DOI: 10.5061/dryad.c866t1gk6
title: Data from: A genomic perspective on cryptic species reveals complex evolutionary dynamics in the gray zone of the speciation continuum

description: The evolutionary dynamics of cryptic species remain poorly understood, and
 their detection relies primarily on methods that quantify divergence,
 assuming that gene flow is absent. Here, we examine how gene flow shapes
 the evolutionary trajectories and species boundaries in Bornean Fanged
 Frogs, a renowned example of cryptic diversity where a single species has
 been split into 18 genetically divergent yet morphologically
 indistinguishable species. We employed target-capture data from over
 13,000 loci to assess lineage independence of 14 nominal species
 distributed across Malaysian Borneo by evaluating both divergence and
 cohesion using network multispecies coalescent (NMSC) and MSC + migration
 approaches. Under the Unified Species Concept, only six of the 14 nominal
 species unambiguously form independently evolving lineages; the remainder
 represent cohesive metapopulation lineages nested within those six
 species. While mitochondrial p-distances varied substantially (up to 10%),
 genome-wide net divergences (Da) were more consistent, ranging from 0.5–2
 %, placing all the hypothesized “cryptic species” within the empirical
 gray zone of the speciation continuum. We show that diversification in the
 gray zone is unpredictable and heavily impacted by gene flow, leading to
 two key phenomena that confound species delimitation: (1) the artifactual
 branch effect, where admixed lineages are inferred as long,
 early-diverging branches, creating an illusion of deep divergence; and (2)
 the species-definition anomaly zone, where intraspecific pairwise sequence
 distances exceed interspecific ones. We further demonstrate that
 divergence in the gray zone varies among metrics and genomic regions,
 reflecting heterogeneity in evolutionary dynamics across the genome.
 Different genomic markers also vary considerably in phylogenetic
 discordance and their ability to retain signatures of gene flow. Loci from
 anchored hybrid enrichment (AHE) and ultraconserved elements (UCE)
 produced less phylogenetic discordance and retained signals of older
 introgression but failed to detect recent migration, making them suitable
 for phylogenetic reconstruction and inferring ancient introgression, but
 not ongoing gene flow. Recognizing the central role of gene flow reframes
 our understanding of cryptic species; rather than being considered as
 genetically distinct units that failed to evolve morphological
 differentiation, they are manifestations of continuous diversification in
 the gray zone. This shift in perspective offers a new and dynamic
 evolutionary framework for identifying and interpreting cryptic
 biodiversity across the Tree of Life.
description: # Data from: A genomic perspective on cryptic species reveals complex
 evolutionary dynamics in the gray zone of the speciation continuum Dataset
 DOI: [10.5061/dryad.c866t1gk6](https://doi.org/10.5061/dryad.c866t1gk6) ##
 Description of the data and file structure All data relevant to the
 reproducibility of this study are made available, including **sequence
 alignments** (16S and genomic), **pairwise p-distance calculations**, raw
 results from the **pixy analysis** (Dxy, Fst, and pi), **SNP dataset** in
 STRUCTURE format, and **phylogenetic trees** (species, gene, and consensus
 trees). ### Files and variables #### File: scripts_others.zip
 **Description:** Various helper bash and Python scripts:\
 **filter_alignments.sh:** subsets alignment files based on a predefined
 list of loci. It reads locus IDs from a text file and copies the
 corresponding `.phy` alignment files from a source directory into a new
 directory for downstream phylogenetic analyses.
 **filter_genetrees.sh:** subsets a collection of gene tree files based on
 a predefined list of IDs **phylip_to_bpp.py:** converts a phylip to bpp
 format **random_columns_from_third.sh:** randomly selects a specified
 number of columns from an input table, starting from the 3rd column
 onward, and prints them together with the first two columns.
 **random_select_100_loci.sh:** randomly subset 100 loci
 **rename_population.sh:** remaps population identifiers in FASTA sequence
 headers using a tab-delimited mapping file **resample-genetrees.sh:**
 randomly subset a user-specified number of genetrees
 **split_vcf_by_marker.sh:** partitions a VCF file into region-specific
 subsets (UCE, AHE, BUSCO, etc.) based on genomic coordinates defined in a
 BED file. #### File: scripts_R.zip **Description:** R scripts for specific
 analyses **snmf_tsne.R:** R script for sNMF and t-SNE analyses
 **divergence_landscape.R:** R script for the divergence landscape analyses
 **nanuq.R:** R script for the NANUQ analyses **p_distances.R:** R script
 for the p-distance comparisons analyses #### File: data.zip
 **Description:** sequence alignments, p-distance calculations, pixy
 results, SNP dataset, and phylogenetic trees **alignments:** Sequence
 alignments for 16S and all genomic loci **p_distances:** Pairwise
 p-distance calculations that are used for the p-distance analyses
 **pixy:** Fst, Dxy, and pi calculations from the pixy analysis. NA=no
 segregating sites between populations in that window; populations are
 identical at this locus **snmf_tsne:** SNP dataset for the snmf and t-SNE
 analyses **Trees:** ASTRAL species trees, individual gene trees by marker
 type, and IQ-TREE consensus trees ## Code/software Tree files can be
 viewed using FigTree. All other files can be viewed using a text editor ##
 Access information Other publicly accessible locations of the data: *
 [https://github.com/chankinonn/kuhlii](https://github.com/chankinonn/kuhlii)