riquet, Simon, & Bierne, 2017).…”