Computational protocol: Hidden Diversity in Sardines: Genetic and Morphological Evidence for Cryptic Species in the Goldstripe Sardinella, Sardinella gibbosa (Bleeker, 1849)

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Protocol publication

[…] Sequences were assembled in Geneious v5.4 and aligned using MUSCLE v3.8.31 . A best-fit nucleotide substitution model was determined using jMODELTEST v2 , . Phylogenetic analysis using maximum likelihood (ML) criteria was inferred from MEGA v5.2.1 using the best-fit nucleotide substitution models, namely, Kimura-2-Parameter (K2P) for 16S, three parameter model (TPM) for control region and Hasegawa-Kishino-Yano (HKY) for the S7 intron. Also included in the analysis for outgroup comparison were the closely related taxa, namely, Sardinella fimbriata, S. hualiensis, S. lemuru, Herkoltsichthys quadrimaculatus and Amblygaster sirm sequences. Further, such species have overlapping geographic distribution with S. gibbosa throughout the Indo-West Pacific . However, we excluded Amblygaster sirm and Herklotsichthys quadrimaculatus as outgroups for control region dataset since they are highly divergent and inclusion of these taxa created large indels in sequence alignment. Allelic state of the nuclear S7 intron was estimated using PHASE v2.1 , as implemented in DnaSP v5.0 . The phylogenetic network was inferred using the median-joining network implemented in NETWORK v4.6 using the default settings. […]

Pipeline specifications

Software tools Geneious, jModelTest, MEGA-V, DnaSP
Applications Phylogenetics, GWAS
Organisms Sardina pilchardus, Danio rerio