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Supporting Data: Phylogeny of Arbacia Gray, 1835 (Echinoidea) reveals diversification patterns in the Atlantic and Pacific Oceans.
<p>This dataset contains:</p> <ol> <li>Appendix S1, metadata asociated with the specimens (collection localities, specimen numbers)</li> <li>The aligned sequence files for each marker: COI_fasta, 16S_fasta, CR_fasta</li> <li>The concatenated sequence file COI + 16S + CRA + 28S Arbacia_supermatrix_fasta and the partition file partitions_concat</li> <li>The Bayesian trees for COI, 16S, CRA, and the supermatrix: BI_tree_16S, BI_tree_COI, BI_tree_CR, BI_tree_Arbacia_supermatrix</li> <li>The ML tree of the supermatrix: ML_tree_Arbacia_supermatrix</li> <li>Appendix S2, which includes various information on the primers used, PCR cycles, etc.</li> <li>Appendix S3, which includes the index calculations for each marker.</li> </ol>
Branching patterns in phylogenies cannot distinguish diversity-dependent diversification from time-dependent diversification
One of the primary goals of macroevolutionary biology has been to explain general trends in long-term diversity patterns, including whether such patterns correspond to an up-scaling of processes occurring at lower scales. Reconstructed phylogenies often show decelerated lineage accumulation over time. This pattern has often been interpreted as the result of diversity-dependent diversification, where the accumulation of species causes diversification to decrease through niche filling. However, other processes can also produce such a slowdown, including time-dependence without diversity-dependence. To test whether phylogenetic branching patterns can be used to distinguish these two mechanisms, we formulated a time-dependent, but diversity-independent model that matches the expected diversity through time of a diversity-dependent model. We simulated phylogenies under each model and studied how well likelihood methods could recover the true diversification mode. Standard model selection criteria always recovered diversity-dependence, even when it was not present. We correct for this bias by using a bootstrap method and find that neither model is decisively supported. This implies that the branching pattern of reconstructed trees contains insufficient information to detect the presence or absence of diversity-dependence. We advocate that tests encompassing additional data, e.g., traits or range distributions, are needed to evaluate how diversity drives macroevolutionary trends.
FIGURE 37 in Patterns of diversification and phylogenetic structure in the dorsolateral head musculature of Neotropical electric eels (Ostariophysi: Gymnotiformes), with a myological synonymy
FIGURE 37 | Patterns of PBS value distribution of myologycal characters per taxonomic level in the phylogeny based on phenotypic data (Figs. 35, 36). Green bars indicate positive PBS values and red bars indicate negative PBS values. Bar for tribes include only non-monogeneric tribes. Taxon legends: A) Characiformes; B) Siluriformes; C) Siluriphysi; D) Gymnotiformes; E) Sternopygoidei; F) Rhamphichthyoidea; G) Sternopygoidea; H) Gymnotidae; I) Hypopomidae; J) Rhamphichthyidae; K) Sternopygidae; L) Apteronotidae; M) Steatogeninae; N) Eigenmanniinae; O) Sternarchorhynchinae; P) Microsternarchini; Q) Gymnotus; R) Brachyhypopomus; S) Akawaio + Hypopomus; T) Gymnorhamphichthys; U) Iracema + Rhamphichthys; V) Steatogenys; W) Hypopygus; X) Sternopygus; Y) Archolaemus + remaining Eigenmanniinae genera (except Japigny) Z) Distocyclus + remaining Eigenmanniinae genera (except Archolaemus and Japigny); A1) Eigenmannia + Rhabdolichops; B1) Rhabdolichops; C1) R. eastwardi + Rhabdolichops spp.; D1) Eigenmannia spp.; E1) Adontosternarchus; F1) Megadontognathus + Apteronotus; G1) Apteronotus; H1) A. cuchillejo + A. spp.1; I1) ((Porotergus + Tenebrosternarchus, Sternarchogiton) + (Compsaraia + "A." bonapartii)); J1) (Porotergus + Tenebrosternarchus, Sternarchogiton); K1) (Tenebrosternarchus, Sternarchogiton); L1) (Compsaraia + "A." bonapartii); M1) Compsaraia; N1) Pariosternarchus + Sternarchella; O1) Sternarchella; P1) Orthosternarchus + Sternarchorhamphus; Q1) Platyurosternarchus + Sternarchorhynchus; R1) Platyurosternarchus; S1) Sternarchorhynchus; T1) G. curupira + Gymnotus subgroups; U1) Gymnotus spp.2,3, 4, 5; V1) Gymnotus spp.3; W1) Gymnotus spp.4; X1) Gymnotus spp.5; Y1) Gymnotus spp.6; Z1) Gymnotus spp.7; A2) B. beebei + Brachyhypopomus subgroups; B2) B. draco + Brachyhypopomus spp.2; C2) Brachyhypopomus spp.3; D2) Hypopygus spp.; E2) Rhabdolichops spp.; F2) Adontosternarchus spp.; G2) Apteronotus spp.1; H2) Apteronotus spp.2 + Apteronotus spp.3; I2) Apteronotus spp.2; J2) Apteronotus spp.3; K2) "A." bonapartii; L2) Sternarchorhynchus spp.
FIGURE 35 in Patterns of diversification and phylogenetic structure in the dorsolateral head musculature of Neotropical electric eels (Ostariophysi: Gymnotiformes), with a myological synonymy
FIGURE 35 | Strict consensus of MPT's resulting from parsimony analysis of character matrix in Peixoto et al. (2019), concatenated with dorsolateral head musculature characters of this study [Score: 795; RI: 0.92; CI: 0.37], with numbered dorsolateral head musculature characters (below branches) and respective characters states (above branches. Black circles indicate homoplasy-free characters and white circles indicate homoplastic characters. Taxon legends: Gymnotus spp.1 (G. panamensis, G. maculosus, and G. cylindricus); Gymnotus spp.2 (G. varzea, G. pantanal, G. obscurus, G. chaviro); Gymnotus spp.3 (G. ucamara, G. sylvius, G. sp, G. omamorum, G. mamiraua, G. bahianus); Gymnotus spp.4 (G. choco and G. ardilai); Gymnotus spp.5 (G. carapo and G. arapaima); Gymnotus spp.6 (G. tigre and G. hehni); Gymnotus spp.7 (G. stenoleucus, G. pedanopterus, G. pantherinus, G. jonasi, G. javari, G. coropinae, G. coatesi, G. cf. anguilaris, and G. cataniapo); Brachyhypopomus spp.1 (B. sp., B. accidentalis, and B. diazi); Brachyhypopomus spp.2 (B. pinnicaudatus; B. sp. 2); Brachyhypopomus spp.3 (B. bullocki and B. brevirostris); Rhabdolichops spp. (R. jegui and R. cf. stewarti); Adontosternarchus spp. (A. nebulosus, A. devenanzii, A. clarkae, A. balaenops); Apteronorus spp.1 (A. caudimaculosus and A. albifrons); Apteronorus spp.2 (A. magdalenensis and A. cuchillo); Apteronorus spp.3 (A. leptorhynchus and A. eschemeyeri); Sternarchorhynchus spp. (S. starski, S. hagedornae, S. galibi, S. sp.).
FIGURE 25 in Patterns of diversification and phylogenetic structure in the dorsolateral head musculature of Neotropical electric eels (Ostariophysi: Gymnotiformes), with a myological synonymy
FIGURE 25 | Lateral view of dorsolateral musculature of Apteronotus bonapartii (Apteronotidae), MPEG 3038, 217.5 mm LEA. Anatomical abbreviations in Tab. 1. Scale bar = 5 mm.
FIGURE 31 in Patterns of diversification and phylogenetic structure in the dorsolateral head musculature of Neotropical electric eels (Ostariophysi: Gymnotiformes), with a myological synonymy
FIGURE 31 | Lateral view of dorsolateral musculature of Compsaraia compsa (Apteronotidae), MZUSP 56206, 123.4 mm LEA. Anatomical abbreviations in Tab. 1. Scale bar = 5 mm.
FIGURE 34 in Patterns of diversification and phylogenetic structure in the dorsolateral head musculature of Neotropical electric eels (Ostariophysi: Gymnotiformes), with a myological synonymy
FIGURE 34 | Same tree as in Fig. 33, with numbered dorsolateral head musculature characters (below branches) and respective character states (above branches). Black squares indicate homoplasy-free characters and white squares indicate homoplastic characters. Table on left indicates support values for each node: BR (Relative Bremer support), BST (Bootstrap), and JCK (Jackknife). Taxon legends as in Fig. 33.
FIGURE 32 in Patterns of diversification and phylogenetic structure in the dorsolateral head musculature of Neotropical electric eels (Ostariophysi: Gymnotiformes), with a myological synonymy
FIGURE 32 | Lateral view of dorsolateral musculature of Tenebrosternarchus preto (Apteronotidae), MPEG 22758, 268.5 mm LEA. A= anterolateral fibers of the levator arcus palatini; P= posterolateral fibers of the levator arcus palatini. Remaining anatomical abbreviations in Tab. 1. Scale bar = 5 mm.
FIGURE 36 in Patterns of diversification and phylogenetic structure in the dorsolateral head musculature of Neotropical electric eels (Ostariophysi: Gymnotiformes), with a myological synonymy
FIGURE 36 | Strict consensus of MPT's resulting from parsimony analysis of character matrix in Peixoto et al. (2019), concatenated with dorsolateral head musculature characters of this study [Score: 795; RI: 0.92; CI: 0.37]. PBS values for general morphological characters and myological characters are indicated below each branch. Circle size is arbitrary; gray indicate neutral values of PBS for myologycal characters. Taxon legends as in Fig. 35.
FIGURE 28 in Patterns of diversification and phylogenetic structure in the dorsolateral head musculature of Neotropical electric eels (Ostariophysi: Gymnotiformes), with a myological synonymy
FIGURE 28 | Lateral view of dorsolateral musculature of Sternarchella terminalis (Apteronotidae), MPEG 3481, 155.3 mm TL [regenerated]. Anatomical abbreviations in Tab. 1. Scale bar = 5 mm.
FIGURE 21 in Patterns of diversification and phylogenetic structure in the dorsolateral head musculature of Neotropical electric eels (Ostariophysi: Gymnotiformes), with a myological synonymy
FIGURE 21 | Lateral view of dorsolateral musculature of Distocyclus conirostris (Sternopygidae), MZUSP 23316, 242.2 mm LEA. Anatomical abbreviations in Tab. 1. Scale bar = 4 mm.
FIGURE 18 in Patterns of diversification and phylogenetic structure in the dorsolateral head musculature of Neotropical electric eels (Ostariophysi: Gymnotiformes), with a myological synonymy
FIGURE 18 | Lateral view of dorsolateral musculature of Rhamphichthys hahni (Rhamphichthyidae), MZUSP 24736, 479.5 mm TL. Anatomical abbreviations in Tab. 1. Scale bar = 20 mm.
FIGURE 15 in Patterns of diversification and phylogenetic structure in the dorsolateral head musculature of Neotropical electric eels (Ostariophysi: Gymnotiformes), with a myological synonymy
FIGURE 15 | Lateral view of dorsolateral musculature of Microsternarchus cf. bilineatus (Hypopomidae), MBUCV-V 7298, 59.2 mm LEA. Anatomical abbreviations in Tab. 1. Scale bar = 1 mm.
FIGURE 12 in Patterns of diversification and phylogenetic structure in the dorsolateral head musculature of Neotropical electric eels (Ostariophysi: Gymnotiformes), with a myological synonymy
FIGURE 12 | Mesial view of suspensorium of Brachyhypopomus janeiroensis (Hypopomidae), MZUSP 22702, 80.9 mm LEA. Anatomical abbreviations in Tab. 1. Scale bar = 4 mm.
FIGURE 11 in Patterns of diversification and phylogenetic structure in the dorsolateral head musculature of Neotropical electric eels (Ostariophysi: Gymnotiformes), with a myological synonymy
FIGURE 11 | Lateral view of dorsolateral musculature of Hypopygus lepturus (Hypopomidae), MZUSP 91426, 55.4 mm LEA. Some fibers of the LO, anterior accidentally removed during dissections. Anatomical abbreviations in Tab. 1. Scale bar = 2 mm.
FIGURE 8 in Patterns of diversification and phylogenetic structure in the dorsolateral head musculature of Neotropical electric eels (Ostariophysi: Gymnotiformes), with a myological synonymy
FIGURE 8 | Rhamphichthys hahni (Rhamphichthyidae), MZUSP 24736, 479.5 mm TL. A. Lateral view of adductor mandibulae, pars ricto-stegalis; B. Mesial view of levator arcus palatini. Anatomical abbreviations in Tab. 1. Scale bars = 10 mm; 2 mm.
FIGURE 7 in Patterns of diversification and phylogenetic structure in the dorsolateral head musculature of Neotropical electric eels (Ostariophysi: Gymnotiformes), with a myological synonymy
FIGURE 7 | Lateral view of dorsolateral musculature of Apteronotus albifrons (Apteronotidae), MZUSP 22251, 150.1 mm LEA. Green indicates the path of recurrent ramus of anteroventral part of anterior lateral line nerve. Anatomical abbreviations in Tab. 1. Scale bar = 5 mm.
FIGURE 5 in Patterns of diversification and phylogenetic structure in the dorsolateral head musculature of Neotropical electric eels (Ostariophysi: Gymnotiformes), with a myological synonymy
FIGURE 5 | Lateral view of adductor mandibulae, pars malaris of Gymnorhamphichthys rosemariae (Rhamphichthyidae), MZUSP 56317. Anatomical abbreviations in Tab. 1. Scale bar = 5 mm.
FIGURE 14 in Patterns of diversification and phylogenetic structure in the dorsolateral head musculature of Neotropical electric eels (Ostariophysi: Gymnotiformes), with a myological synonymy
FIGURE 14 | Lateral view of dorsolateral musculature of Brachyhypopomus janeiroensis (Hypopomidae), MZUSP 22702, 80.9 mm LEA. Anatomical abbreviations in Tab. 1. Scale bar = 3 mm.
FIGURE 10 in Patterns of diversification and phylogenetic structure in the dorsolateral head musculature of Neotropical electric eels (Ostariophysi: Gymnotiformes), with a myological synonymy
FIGURE 10 | Electrophorus cf. electricus (Gymnotidae), MZUSP 85509, 488.2 mm LEA. A. Lateral view of dorsolateral head muscles; B. Posterior portion of dorsolateral head muscles. Adductor mandibulae dissected in B. LO, anterior not visible in lateral view. Anatomical abbreviations in Tab. 1. Scale bar = 10 mm.
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