Data from: Repetitive DNA profiles reveal evidence of rapid genome evolution and reflect species boundaries in ground beetles

Genome architecture is a complex, multidimensional property of an organism
defined by the content and spatial organization of the genome’s component
parts. Comparative study of entire genome architecture in model organisms
is shedding light on mechanisms underlying genome regulation, evolution,
and diversification; but such studies require costly analytical approaches
which make extensive comparative study impractical for most groups.
However, lower-cost methods that measure a single architectural component
(e.g., distribution of one class of repeats) have potential as a new data
source for evolutionary studies insofar as that measure correlates with
more complex biological phenomena, and for which it could serve as part of
an explanatory framework. We investigated copy number variation (CNV)
profiles in ribosomal DNA (rDNA) as a simple measure reflecting the
distribution of rDNA subcomponents across the genome. We find that
signatures present in rDNA CNV profiles strongly correlate with species
boundaries in the breve species group of Bembidion, and vary across
broader taxonomic sampling in Bembidion subgenus Plataphus. Profiles of
several species show evidence of re-patterning of rDNA-like sequences
throughout the genome, revealing evidence of rapid genome evolution
(including among sister pairs) not evident from analysis of traditional
data sources such as multi-gene data sets. Major re-patterning of
rDNA-like sequences has occurred frequently within the evolutionary
history of Plataphus. We confirm that CNV profiles represent an aspect of
genomic architecture (i.e., the linear distribution of rDNA components
across the genome) via fluorescence in-situ hybridization. In at least one
species, novel rDNA-like elements are spread throughout all chromosomes.
We discuss the potential of copy number profiles of rDNA, or other
repeats, as a low-cost tool for incorporating signal of genomic
architecture variation in studies of species delimitation and genome
evolution.