Computational protocol: Evolution of the locomotory system in eels (Teleostei: Elopomorpha)

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Protocol publication

[…] Detailed measurements of extinct specimens were conducted with tpsUtil v.1.58 and tpsDig v.1.40 and combined with data of extant anguilliforms ([]; Additional file : Table S1). The relationship between body length and number of vertebrae was analysed with linear regression analyses conducted by SPSS 20.0. (IBM, Armonk, USA).The ‘vertebrate shape index’ (VSI) is employed here, which represents a metric of the body shape and, therefore, describes the shape diversity in vertebrates []. It quantifies the shape of the body by the computation of different morphometric indices of the investigated fishes. Comparison of VSI among extinct and extant anguilliforms was scrutinized with principal component analyses (Figs.  and , Additional file : Table S1) using the following formula []:VSI=Laxis1/Laxis2+LheadinvertebraexARhead+NPCVxARPCV+NCVxARCV.Abbreviations of the VSI index are as follows:ARCV - mean aspect ratio of the length of three selected caudal vertebrae to their height in the dimension of Laxis2; ARhead - ratio of head length to its length in the dimension of Laxis2; ARPCV - mean aspect ratio of three selected precaudal vertebrae to their height in the dimension of Laxis2; Laxis1 - standard length; Laxis2 - length of secondary body axis (maximum body depth or width; in extinct anguilliforms body depth is used); Lhead in vertebrae - head length quantified as the number of vertebrae spanning the anterio-posterior length of the head; NPCV - number of precaudal vertebrae; NCV - number of caudal vertebrae; VSI - vertebrate shape index. [...] Structural features of the postcranial body including secondarily ossified soft tissues (myoseptal tendons) were studied in extinct anguilliforms by light microscopy and visualized with polarized light (VHX 1000; Keyence, Osaka, Japan) (Figs.  and , Additional file : Table S1, Additional file : Note 1). The morphological terminology for myosepta and the definition of the axial position in anguilliform swimmers employed here follows previous studies (e.g., [, , , ]). The number of traversed vertebrae by the epineural (ENB) and epipleural bones (EPB) provides a fairly accurate estimate of the length of the lateral tendon. The total length of the lateral tendon and, therefore of the myoseptum, is calculated by adding one additional segment (N) based on comparative investigations in extant eels [] and the corresponding distance between the lateral tendon and ENB, respectively EPB (Figs.  and , Additional file : Table S1). Detailed measurements of ENB and EPB lengths were taken in millimetres with a stereomicroscope (Nikon SMZ 1500, Chiyoda, Japan) using a 2 mm standard scale bar slide with 20 subdivisions ([]; Additional file : Table S1). Resulting myoseptal length is expressed in relation to total body length and compared to previously published data [, , ]. We established the ancestral states of myoseptal length with Mesquite 3.02 [] by using the ancestral state module and the parsimony method without estimated time divergences (Additional file : Figure S1).Fig. 3The influence of the phylogenetic signal in the principal component analysis was determined with Bloomberg’s K-value and Pagel’s λ. The analyses were carried out with Mesquite 3.02 [], R-Studio v. 0.99.484 [], and the packages ape 3.4 [, ], phylobase v.0.8.2 [], geiger v.2.0.6 [] and phytools v.0.5-10 [] following previous procedures []. For a detailed list of results see Additional file : Table S1. […]

Pipeline specifications

Software tools APE, GEIGER, Phytools
Application Phylogenetics
Diseases Hypertension