DOI: 10.5061/dryad.zpc866tmh
title: Code from: Museomics unravels cryptic diversity in an endemic group of New Guinean songbirds

description: 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.
description: # Code from: Museomics unravels cryptic diversity in an endemic group of
 New Guinean songbirds Dataset DOI:
 [10.5061/dryad.zpc866tmh](10.5061/dryad.zpc866tmh) ## Description of the
 data and file structure Nextflow code used to produce the findings as
 presented in: *Museomics unravels cryptic diversity in an endemic group of
 New Guinean songbirds* ### Files and variables #### File:
 nf-polish-main.zip **Description**: A reproducible pipeline for polishing
 DNA reads, with a particular focus on sequence data for historical
 specimens. Taken from Github repository:
 [https://github.com/MozesBlom/nf-polish](https://github.com/MozesBlom/nf-polish). It includes the config script with all parameter settings used for the study. #### File: nf-umap-main.zip **Description:** A nextflow DNA read mapping workflow to use on sequences obtained from natural history museum specimens. Taken from Github repository: [https://github.com/IngoMue/nf-umap](https://github.com/IngoMue/nf-umap). It includes the config script with all parameter settings used for the study. #### File: nf-var-main.zip **Description**: A reproducible pipeline to call variants -- for phylogenomic inference. v0.1. Taken from Github repository: [https://github.com/MozesBlom/nf-var](https://github.com/MozesBlom/nf-var). It includes the config script with all parameter settings used for the study. #### File: nf-phylo-main.zip **Description:** A reproducible pipeline for phylogenomic inference using whole-genome data. v1.0. Taken from Github repository: [https://github.com/MozesBlom/nf-phylo](https://github.com/MozesBlom/nf-phylo). It includes the config script with all parameter settings used for the study. ## Code/software YAML files to reproduce the software environments (incl. explicit software versions) for scientific reproduction have been included for each nextflow workflow. ## Access information Data was derived from the following sources: * All raw sequencing reads have been uploaded to the European * Nucleotide Archive and can be publicly accessed via project number: PRJEB80871.