Abstract
Genome size varies significantly across eukaryotic taxa and the largest changes are typically driven by macro-mutations such as whole genome duplications (WGDs) and proliferation of repetitive elements. These two processes may affect the evolutionary potential of lineages by increasing genetic variation and changing gene expression. Here, we elucidate the evolutionary history and mechanisms underpinning genome size variation in a species-rich group of Neotropical catfishes (Corydoradinae) with extreme variation in genome size—0.6 to 4.4 pg per haploid cell. First, genome size was quantified in 65 species and mapped onto a novel fossil-calibrated phylogeny. Two evolutionary shifts in genome size were identified across the tree—the first between 43 and 49 Ma (95% highest posterior density (HPD) 36.2–68.1 Ma) and the second at approximately 19 Ma (95% HPD 15.3–30.14 Ma). Second, restriction-site-associated DNA (RAD) sequencing was used to identify potential WGD events and quantify transposable element (TE) abundance in different lineages. Evidence of two lineage-scale WGDs was identified across the phylogeny, the first event occurring between 54 and 66 Ma (95% HPD 42.56–99.5 Ma) and the second at 20–30 Ma (95% HPD 15.3–45 Ma) based on haplotype numbers per contig and between 35 and 44 Ma (95% HPD 30.29–64.51 Ma) and 20–30 Ma (95% HPD 15.3–45 Ma) based on SNP read ratios. TE abundance increased considerably in parallel with genome size, with a single TE-family (TC1-IS630-Pogo) showing several increases across the Corydoradinae, with the most recent at 20–30 Ma (95% HPD 15.3–45 Ma) and an older event at 35–44 Ma (95% HPD 30.29–64.51 Ma). We identified signals congruent with two WGD duplication events, as well as an increase in TE abundance across different lineages, making the Corydoradinae an excellent model system to study the effects of WGD and TEs on genome and organismal evolution.
Highlights
There is spectacular variation in genome size across the animal and plant kingdoms, with 200 000-fold variation reported across the eukaryotes [1]
We elucidate for the first time the evolutionary history of genome size change within the Neotropical Corydoradinae catfishes
restriction-siteassociated DNA (RAD) sequencing revealed that there have been at least two positive shifts in haplotype diversity per contig and SNP read ratio across the tree which are indicative of whole genome duplications (WGDs)
Summary
There is spectacular variation in genome size across the animal and plant kingdoms, with 200 000-fold variation reported across the eukaryotes [1]. To establish whether changes in genome size expansion could be indicative of polyploidy, we searched for signals of WGD in the RAD sequencing data using two-sequence-based methods: haplotype diversity per contig and bi-allelic SNP frequency distribution. For both of these sequence-based methods, only putative coding regions were used to avoid noise. BIC was used as the model selection criterion for all analyses
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