On the taxonomy and systematics of the recently described Lycodon deccanensis Ganesh, Deuti, Punith, Achyuthan, Mallik, Adhikari, Vogel, 2020 (Serpentes, Colubridae) from India

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Abstract

Lycodon deccanensis Ganesh, Deuti, Punith, Achyuthan, Mallik, Adhikari, Vogel, 2020 was recently described from the Mysore plateau of Karnataka based solely on morphology but lacking in-depth descriptions and comparisons. A scrutiny of the description reveals that the type series, of two specimens, comprise specimens of two different species along with discrepancies throughout the paper. Surveys conducted near the type locality of the species led to the discovery of additional specimens, which allow us to provide an elaborate description of the species and present data on its phylogenetic relationship with members of the genus and comments on the systematics of Lycodon of India. Results from molecular phylogenetics suggest that Lycodon deccanensis is a member of the L. aulicus clade based on molecular data for mitochondrial cytochrome b gene and shows an un-corrected p-distance (sequence divergence) of 14–17% from other members of the Lycodon aulicus clade.

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Sudhir Kumar, Glen Stecher, Michael KaWah Li … (2018)

The Molecular Evolutionary Genetics Analysis (Mega) software implements many analytical methods and tools for phylogenomics and phylomedicine. Here, we report a transformation of Mega to enable cross-platform use on Microsoft Windows and Linux operating systems. Mega X does not require virtualization or emulation software and provides a uniform user experience across platforms. Mega X has additionally been upgraded to use multiple computing cores for many molecular evolutionary analyses. Mega X is available in two interfaces (graphical and command line) and can be downloaded from www.megasoftware.net free of charge.

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IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era

Bui Minh, Heiko Schmidt, Olga Chernomor … (2020)

Abstract IQ-TREE (http://www.iqtree.org, last accessed February 6, 2020) is a user-friendly and widely used software package for phylogenetic inference using maximum likelihood. Since the release of version 1 in 2014, we have continuously expanded IQ-TREE to integrate a plethora of new models of sequence evolution and efficient computational approaches of phylogenetic inference to deal with genomic data. Here, we describe notable features of IQ-TREE version 2 and highlight the key advantages over other software.

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Fredrik Ronquist, John P. Huelsenbeck (2003)

MrBayes 3 performs Bayesian phylogenetic analysis combining information from different data partitions or subsets evolving under different stochastic evolutionary models. This allows the user to analyze heterogeneous data sets consisting of different data types-e.g. morphological, nucleotide, and protein-and to explore a wide variety of structured models mixing partition-unique and shared parameters. The program employs MPI to parallelize Metropolis coupling on Macintosh or UNIX clusters.