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. geisleroru..., , # 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 ...,