Computational protocol: High Connectivity of Animal Populations in Deep-Sea Hydrothermal Vent Fields in the Central Indian Ridge Relevant to Its Geological Setting

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Protocol publication

[…] The obtained forward and reverse sequences were assembled into contigs by using the program ATGC (Genetyx® Version 6, Genetyx, Tokyo, Japan), and aligned by eye. All of the detected haplotypes were used for phylogenetic analyses in neighbor-joining (NJ) and maximum likelihood (ML) algorithms. The phylogeny of each animal was clarified by using the software package MEGA 5 . The molecular phylogenetic tree was reconstructed with previously published data in DNA databanks (NCBI, DDBJ, and EMBL; accession numbers are shown in the phylogenetic trees). Additionally, all of the obtained sequences were used for population-level analyses. The parsimonious haplotype network of each species was estimated by using the software package TCS 1.21 . For each population, we estimated genetic diversity indices (H?: gene diversity, π: nucleotide diversity, and mismatch distribution), and conducted statistical tests for genetic structure, by using Arlequin ver. 3.11 . In mismatch distribution analysis, we applied the goodness-of-fit test to compare the observed mismatch distribution, with the mismatch distribution obtained by using the sudden expansion model. For those species with more than three populations (R. kairei and Alviniconcha sp. type 3), we used analysis of molecular variance (AMOVA) to examine the genetic structure between northern segment populations (Dodo and Solitaire fields), and populations near the triple junction (Edmond and Kairei fields). The relative number of migrants per generation was estimated by using MIGRATE ver. 3.2.1 . A part of the population-level analyses included the previously reported sequences for the scaly-foot gastropod . […]

Pipeline specifications

Software tools MEGA, Arlequin
Databases DDBJ ATGC
Applications Phylogenetics, Population genetic analysis
Organisms Austinograea rodriguezensis, Rimicaris kairei