Data from: Chromosomal speciation in the genomics era: disentangling phylogenetic evolution of rock-wallabies

The association of chromosome rearrangements with speciation is well
established, and there is a long history of theory and evidence relating
to “chromosomal speciation”. Genomic sequencing has the potential to
provide new insights into how reorganization of genome structure promotes
divergence, and in model systems has demonstrated reduced gene flow in
rearranged segments. However, there are limits to what we can understand
from a small number of model systems, which each only tell us about one
episode of chromosomal speciation. Progressing from patterns of
association between chromosome (and genic) change, to understanding
processes of speciation requires both comparative studies across diverse
systems and integration of genome-scale sequence comparisons with other
lines of evidence. Here we showcase a promising example of chromosomal
speciation in a non-model organism, the endemic Australian marsupial genus
Petrogale. We present initial phylogenetic results from exon-capture that
resolve a history of divergence associated with extensive and repeated
chromosome rearrangements. Yet it remains challenging to disentangle gene
tree heterogeneity caused by recent divergence and gene flow in this and
other such recent radiations. We outline a way forward for better
integration of comparative genomic sequence data with evidence from
molecular cytogenetics, and analyses of shifts in the recombination
landscape and potential disruption of meiotic segregation and epigenetic
programming. In all likelihood, chromosome rearrangements impact multiple
cellular processes and these effects need to be considered together, along
with those of genic divergence. Understanding the effects of chromosome
rearrangements together with genic divergence will require development of
more integrative theory and inference methods. Together, new data and
analysis tools will combine to shed light on long standing questions of
how chromosome and genic divergence promote speciation.