DOI: 10.5061/dryad.hdr7sqvnc
title: Phylogenomics of fresh and formalin specimens resolves the systematics of old world mud snakes (Serpentes: Homalopsidae) and expands biogeographic inference

description: The known biodiversity of Asia and Australasia is continuously expanding
 with more focused studies on systematics of various groups and the
 respective biogeography. Historically, fluctuating sea-levels and cyclic
 connection and separation of now-disjunct landmasses have been invoked to
 explain the accumulation of biodiversity via species pump mechanisms.
 However, recent research has shown that geological shifts of the mainland
 and dispersal events may be better explanations of the biodiversity in
 these regions. We investigate these processes using the poorly-studied and
 geographically widespread Mud Snakes (Serpentes: Homalopsidae) using a
 target capture approach of ~4,800 nuclear loci from fresh tissues and
 supplemental mitochondrial data from formalin tissues from museum
 specimens. We use these datasets to reconstruct the first resolved
 phylogeny of the group, identify their biogeographic origins, and test
 hypotheses regarding the roles of sea-level change and habitat selection
 on their diversification. Divergence dating and ancestral range estimation
 yielded support for an Oligocene origin and diversification from mainland
 Southeast Asia and Sundaland in the rear-fanged group ~20 million years
 ago, followed by eastward and westward dispersal. GeoHiSSE models indicate
 that niche expansion of ancestral rear-fanged lineages into aquatic
 environments did not impact their diversification rates. Our results
 highlight that Pleistocene sea-level changes and habitat specificity did
 not primarily lead to the extant species richness of Homalopsidae, and
 that, alternatively, geological shifts in mainland Southeast Asia may be a
 major driver of diversity in this group. We also emphasize the importance
 of using fresh and degraded tissues, and both nuclear and mitochondrial
 DNA, for filling in knowledge gaps in poorly known, but highly diverse and
 conceptually important groups, constituting a non-traditional model study
 system for understanding transitions between terrestrial, marine, and
 freshwater environments.
description: Data was collected using target capture approach, using the
 Squamate Conserved Loci v2 probeset from Singhal et a. 2017.
description: Text editor applications (e.g., Notepad++) can be used to open
 .nexus, .phylip, .docx, and .tre files. The .tre and .tree files can also
 be opened using FigTree phylogenetic tree visualizer. Adobe or another
 version of PDF viewer will be needed to viwe .pdf files.
description: # Museumomics Expands Biogeographic Inference and Resolves the Systematics
 of Old World Mud Snakes (Serpentes: Homalopsidae) Corresponding Author:
 Justin M. Bernstein (University of Kansas, Center for Genomics); email:
 [jmbernst223@gmail.com](mailto:jmbernst223@gmail.com) Date of Data
 Collection: 2020-2021 \#Supplementary Material files include specimen and
 sequencing data for all specimens used in this study. Code is provided for
 the GeoHiSSE analysis, with models and \#parameters described in
 Supplementary Material Text S1. Further details are found within the files
 themselves. \#Data and File Overview Supplementary Appendix S1. Specimens
 included in this study for genomic and sanger (cyt-b) sequencing. (Excel
 spreadsheet; created 1/13/2022). Supplementary Text S1. Phylogenomic,
 GeoHiSSE, and BioGeoBEARS models and results for the nuclear species tree
 (Microsoft Word Document; created 1/23/2023). Supplementary Figure S1.
 Species tree of Homalopsidae using UCEs, AHEs, and NPCGs of fresh
 specimens. (PDF; created 8/24/2022). Supplementary Figure S2. Concatenated
 phylogeny of Homalopsidae using UCEs, AHEs, and NPCGs of fresh specimens.
 (PDF; created 8/24/2022). Supplementary Figure S3. Dated concatenated
 phylogeny of Homalopsidae. (PDF; created 8/24/2022). Supplementary Figure
 S4. Dated cyt-b phylogeny of Homalopsidae with support values. (PDF;
 created 8/24/2022). Supplementary Figure S5. Ancestral range estimations
 from BioGeoBEARS using the cyt-b tree (DEC+J model). (PDF; created
 8/24/2022). Supplementary Figure S6. Ancestral state reconstructions of
 habitat preference in Homalopsidae. (PDF; created 8/24/2022).
 Supplementary Data D1. R code for model setup and GeoHiSSE analyses. (.R
 file for R/RStudio; created 8/24/2022). Supplementary Data D2. Input
 time-calibrated nuclear species tree for GeoHiSSE analysis. (.tre file;
 created 8/24/2022). Supplementary Data D3. Input state matrix for nuclear
 species tree GeoHiSSE analysis. (CSV file; created 8/24/2022).
 Supplementary Data D4. Input time-calibrated cyt-b tree for GeoHiSSE
 analysis. (CSV file; created 8/24/2022). Supplementary Data D5. Input
 state matrix for cyt-b GeoHiSSE analysis. (CSV file; created 8/24/2022).
 Supplementary Data D6. R code for ancestral state reconstructions (.R file
 for R/RStudio; created 8/24/2022). Supplementary Data D7. Input data for
 homalopsid habitat states for ancestral state reconstruction Case 1 (CSV
 file; created 8/24/2022). Supplementary Data D8. Input data for homalopsid
 habitat states for ancestral state reconstruction Case 2 (CSV file;
 created 8/24/2022). Supplementary Data D9. Input data for homalopsid
 habitat states for ancestral state reconstruction Case 3 (CSV file;
 created 8/24/2022). Supplementary Data D10. Input data for homalopsid
 habitat states for ancestral state reconstruction Case 4 (CSV file;
 created 8/24/2022). Supplementary Data D11. Input data for homalopsid
 habitat states for ancestral state reconstruction Case 5 (CSV file;
 created 8/24/2022). Supplementary Data D12. Input tree for ancestral state
 reconstruction (all Cases (CSV file; created 8/24/2022). Any files for
 Supplementary Data that that contain NAs represent data for which no
 natural history or state informatoin exists for the respective taxon.
 ###The below files on Dryad will be part of Supplementary Material as
 additional files in the Supplementary_Alignments.zip###
 Locus-Alignments_for_Formalin-Fresh_ASTRAL-Tree.zip. = Zipped folder of
 nexus alignments for all loci used in the ASTRAL species tree analysis
 containing formalin-preserved and fresh specimens (175 .nex files in a
 .zip; created 4/1/2022) Locus-Alignments_for_Fresh_ASTRAL-Tree.zip. =
 Zipped folder of nexus alignments for all loci used in the ASTRAL species
 tree analysis containing fresh specimens only (4837 .nexus files in a
 .zip; created 4/1/2022) CYTB_tree-RAxML = Contains constraint tree,
 alignment file, and tree file from the cyt-b analysis in RAxML-NG (.phy
 file, .tre file, .bestTree.support file; created 8/24/2022)
 Homalopsidae_Formalin-Fresh_ASTRAL-input-trees.tre = List of input trees
 for the ASTRAL species tree analysis containing formalin-preserved and
 fresh specimens (.tre file; created 4/1/2022)
 Homalopsidae_Fresh_ASTRAL-input-trees.nex = List of input trees for the
 ASTRAL species tree analysis containing only fresh specimens (.nex file;
 created 4/1/2022) Homalopsidae_Fresh_IQTREE-Concatenated-Alignment.nex =
 concatenated alignment for the concatenated nuclear tree for Homalopsidae
 (.nex file; created 8/24/2022). TREES_FOR_SYSBIO_FRESH_ASTRAL.zip = A
 zipped folder containing all locus trees from fresh specimens only when
 input into IQ-TREE for phylogenetic reconstruction. These are the
 resulting output trees from this ananlysis. (.zip file; created
 8/24/2022).