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R-code and Output from Comparative Analysis of Dominance Steepness and Directional Consistency

Figure S1: 3D iso-surfaces of vorticity magnitude 10 Hz (red) and -10 Hz (green) as calculated by CFD for the original model of (a) A. guineensis, (b) L. triqueter, (c) L. cornuta, (d) O. cubicus, and (e) R. rhinorhynchus; and (‘) their corresponding reduced-keel models; (I) with their rostro-caudal axis parallel, (II) at a 20° pitch angle of attack, and (III) at a -20° yaw angle of attack in a water flow of 0.5 m s-1. From left to right, views are lateral, dorsal, and frontal. Figure S2: Outline plot of percentage differences in the studied coefficients (drag coefficient CD, pitch and yaw moment coefficient CMpitch and CMyaw, rotational drag moment coefficient CrotD, rotational added mass moment coefficient CrotAM), of the reduced-keel model relative to the original model for A. guineensis (turquoise), L. triqueter (red), L. cornuta (blue), O. cubicus (green), and R. rhinorhynchus (black). See Tables 1 to 4 for numerical data.

During the Last Glacial Maximum (LGM), global sea levels were 120‐130 m lower than today, resulting in the emergence of most continental shelves and extirpation of subtidal organisms from these areas. During the interglacial periods, rapid inundation of shelf regions created a dynamic environment for coastal organisms, such as the charismatic leafy seadragon (Phycodurus eques, Syngnathidae), a brooder with low dispersal ability inhabiting kelp beds in temperate Australia. Reconstructions of the paleoshoreline revealed that the increase of shallow areas since the LGM was not uniform across the species’ range and we investigated the effects of these asymmetries on genetic diversity and structuring. Using targeted capture of 857 variable Ultraconserved Elements (UCEs, 2845 SNPs) in 68 individuals, we found that the regionally different shelf topographies were paralleled by contrasting population genetic patterns. In the west, populations may not have persisted through sea‐level lows because shallow seabed was very limited. Shallow genetic structure, weak expansion signals and a westward cline in genetic diversity indicates a postglacial recolonization of the western part of the range from a more eastern location following sea‐level rise. In the east, shallow seabed persisted during the LGM and increased considerably after the flooding of large bays, which resulted in strong demographic expansions, deeper genetic structure and higher genetic diversity. This study suggests that postglacial flooding with rising sea levels produced locally variable signatures in colonizing populations.

The fish clade Pelagiaria, which includes tunas as its most famous members, evolved remarkable morphological and ecological variety in a setting not generally considered conducive to diversification: the open ocean. Relationships within Pelagiaria have proven elusive due to short internodes subtending major lineages suggestive of rapid early divergences. Using a novel sequence dataset of over 1000 ultraconserved DNA elements (UCE) for 94 of the 286 species of Pelagiaria (greater than 70% of genera), we provide a time-calibrated phylogeny for this widely distributed clade. Some inferred relationships have clear precedents (e.g. the monophyly of ‘core’ Stromateoidei, and a clade comprising ‘Gempylidae’ and Trichiuridae), but others are unexpected despite strong support (e.g. Chiasmodontidae + Tetragonurus). Relaxed molecular clock analysis using node-based fossil calibrations estimates a latest Cretaceous origin for Pelagiaria, with crown-group families restricted to the Cenozoic. Estimated mean speciation rates decline from the origin of the group in the latest Cretaceous, although credible intervals for root and tip rates are broad and overlap in most cases, and there is higher-than-expected partitioning of body shape diversity (measured as fineness ratio) between clades concentrated during the Palaeocene–Eocene. By contrast, more direct measures of ecology show either no substantial deviation from a null model of diversification (diet) or patterns consistent with evolutionary constraint or high rates of recent change (depth habitat). Collectively, these results indicate a mosaic model of diversification. Pelagiarians show high morphological disparity and modest species richness compared to better-studied fish radiations in contrasting environments. However, this pattern is also apparent in other clades in open-ocean or deep-sea habitats, and suggests that comparative study of such groups might provide a more inclusive model of the evolution of diversity in fishes.

Methods of phylogeny reconstruction, Malawi-wide convergence, and Table of Malawi-wide convergence model scores

International audience; Understanding why some groups of organisms are more diverse than others is a central goal in macroevolution. Evolvability, or lineages’ intrinsic capacity for evolutionary change, is thought to influence disparities in species diversity across taxa. Over macroevolutionary time scales, clades that exhibit high evolvability are expected to have higher speciation rates. Cone snails (family: Conidae, >900 spp.) provide a unique opportunity to test this prediction because their venom genes can be used to characterize differences in evolvability between clades. Cone snails are carnivorous, use prey-specific venom (conotoxins) to capture prey, and the genes that encode venom are known and diversify through gene duplication. Theory predicts that higher gene diversity confers a greater potential to generate novel phenotypes for specialization and adaptation. Therefore, if conotoxin gene diversity gives rise to varying levels of evolvability, conotoxin gene diversity should be coupled with macroevolutionary speciation rates. We applied exon capture techniques to recover phylogenetic markers and conotoxin loci across 314 species, the largest venom discovery effort in a single study. We paired a reconstructed timetree using 12 fossil calibrations with species-specific estimates of conotoxin gene diversity and used trait-dependent diversification methods to test the impact of evolvability on diversification patterns. Surprisingly, did not detect any signal for the relationship between conotoxin gene diversity and speciation rates, suggesting that venom evolution may not be the rate-limiting factor controlling diversification dynamics in Conidae. Comparative analyses showed some signal for the impact of diet and larval dispersal strategy on diversification patterns, though whether or not we detected a signal depended on the dataset and the method. If our results remain true with increased sampling in future studies, they suggest that the rapid evolution of Conidae venom may cause other factors to become more critical to diversification, such as ecological opportunity or traits that promote isolation among lineages.

For tropical marine species, hotspots of endemism occur in peripheral areas furthest from the center of diversity, but the evolutionary processes that lead to their origin remain elusive. We test several hypotheses related to the evolution of peripheral endemics by sequencing ultraconserved element (UCE) loci to produce a genome-scale phylogeny of 47 butterflyfish species (family Chaetodontidae) that includes all shallow water butterflyfish from the coastal waters of the Arabian Peninsula (i.e., Red Sea to Arabian Gulf) and their close relatives. Bayesian tree building methods produced a well-resolved phylogeny that elucidated the origins of butterflyfishes in this hotspots of endemism. We show that UCEs, often used to resolve deep evolutionary relationships, represent an important tool to assess the mechanisms underlying recently diverged taxa. Our analyses indicate that unique environmental conditions in the coastal waters of the Arabian Peninsula probably contributed to the formation of endemic butterflyfishes. Older endemic species are also associated with narrow versus broad depth ranges, suggesting that adaptation to deeper coral reefs in this region occurred only recently (

Electronic Supplemental Material including Appendix S1, Appendix S2, Appendix S3, Figure S1, Figure S2, Figure S3 and Figure S4.

BackgroundFlatfish cranial asymmetry represents one of the most remarkable morphological innovations among vertebrates, and has fueled vigorous debate on the manner and rate at which strikingly divergent phenotypes evolve. A surprising result of many recent molecular phylogenetic studies is the lack of support for flatfish monophyly, where increasingly larger DNA datasets of up to 23 loci have either yielded a weakly supported flatfish clade or indicated the group is polyphyletic. Lack of resolution for flatfish relationships has been attributed to analytical limitations for dealing with processes such as nucleotide non-stationarity and incomplete lineage sorting (ILS). We tackle this phylogenetic problem using a sequence dataset comprising more than 1,000 ultraconserved DNA element (UCE) loci covering 45 carangimorphs, the broader clade containing flatfishes and several other specialized lineages such as remoras, billfishes, and archerfishes.ResultsWe present a phylogeny based on UCE loci that unequivocally supports flatfish monophyly and a single origin of asymmetry. We document similar levels of discordance among UCE loci as in previous, smaller molecular datasets. However, relationships among flatfishes and carangimorphs recovered from multilocus concatenated and species tree analyses of our data are robust to the analytical framework applied and size of data matrix used. By integrating the UCE data with a rich fossil record, we find that the most distinctive carangimorph bodyplans arose rapidly during the Paleogene (66.0-23.03Ma). Flatfish asymmetry, for example, likely evolved over an interval of no more than 2.97 million years.ConclusionsThe longstanding uncertainty in phylogenetic hypotheses for flatfishes and their carangimorph relatives highlights the limitations of smaller molecular datasets when applied to successive, rapid divergences. Here, we recovered significant support for flatfish monophyly and relationships among carangimorphs through analysis of over 1,000 UCE loci. The resulting time-calibrated phylogeny points to phenotypic divergence early within carangimorph history that broadly matches with the predictions of adaptive models of lineage diversification.

Sagittalarva Victor, n. gen. Type species: Sagittalarva inornata (Gilbert, 1890), Baja California, Mexico; here designated. Diagnosis. Dorsal rays IX, 12; anal rays III, 12; pectoral rays 13 (12 plus uppermost rudimentary ray); lateral-line continuous, inclined sharply downward below soft portion of dorsal fin, the pored scales 27, canals on scales with a single pore; head naked except for a set of small scales on each side of nape forward of the dorsal-fin origin; scales on thorax much smaller than body scales; jaws with a single pair of enlarged canine teeth at the front of the upper jaw (one tooth per side) and a single pair at the front of the lower jaw (one tooth per side) which fit between the upper pair when the mouth is closed; teeth behind enlarged canines in a regular row of caniniform to conical teeth; no posterior canine at the corner of the mouth; posterior half of upper lip with a dorsal fleshy flap, variably developed; 10 + 6 gill rakers, larger ones serrated and branched; snout long and pointed, snout length 3.3���3.4 in HL for fish over 70 mm SL (3.36 in holotype); body slender, depth of body 4.6���4.7 in SL for fish over 70 mm SL (4.57 in holotype, ���depth 5 2 / 3 in length��� in Gilbert (1890) must refer to TL); body very compressed, body width 9.0- 10.5 % SL; dorsal-fin spines pungent, first spine shortest, subsequent spines and rays progressively longer; caudal fin only slightly rounded. Mid to late-stage larvae (7���14 mm SL) slender, flattened, and dart-shaped with marked horizontal symmetry (symmetrical above and below the lateral midline); forehead low and straight; mouth small, terminal, and at the level of the lateral midline; snout long and sharply pointed; melanophore pigment limited to the tip of the upper and lower jaws and a few small melanophores along the edge of the caudal-fin and posterior dorsal and anal-fin membranes. Etymology. The name Sagittalarva derives from the combination of sagitta, arrow or dart in Latin, and larva, originally ghost or mask in Latin and first applied to immature forms by Linnaeus, referring to the unusual dartshaped larva of the Cape Wrasse; both nouns and the combination are feminine. Remarks. A single pair of enlarged canines at the tip of each of the upper and lower jaws with no canine at the corner of the jaw and rows of caniniform to conical teeth along the jaws (Fig. 1) separates Sagittalarva from all other New World julidines as well as from Pseudojuloides. All western Atlantic Halichoeres differ in having a prominent canine at the corner of the jaw and all but two have two pairs of enlarged canines in the lower jaw (H. maculipinna and its Brazilian sibling have only a single pair of enlarged canines at the lower jaw). Most eastern Pacific Halichoeres also have the canine at the corner of the jaw and the exceptions have two pairs of enlarged canines at the tip of the lower jaw (H. notospilus (G��nther), H. adustus (Gilbert, 1890), and H. insularis Allen & Robertson, 1992) or more than a single enlarged pair at both the upper and lower jaw tips (H. melanotis, H. salmofasciatus, and H. malpelo Allen & Robertson, 1992; as well as Oxyjulis californica). Species of Thalassoma do not have a particularly enlarged pair of canines, while Pseudojuloides have flattened chisel-like incisiform teeth behind a pair of canines (Fig. 2). There is some ambiguity in the literature for the pectoral fin-ray counts for eastern Pacific Halichoeres species, with counts of 12 or 13 inconsistently cited in descriptions and guides. All of the species were examined but H. malpelo and they all have 13 total rays (12 plus one upper rudimentary). The species description for H. malpelo also reports 13 pectoral rays (Allen & Robertson 1992; 1994). In all species, the uppermost pectoral ray is a short unbranched ray, more obvious on smaller individuals and sometimes not grossly visible in adults. The next ray is typically the largest ray of the pectoral-fin series and should be counted as the second ray from the top (Randall & Allen 2010). The larvae of New World Halichoeres and Thalassoma species differ markedly in morphology from larval Sagittalarva inornata. They have relatively stout bodies that are not horizontally symmetrical, relatively short snouts, and different patterns of melanophores (Watson et al. 1996; Beltr��n-Leon & Herrera 2000; Jones et al. 2006; Victor 2012 and unpublished data) (Fig. 3). None have melanophores on the head and the basic complement is melanophores on the membranes between adjacent fin rays in discrete patches spaced out along the length of the dorsal and anal fins. On most larval Halichoeres there are three patches on the dorsal fin (front, mid, and rear) and two on the anal fin (front and rear). Halichoeres maculipinna larvae have only the rear patch on the dorsal and anal fins. Larval Thalassoma generally have very few melanophores: T. bifasciatum (Bloch) larvae have a patch on the membranes of the first few dorsal spines and isolated small edge melanophores along the rim of the dorsal, caudal, and anal fin membranes (these are similar to the melanophores on larval S. inornata). Larvae of other Thalassoma in the literature are typically shown with no melanophores, although the small fin-edge melanophores are present on well-preserved larvae of the eastern Pacific species and some western Pacific species as well (Victor 2012). It is likely that they occur on all Thalassoma larvae. The larvae of Pseudojuloides cerasinus (Snyder) have been identified by DNA-barcode matching (collected from Hawaii by David Carlon, pers. comm. and in BOLD project FLHI) as well as by morphology (Miller et al. 1979, as Labrid L 3, 7.2 mm SL). They differ markedly from Sagittalarva inornata larvae, having a short upturned snout and some very different markings from other labrid larvae, in particular distinctive internal melanophores along myomere edges within the musculature of the rear body, in addition to patches of melanophores on the membranes between the last few dorsal and anal-fin rays (Fig. 4). Bruce Mundy (pers.comm.) identified larval P. cerasinus in his Hawaiian collections and found both the internal and fin-membrane melanophores as well as additional melanophores over the cranium and a complex pattern of erythrophores (usually lost in preservation) on fresh late-stage P. cerasinus larvae., Published as part of Victor, Benjamin C., Alfaro, Michael E. & Sorenson, Laurie, 2013, Rediscovery of Sagittalarva inornata n. gen., n. comb. (Gilbert, 1890) (Perciformes: Labridae), a long-lost deepwater fish from the eastern Pacific Ocean: a case study of a forensic approach to taxonomy using DNA barcoding, pp. 551-570 in Zootaxa 3669 (4) on pages 557-560, DOI: 10.11646/zootaxa.3669.4.8, http://zenodo.org/record/221559

Victor, Benjamin C., Alfaro, Michael E., Sorenson, Laurie (2013): Rediscovery of Sagittalarva inornata n. gen., n. comb. (Gilbert, 1890) (Perciformes: Labridae), a long-lost deepwater fish from the eastern Pacific Ocean: a case study of a forensic approach to taxonomy using DNA barcoding. Zootaxa 3669 (4): 551-570, DOI: http://dx.doi.org/10.11646/zootaxa.3669.4.8

Massively parallel DNA sequencing techniques are rapidly changing the dynamics of phylogenetic study design by exponentially increasing the discovery of phylogenetically useful loci. This increase in the number of phylogenetic markers potentially provides researchers the opportunity to select subsets of loci best-addressing particular phylogenetic hypotheses based on objective measures of performance over different time scales. Investigators may also want to determine the power of particular phylogenetic markers relative to each other. However, currently available tools are designed to evaluate a small number of markers and are not well-suited to screening hundreds or thousands of candidate loci across the genome. TAPIR is an alternative implementation of Townsend's estimate of phylogenetic informativeness (PI) that enables rapid estimation and summary of PI when applied to data sets containing hundreds to thousands of candidate, phylogenetically informative loci., Comment: 13 pages, 1 figure, 1 supplementary table, 3 supplementary figures

In recent years, a suite of methods has been developed to fit multiple rate models to phylogenetic comparative data. However, most methods have limited utility at broad phylogenetic scales because they typically require complete sampling of both the tree and the associated phenotypic data. Here, we develop and implement a new, tree?based method called MECCA (Modeling Evolution of Continuous Characters using ABC) that uses a hybrid likelihood/approximate Bayesian computation (ABC)?Markov?Chain Monte Carlo approach to simultaneously infer rates of diversification and trait evolution from incompletely sampled phylogenies and trait data. We demonstrate via simulation that MECCA has considerable power to choose among single versus multiple evolutionary rate models, and thus can be used to test hypotheses about changes in the rate of trait evolution across an incomplete tree of life. We finally apply MECCA to an empirical example of body size evolution in carnivores, and show that there is no evidence for an elevated rate of body size evolution in the pinnipeds relative to terrestrial carnivores. ABC approaches can provide a useful alternative set of tools for future macroevolutionary studies where likelihood?dependent approaches are lacking.