DOI: 10.5061/dryad.7d7wm3876
title: Data from: Uncovering new lineages in the Sunda Pangolin (<em>Manis javanica</em>) with museum mitogenomics

description: Accurately identifying evolutionarily significant units (ESUs) is crucial
 for conservation planning, especially for species like pangolins
 threatened by overhunting and habitat loss. ESUs help categorize different
 pangolin populations, aiding in understanding their genetic diversity and
 distribution, which is vital for targeted conservation efforts. This
 research generated mitochondrial genomes from historical museum specimens
 of Sunda pangolins (Manis javanica) from underrepresented locations,
 uncovering a new evolutionary lineage from the Mentawai Islands. The novel
 sequences provide resources for forensic labs tracing the origin of
 confiscated scales and limit the potential distribution of the
 "mysterious pangolin." The Mentawai Archipelago represents a
 divergent ESU with a small distribution, important for conservation
 planning. Additionally, this research confirmed the presence of two major
 M. javanica lineages in Java and extended the known distribution to Bali
 and East Kalimantan. These findings support the "Out of Borneo"
 hypothesis and suggest a recent colonization of pangolins across Indochina
 and west Sundaland. This study also highlights the need for further
 investigation into the taxonomic status of these lineages and their
 management as subspecies.
description: # Uncovering New Lineages in the Sunda Pangolin (*Manis javanica*) with
 Museum Mitogenomics Dataset DOI:
 [10.5061/dryad.7d7wm3876](10.5061/dryad.7d7wm3876) ## Description of the
 data and file structure This research generated mitochondrial genomes from
 historical museum specimens of Sunda pangolins (*Manis javanica*) from
 underrepresented locations, uncovering a new evolutionary lineage from the
 Mentawai Islands that diverged from mainland and west Sundaland
 populations around 760 thousand years ago. The novel sequences provide
 resources for forensic labs tracing the origin of confiscated scales and
 shed light into the potential distribution of the "mysterious
 pangolin". ### Files and variables #### File:
 IQTREE_input_alignment.fasta **Description:** Mitochondrial genome
 alignment used in IQTREE phylogenetic analysis. #### File:
 IQTREE_mtgenome_input_partitions.nex **Description:** Mitochondrial genome
 alignment partition used in IQTREE phylogenetic analysis. #### File:
 IQTREE_mitogenome_sp_partition_merge.contree **Description:** Maximum
 likelihood phylogenetic tree inferred from mitochondrial genomes (15,254
 bp) with IQTREE (Figure 1). #### File: BEAST_input_relaxed.xml
 **Description:** BEAST analysis input file. #### File:
 BEAST_MCC_Manis_final **Description:** Maximum Clade Credibility (MCC)
 timetree inferred from mitochondrial genomes (11,510 bp) using BEAST
 (Figure S3). #### File: BEAST_input_alignments_BEAST.zip
 **Description:** Mitochondrial genome alignments input (and excluded) in
 BEAST.  This ZIP file contains two directories representing those
 partition alignments included and excluded from the BEAST analysis due to
 saturation. ### File: cytb_genetic_distance_plot.zip
 **Description:** Input and R code to generate *Cytochrome b* genetic
 distance plot (Figure S2).  #### File: cytb_input_tree_final.fasta
 **Description:** *Cytochrome b* alignment used in IQTREE phylogenetic
 analysis. #### File: cytb.contree **Description:** Maximum likelihood
 phylogenetic tree inferred from *Cytochrome b* (1,040 bp) with IQTREE
 (Figure S1). ## Code/software These analyses have been run on IQTREE,
 BEAST, and R. All code–which was used to compute the genetic distance
 plot–is provided in "cytb_genetic_distances_plot.R", which is
 found in "cytb_genetic_distance_plot.zip". ## Access information
 Other publicly accessible locations of the data: * Newly generated
 mitogenome sequences, along with previously published ones, including
 their GenBank accession numbers and associated metadata, are listed in
 Table S1. Data was derived from the following sources: * GenBank