Computational protocol: Cryptic Diversity and Venom Glands in Western Atlantic Clingfishes of the Genus Acyrtus (Teleostei: Gobiesocidae)

Similar protocols

Protocol publication

[…] Protocols for DNA extraction and subsequent amplification of the cytochrome oxidase 1 (COI) gene from tissue samples follow those utilized by recent studies on Caribbean fishes –, –. In addition to members of the genus Acyrtus, we also obtained COI data for eight other New World gobiesocid taxa included within the subfamily Gobiesocinae (Acyrtops beryllinus, Arcos nudus, Gobiesox maeandricus, G. strumosus, Rimicola muscarum, Sicyases sanguineus, Tomicodon briggsi and T. reitzae), two from the Lepadogastrinae (Apletodon dentatus and Lepadogaster purpurea), and one from the Diplocrepinae (Parvicrepis parvipinnis), which served as outgroups in phylogenetic analyses. Obtained sequences were aligned by eye using TextWrangler vs. 2.3 (Barebones Software Inc). The aligned data set was subsequently viewed in MacClade vs. 4.05 to check for spurious stop codons and trimmed to ensure all taxa had sequences of similar length, resulting in a final aligned data set 621bp in length. GenSeq nomenclature for DNA sequences and GenBank information are presented along with museum catalog numbers for voucher specimens in .Maximum parsimony (MP) analysis of the final data set was conducted with heuristic searches in PAUP* v. 4.0b10 , utilizing tree-bisection and reconnection branch swapping (TBR) with the MULTREES option effective for 1000 random addition sequence replicates. All characters were equally weighted and left unordered. The resulting equally parsimonious cladograms were rooted using P. parvipinnis and summarized using a strict consensus method. Nodal support was estimated using non-parametric bootstrapping for 1000 pseudoreplicates, utilizing a random addition sequence and TBR branch swapping.Means of the corrected genetic distances within and between genetic lineages of Acyrtus corresponding to exclusive lineages obtained in resulting phylogenetic hypotheses were calculated with MEGA4.0 , using “within group means”, “between groups means”, and “net between groups means” options. Standard errors of the genetic distances were calculated using 1000 bootstrap replicates. […]

Pipeline specifications

Software tools MacClade, PAUP*, MEGA
Application Phylogenetics