Code from: Museomics unravels cryptic diversity in an endemic group of New Guinean songbirds

Deciphering cryptic diversity can have substantial implications for our
understanding of evolutionary processes and species conservation. Birds
are arguably among the best studied organismal groups, but even in avian
clades there are some genera that have not been thoroughly surveyed. This
is particularly true for taxa that occur in hyperdiverse biogeographic
regions. In this study, we focus on an endemic group of New Guinean birds,
the jewel-babblers (genus: Ptilorrhoa), and study the diversification
history of all known taxa. We assemble a de novo genome using linked-read
sequencing and genomic data for 40 historical specimens. Both phylogenomic
and population-genomic analyses strongly support the recovery of a cryptic
species and shed new light on the diversification history of this group.
The blue jewel-babbler (Ptilorrhoa caerulescens) is a paraphyletic species
complex and P. c. nigricrissus is more closely related to the
phenotypically distinct and sexually dimorphic P. geislerorum, than to
other P. caerulescens subspecies. These findings demonstrate that even in
well-studied groups such as birds, cryptic diversity can still be a
prevalent reality. Moreover, by deciphering cryptic diversity, we shed new
light on the processes driving speciation within Ptilorrhoa and the need
to potentially revise the taxonomic status of all subspecies.