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Phylogenomics of fresh and formalin specimens resolves the systematics of old world mud snakes (Serpentes: Homalopsidae) and expands biogeographic inference

Cite this dataset

Bernstein, Justin (2024). Phylogenomics of fresh and formalin specimens resolves the systematics of old world mud snakes (Serpentes: Homalopsidae) and expands biogeographic inference [Dataset]. Dryad. https://doi.org/10.5061/dryad.hdr7sqvnc

Abstract

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.

README: 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
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).

Methods

Data was collected using target capture approach, using the Squamate Conserved Loci v2 probeset from Singhal et a. 2017.

Usage notes

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.

Funding

National Science Foundation, Award: DEB 2224119

National Science Foundation, Award: DEB 0743491

National Science Foundation, Award: DEB 1654388

National Science Foundation, Award: DEB 0804115

National Institute of General Medical Sciences, Award: 2P20GM103432

Field Museum of Natural History's Grainger Bioinformatics Center