What is <i>Sphenomorphus maculatus</i> (Blyth, 1853) (Reptilia: Squamata: Scincidae)? Validating cryptic diversity and the designation of a neotype [Supplementary Material]
Creators: name: Borah, Pranoy Kishore
name: Grismer, L. Lee
name: Das, Abhijit
name: Purkayastha, Jayaditya
name: Deuti, Kaushik
name: Lalremsanga, Hmar Tlawmte
name: Datta-Roy, Aniruddha
Publisher: name: figshare
Year: 2024
Subjects: classificationCode: 310914
subject: Vertebrate biology
classificationCode: 310410
subject: Phylogeny and comparative analysis

description: <br>AbstractThe Spotted Litter Skink, Sphenomorphus maculatus, initially described by Edward Blyth in 1853, lacks a taxonomic reference point, as the holotype was lost in 1868. A preliminary molecular phylogenetic analysis revealed indications of cryptic diversity within S. maculatus across its range in Northeast India. We aimed to pinpoint the precise type locality, concluding that it corresponds to the peripheral forested regions surrounding Guwahati, India. To establish a robust taxonomic foundation for future investigations, we designate a neotype under the provisions of the ICZN Code (Article 75). We also provide a comprehensive redescription of the neotype. This analysis and redescription were based on recently collected specimens from the identified type locality, and approximate areas based on the movements of Col. Jenkins, who was the original collector of the holotype. Genetic data from six loci of the neotype and from the other specimens were deposited in GenBank, contributing valuable information for future reference.Description of the Data and File StructureThe supplementary materials provided alongside our paper consist of various datasets and protocols crucial for understanding the methodologies and results presented in our research on <i>Sphenomorphus maculatus</i>. These files are integral for replicating our analyses and understanding the intricate details of our study. The files are structured as follows:<b>S1: PCR Protocol</b>This document outlines the specific polymerase chain reaction (PCR) protocols used in our study. It includes details on the reagents, cycling conditions, and modifications to standard protocols that were necessary for our work.<b>S2: Partition Blocks for the ML Analysis</b>This file contains information on the partitioning scheme used for our Maximum Likelihood (ML) phylogenetic analysis. It details the 14 partitions applied across the six loci included in our study, which is critical for replicating the ML analysis using the IQ-Tree Web Server.<b>S3: Large Sphenomorphine Tree</b>This supplementary file includes the comprehensive phylogenetic tree of various sphenomorphine lizards, generated using the same loci and ML parameters described in our methods section. It provides a broader context for the evolutionary relationships within this group.<b>S4: p-Distances Based on the Large Sphenomorphine Tree</b>This dataset includes the uncorrected pairwise distances (p-distances) calculated for all members of the large sphenomorphine phylogenetic tree. It supports the genetic divergence metrics discussed in our paper.<b>S5: Morphometric and Meristic Data for All Specimens Used in Figure 1 (Except PKB51)</b>This file contains detailed morphometric and meristic measurements for the specimens included in our study. These measurements are essential for understanding the morphological variation and for performing the multiple factor analysis (MFA).<b>S6: Data Used for the MFA Analysis</b>This dataset includes all the normalized morphometric and meristic data used in the MFA analysis. It is structured to facilitate replication of the MFA, showing how different morphological traits contribute to the observed patterns.<b>S7: Contributions of Quantitative Variables to Dimensions in the MFA Analysis</b>This file details the contributions of various quantitative variables to the dimensions identified in the MFA. It helps interpret the MFA results by showing which traits are most influential.<b>S8: MFA Variance Data</b>This supplementary material provides the variance explained by each dimension in the MFA. It is crucial for understanding the distribution of variance across different morphological traits.<b>S9: Character Contribution to the MFA Analysis</b>This file outlines the contribution of individual characters to the MFA, further aiding in the interpretation of the MFA results.Relationships Between Data FilesThe files are interconnected in the following ways:<b>S1</b> provides the PCR protocol essential for the initial molecular work, which underpins the phylogenetic analyses presented in <b>S3</b>.<b>S2</b> details the partitioning scheme that is crucial for understanding the phylogenetic tree in <b>S3</b>.<b>S3</b> and <b>S4</b> are linked as the tree in <b>S3</b> is used to calculate the p-distances in <b>S4</b>.<b>S5</b> provides the raw morphological data, which is processed and normalized to create <b>S6</b>.<b>S6</b>, <b>S7</b>, <b>S8</b>, and <b>S9</b> collectively provide the full dataset and detailed results of the MFA, which correlates morphological data with the phylogenetic results in <b>S3</b>.Missing Data Codes and Abbreviations<b>Missing Data</b>: Represented as 'NA' in the datasets.<b>Abbreviations</b>: Standard morphological abbreviations are used (e.g., SVL for snout-vent length).Sharing/Access InformationLinks to Other Publicly Accessible Locations of the Data:To be provided upon paper acceptance and GenBank accession number confirmation.Data Was Derived From the Following Sources:The primary data was collected from fieldwork conducted between 2021 and 2024 across northeastern India. Tissue samples were processed and sequences were obtained from Barcode Biosciences Pvt. Ltd., Bangalore, India. Additional comparative sequences were sourced from GenBank.Code/Software<br>The analysis was conducted using the following software:<b>MEGA v5.2</b> for sequence alignment and p-distance calculation.<b>IQ-Tree Web Server</b> for Maximum Likelihood phylogenetic analysis.<b>R (R Core Team 2022)</b> for statistical analysis, including the GroupStruct R program (Ver. 1.0, Chan &amp; Grismer 2021) for normalizing morphometric data and conducting MFA.<br>Scripts and WorkflowDetailed R scripts and protocols used in the analysis can be found on the R package information page. These scripts facilitate replication of the study's results and each script is annotated to guide users through the analysis workflow, ensuring transparency and reproducibility. The scripts are essential for normalizing morphometric data and performing the MFA analysis.