Rapid evolutionary divergences in reef fishes of the family Acanthuridae (Perciformes: Teleostei)

An enigmatic pelagic fish with internalized red muscle: A future regional endotherm or forever an ectotherm?

Ectothermy and endothermy in extant fishes are defined by distinct integrated suites of characters. Although only ⁓0.1% of fishes are known to have endothermic capacity, recent discoveries suggest that there may still be uncommon pelagic fish species with yet to be discovered endothermic traits. Among the most rarely encountered marine fishes, the louvar Luvarus imperialis is a remarkable example of adaptive evolution as the only extant pelagic species in the order Acanthuriformes (including surgeonfishes, tangs, unicornfishes and Moorish idol). Magnetic resonance imaging and gross necropsy did not yield evidence of cranial or visceral endothermy but revealed a central-posterior distribution of myotomal red muscle that is a mixture of the character states typifying ectotherms (lateral-posterior) and red muscle endotherms (central-anterior). Dissection of a specimen confirmed, and an osteological proxy supported, that L. imperialis has not evolved the vascular rete that is vital to retaining heat in the red muscle. The combination of presumably relying on caudal propulsion while exhibiting internal red muscle without associated retia is unique to L. imperialis among all extant fishes, raising the macroevolutionary question of whether this species - in geologic timescales - will remain an ectotherm or evolve red muscle endothermy.

The complete mitochondrial genome sequence of Ctenochaetus tominiensis (Actinopteri, Acanthuridae)

We sequenced and annotated the complete mitochondrial genome of Ctenochaetus tominiensis (Randall 1955) from Indonesia. The genome was assembled into a circular molecule of 16,429 bp with 44.45% GC content. This genome consisted of 13 protein-coding genes (PCGs), 22 tRNA genes, two rRNA genes, and 1D-loop. Phylogenetic analysis based on 13 PCGs showed that Ctenochaetus and Acanthurus were recovered in a single clade. The mitochondrial genome of C. tominiensis is helpful for species identification and phylogenetic position of fish.

Evolutionary History and Taxonomic Reappraisal of Coral Reef Rabbitfishes (Siganidae): Patterns of Lineage Diversification and Speciation

Simple Summary

Herbivorous fish are recognized as being ecologically important to the health and survival of coral reef ecosystems because they remove algal turfs growing on corals. Apart from being one of the major components of herbivorous fish communities, rabbitfish are also characterized by possessing rabbit-like mouths. A total of 29 species of rabbitfish are confined to a single genus, Siganus, fish that are highly sought after for the aquarium trade and for food by humans. Natural hybridization between some species that have parapatric distributions across the Indo-West Pacific region may have homogenized their genotypic and morphological features. Relatively little is known, however, about how environmental factors may affect phylogenetic relationships among these siganid species. Based on sequencing of eight siganid species collected from the South China Sea and meta-analysis of sequences from ten siganid species retrieved from the NCBI database, we applied an integrated morphological–molecular approach to elucidate phylogenetic relationships and demographic histories of these species. Our results highlight that diversification and speciation of siganid species were influenced by a series of paleo-climatic events, changes to natural geographical distributions, and associated environmental changes. The target species were differentiated by body shape, and two morphometric parameters, notably body depth and snout length. Our results provide considerable baseline knowledge for strategizing improvement of both breeding and conservation programs for rabbitfish.

Abstract

Rabbitfish (Siganidae) are coral reef fish that are distributed across diverse habitats that include estuaries, mangroves, reefs, and even seaweed mats. Given their ecological diversity and natural widespread distributions across the Indo-Pacific region, we were interested to investigate the evolutionary history of this group and patterns of divergence that have contributed to their present-day distributions. In the present study, samples were collected from the South China Sea to study taxonomic and phylogenetic relationships, and divergence times. We investigated the taxonomic relationships among modern rabbitfish species, reconstructed their molecular phylogeny, and estimated divergence times among selected lineages based on a fragment of the mtDNA cytochrome oxidase I (COI) and sequences of the nuclear rhodopsin retrogene (RHO). Our results indicate that modern rabbitfish likely originated in the Indo-West Pacific during the late Eocene [37.4 million years ago (mya)], following which they diverged into three major clades during the Pliocene/Pleistocene. Subsequent diversification and origins of the majority of siganids may likely be associated with episodes of paleo-oceanographic events, including greenhouse and glaciation events (Eocene–Miocene) as well as major plate tectonic events (Pliocene–Pleistocene). Some modern siganid species may naturally hybridize with congeneric species where their geographical ranges overlap. A comprehensive taxonomic analysis revealed that the phylogeny of Siganidae (cladogenesis of Clades I, II, and III) is characterized by divergence in several external morphological characters and morphometric parameters. Our study demonstrates that morphological characteristics, geographical heterogeneity, and environmental change have contributed to siganids’ historical diversification.

Utility of characters evolving at diverse rates of evolution to resolve quartet trees with unequal branch lengths: analytical predictions of long-branch effects

BACKGROUND

The detection and avoidance of "long-branch effects" in phylogenetic inference represents a longstanding challenge for molecular phylogenetic investigations. A consequence of parallelism and convergence, long-branch effects arise in phylogenetic inference when there is unequal molecular divergence among lineages, and they can positively mislead inference based on parsimony especially, but also inference based on maximum likelihood and Bayesian approaches. Long-branch effects have been exhaustively examined by simulation studies that have compared the performance of different inference methods in specific model trees and branch length spaces.

RESULTS

In this paper, by generalizing the phylogenetic signal and noise analysis to quartets with uneven subtending branches, we quantify the utility of molecular characters for resolution of quartet phylogenies via parsimony. Our quantification incorporates contributions toward the correct tree from either signal or homoplasy (i.e. "the right result for either the right reason or the wrong reason"). We also characterize a highly conservative lower bound of utility that incorporates contributions to the correct tree only when they correspond to true, unobscured parsimony-informative sites (i.e. "the right result for the right reason"). We apply the generalized signal and noise analysis to classic quartet phylogenies in which long-branch effects can arise due to unequal rates of evolution or an asymmetrical topology. Application of the analysis leads to identification of branch length conditions in which inference will be inconsistent and reveals insights regarding how to improve sampling of molecular loci and taxa in order to correctly resolve phylogenies in which long-branch effects are hypothesized to exist.

CONCLUSIONS

The generalized signal and noise analysis provides analytical prediction of utility of characters evolving at diverse rates of evolution to resolve quartet phylogenies with unequal branch lengths. The analysis can be applied to identifying characters evolving at appropriate rates to resolve phylogenies in which long-branch effects are hypothesized to occur.

An integrated phylogenomic approach toward pinpointing the origin of mitochondria

Overwhelming evidence supports the endosymbiosis theory that mitochondria originated once from the Alphaproteobacteria. However, its exact position in the tree of life remains highly debated. This is because systematic errors, including biased taxonomic sampling, high evolutionary rates and sequence composition bias have long plagued the mitochondrial phylogenetics. In this study, we address this issue by 1) increasing the taxonomic representation of alphaproteobacterial genomes by sequencing 18 phylogenetically novel species. They include 5 Rickettsiales and 4 Rhodospirillales, two orders that have shown close affiliations with mitochondria previously, 2) using a set of 29 slowly evolving mitochondria-derived nuclear genes that are less biased than mitochondria-encoded genes as the alternative “well behaved” markers for phylogenetic analysis, 3) applying site heterogeneous mixture models that account for the sequence composition bias. With the integrated phylogenomic approach, we are able to for the first time place mitochondria unequivocally within the Rickettsiales order, as a sister clade to the Rickettsiaceae and Anaplasmataceae families, all subtended by the Holosporaceae family. Our results suggest that mitochondria most likely originated from a Rickettsiales endosymbiont already residing in the host, but not from the distantly related free-living Pelagibacter and Rhodospirillales.

Sequential steps of chromosomal differentiation in Atlantic surgeonfishes: evolutionary inferences

Surgeonfishes are a species-rich group and a major biomass on coral reefs. Three species are commonly found throughout South Atlantic, Acanthurus bahianus, A. chirurgus, and A. coeruleus. In this paper, we present the first cytogenetic data of these species, revealing a sequential chromosomal diversification. A. coeruleus was characterized by a relatively conserved karyotype evolved by pericentric inversions of some pairs (2n = 48, 2sm + 4st + 42a). In contrast, the karyotypes of A. bahianus (2n = 36) and A. chirurgus (2n = 34) were highly differentiated by the presence of six large metacentric pairs in A. bahianus (12m + 2sm + 4st + 18a) and A. chirurgus (12m + 2sm + 4st +1 6a) probably derived by chromosomal fusions that corroborate their closer relationship. A discernible in tandem fusion represents an autapomorphic character to A. chirurgus. In spite of macrostructure variation, single nucleolar organizer regions (NORs) on short arms of a subtelocentric pair and similar distribution of C-bands were observed in the three species. Overlapping of chromosomal data with molecular phylogeny indicated pericentric inversions which took place nearly at 19 Ma while centric fusions are as recent as 5 Ma. A physical mapping of coding and noncoding sequences in Acanthurus could clarify the role of additional rearrangements during their chromosomal evolution.

Protocruzia, a highly ambiguous ciliate (Protozoa; Ciliophora): very likely an ancestral form for Heterotrichea, Colpodea or Spirotrichea? With reevaluation of its evolutionary position based on multigene analyses

The ciliate genus Protocruzia belongs to one of the most ambiguous taxa considering its systematic position, possible as a member of the classes Heterotrichea, Spirotrichea or Karyorelictea, which is tentatively placed into Spirotrichea in Lynn's 2008 system. To test these hypotheses, multigene trees (Bayesian inference, evolutionary distance, maximum parsimony, and maximum likelihood) were constructed using the small subunit rRNA (SSU rRNA) gene, internal transcribed spacer 2 (ITS2) and a protein coding gene (histone H4). All analyses agree that: (1) four morphotypes of Protocruzia from different geographical origins group together and form a monophyletic clade, which cannot be assigned to any of the eleven described ciliate classes; (2) it is invariably positioned on an isolated branch separated from the class Spirotrichea suggesting that this clade should be clearly removed from Spirotrichea; (3) this leads us to hypothesize that this taxon may indeed represent a lineage on a class rank. Based on the fact that it is, both morphologically and in molecular features, closely related to heterotrichs, Colpodea and Oligohymenophorea, Protocruziida might be an ancestral form for the subphylum Intramacronucleata in the evolutionary line from the class Heterotrichea (subphylum Postciliodesmatophora) to higher taxa.

Ecological speciation in marine v. freshwater fishes

Absolute barriers to dispersal are not common in marine systems, and the prevalence of planktonic larvae in marine taxa provides potential for gene flow across large geographic distances. These observations raise the fundamental question in marine evolutionary biology as to whether geographic and oceanographic barriers alone can account for the high levels of species diversity observed in marine environments such as coral reefs, or whether marine speciation also operates in the presence of gene flow between diverging populations. In this respect, the ecological hypothesis of speciation, in which reproductive isolation results from divergent or disruptive natural selection, is of particular interest because it may operate in the presence of gene flow. Although important insights into the process of ecological speciation in aquatic environments have been provided by the study of freshwater fishes, comparatively little is known about the possibility of ecological speciation in marine teleosts. In this study, the evidence consistent with different aspects of the ecological hypothesis of speciation is evaluated in marine fishes. Molecular approaches have played a critical role in the development of speciation hypotheses in marine fishes, with a role of ecology suggested by the occurrence of sister clades separated by ecological factors, rapid cladogenesis or the persistence of genetically and ecologically differentiated species in the presence of gene flow. Yet, ecological speciation research in marine fishes is still largely at an exploratory stage. Cases where the major ingredients of ecological speciation, namely a source of natural divergent or disruptive selection, a mechanism of reproductive isolation and a link between the two have been explicitly documented are few. Even in these cases, specific predictions of the ecological hypothesis of speciation remain largely untested. Recent developments in the study of freshwater fishes illustrate the potential for molecular approaches to address specific questions related to the ecological hypothesis of speciation such as the nature of the genes underlying key ecological traits, the magnitude of their effect on phenotype and the mechanisms underlying their differential expression in different ecological contexts. The potential provided by molecular studies is fully realized when they are complemented with alternative (e.g. ecological, theoretical) approaches.

Phylogenetic relationships among families of Gadiformes (Teleostei, Paracanthopterygii) based on nuclear and mitochondrial data

Phylogenetic hypotheses among Gadiformes fishes at the suborder, family, and subfamily levels are controversial. To address this problem, we analyze nuclear and mitochondrial DNA (mtDNA) sequences for the most extensive taxonomic sampling compiled to date, representing all of the recognized families and subfamilies in the order (except the monotypic family Lyconidae). Our study sampled 117 species from 46 genera, comprising around 20% of the species described for the order (more than 60% of all genera in the order) and produced 2740 bp of DNA sequence data for each species. Our analysis was successful in confirming the monophyly of Gadiformes and most of the proposed families for the order, but alternative hypotheses of sister-group relationships among families were poorly resolved. Our results are consistent with dividing Gadiformes into 12 families in three suborders, Muraenolepidoidei, Macrouroidei, and Gadoidei. Muraenolepidoidei contains the single family Muraenolepididae. The suborder Macrouroidei includes at least three families: Macrouridae, Macruronidae and Steindachneriidae. Macrouridae is deeply divided into two well-supported subfamilies: Macrourinae and Bathygadinae, suggesting that Bathygadinae may be ranked at the family level. The suborder Gadoidei includes the families: Merlucciidae, Melanonidae, Euclichthyidae, Gadidae, Ranicipitidae, and Bregmacerotidae. Additionally, Trachyrincinae could be ranked at family level including two subfamilies: Trachyrincinae and Macrouroidinae within Gadoidei. Further taxonomic sampling and sequencing efforts are needed in order to corroborate these relationships.

Complete mitochondrial genome of the rabbitfish Siganus fuscescens (Perciformes, Siganidae)

We determined the complete nucleotide sequence of the mitochondrial genome for the rabbitfish Siganus fuscescens (Perciformes, Siganidae). This mitochondrial genome, consisting of 16,491 base pairs (bp), included 13 protein-coding genes, 2 ribosomal RNAs, 22 transfer RNAs, and a noncoding control region similar those found in other vertebrates; the gene order was identical to that of typical vertebrates. Most of the genes of S. fuscescens were encoded on the H-strand, while the ND6 and eight tRNA (Gln, Ala, Asn, Cys, Tyr, Ser [UCN], Glu, and Pro) genes were encoded on the L-strand. The reading frames of ATPase 8 and 6 and those of ND4L and ND4 overlapped by ten and seven nucleotides, respectively. All mitochondrial protein-coding genes began with an ATG start codon, except for CO1, which started with GTG. Open reading frames of S. fuscescens ended with TAA (ND1, CO1, ATPase 8, ND4L, ND5 and ND6), and the remainder had incomplete stop codons, either TA (ATPase 6 and CO3) or T (ND2, CO2, ND3, ND4, and Cytb). The origin of L-strand replication in S. fuscescens was located in a cluster of five tRNA genes (WANCY) and was 34 nucleotides in length. A major noncoding region between the tRNA-Pro and tRNA-Phe genes (828 bp) was considered to be the control region (D-loop). Within this sequence, we identified a conserved sequence block characteristic of this region. The rabbitfish was grouped with Siganus canaliculatus in most parsimony analyses, which showed 100% bootstrap support for their divergence. These findings are useful for inferring phylogenetic relationships and identification within the suborder Acanthuroidei.

Phylogenetic relationships and natural hybridization in rabbitfishes (Teleostei: Siganidae) inferred from mitochondrial and nuclear DNA analyses

Phylogenetic relationships of rabbitfishes (the family Siganidae), ecologically important components as primary consumers in coral reef communities, were studied using mitochondrial cytochrome b gene and nuclear ITS1 (internal transcribed spacer 1) sequence analyses. The analyses of 19 out of 22 species known in the Western Pacific region revealed that siganids are genetically clustered into three major clades, which are characterized by some morphological and ecological traits. Between closely related species, such as Siganus guttatus-S. lineatus and S. virgatus-S. doliatus, and also between two morphs recognized in S. corallinus, small but discernible genetic differentiation was found, implying that the components of each pair are incipient species. On the other hand, between some species, such as S. fuscescens-S. canaliculatus and S. unimaculatus-S.vulpinus, individuals of the components of each pair were found to construct a genetic mosaic, suggesting that the components are genetic color morphs within a single biological species, respectively. Moreover, evidence from morphological characters, mtDNA, and nuclear DNA gave an inconsistent picture of identity and relationships for several individuals. They were regarded as hybrids or individuals with hybrid origin. Such instances were observed not only between closely related species, such as S. guttatus-S. lineatus, S. virgatus-S. doliatus, and two morphs (incipient species) in S. corallinus, respectively, but also between distantly related ones, such as S. corallinus-S. puellus. In fact, more than half of the species examined (11/20, when treating the two morphs in S. corallinus as independent species) were involved in hybridization. These suggest that hybridization is much more prevalent in marine fishes than previously assumed, and may have some relevance to their diversification.

Deciphering ancient rapid radiations

A deeper phylogenetic understanding of ancient patterns of diversification would contribute to solving many problems in evolutionary biology, yet many of these phylogenies remain poorly resolved. Ancient rapid radiations pose a major challenge for phylogenetic analysis for two main reasons. First, the pattern to be deciphered, the order of divergence among lineages, tends to be supported by small amounts of data. Second, the time since divergence is large and, thus, the potential for misinterpreting phylogenetic information is great. Here, we review the underlying causes of difficulty in determining the branching patterns of diversification in ancient rapid radiations, and review novel data exploration tools that can facilitate understanding of these radiations.

Mating preferences, sexual selection and patterns of cladogenesis in ray-finned fishes

Evolutionary theory predicts that sexual selection may increase taxonomic diversity when emergent mating preferences result in reproductive isolation and therefore speciation. This theory has been invoked to explain patterns of diversity in ray-finned fishes (most notably in the cichlids), but the theory has not been tested comparatively in fish. Additionally, several other unrelated factors have been identified as promoters of cladogenesis, so it is unclear how important sexual selection might be in diversification. Using sister-clade analysis, I tested the relationship between the presence of sexually selected traits and taxonomic diversification in actinopterygiian fishes, a large clade that shows substantial diversity in mating preferences and related sexually selected traits. In all identified sister-families that differed with regard to the proportion of species manifesting sexually selected traits, sexual selection was correlated with increased diversification, and this association was significant across all sister clades (P=0.02). This suggests that sexual selection, when present, is a substantial driver of diversification in the ray-finned fishes, and lends further empirical support to the theoretical link between mating preferences and accelerated cladogenesis.

Patterns of lineage diversification in rabbitfishes

Fishes of the tropical Indo-Pacific family Siganidae comprise 28 species, characterized by their body proportions and their colour patterns. A mitochondrial phylogeny of 20 Siganidae species was produced to infer their evolutionary history. Three distinct, major clades were found, that also correspond to the early radiation of the family into three major ecological types: fusiform species that also live in schools on the inshore reef flats (S. canaliculatus, S. fuscescens, S. luridus, S. rivulatus, S. spinus, S. sutor); deep-bodied species including brightly coloured ones whose adults live in pairs on the reef front (S. corallinus, S. doliatus, S. puellus, S. punctatus, S. unimaculatus, S. virgatus, S. vulpinus), and species that live in small schools in mangroves, estuaries and estuarine lakes (S. guttatus, S. javus, S. lineatus, S. randalli, S. vermiculatus); and a third clade including a cosmopolitan species, S. argenteus, the only species of the family known to possess a pelagic, prejuvenile stage and S. woodlandi, a recently described species from New Caledonia and morphologically close to S. argenteus. The partition of the genus into two sub-genera, Lo (erected for S. unimaculatus, S. vulpinus and three related species possessing a tubular snout) and Siganus (all the other species), had no phylogenetic rationale. The present results indicate that the tubular snout, which apparently results from ecological specialization, is a recent acquisition within the deep-body clade. The Western Indian Ocean endemic S. sutor appeared as the sister-species of the Red Sea endemic S. rivulatus within a well-supported subclade that also included S. canaliculatus and S. fuscescens. S. spinus did not appear as sister-species to S. luridus. S. lineatus haplotypes formed a paraphyletic group with S. guttatus, and an early isolation of Maldives S. lineatus was suggested. Unexpectedly, S. randalli did not appear as the sister-species of S. vermiculatus, but its haplotypes instead were embedded within the West Pacific S. lineatus haplogroup, suggesting recent introgression. Among currently-recognized sister-species with parapatric distribution, S. doliatus and S. virgatus haplotypes formed a single, unresolved haplogroup, as did S. unimaculatus and S. vulpinus. The occurrence of two distinct clades within S. fuscescens was confirmed.

Contrasting patterns of genetic structure in two species of the coral trout Plectropomus (Serranidae) from east and west Australia: Introgressive hybridisation or ancestral polymorphisms

Inter-specific genetic relationships among regional populations of two species of grouper (Plectropomus maculatus and Plectropomus leopardus) were examined using mitochondrial and nuclear markers. mtDNA revealed contrasting regional inter-specific patterns whilst nuclear markers revealed contrasting patterns among markers, irrespective of region. In eastern Australia (EA) the species form a single mtDNA lineage, but the two species are reciprocally monophyletic in Western Australia (WA). This supports previous evidence for hybridisation between these species on the east coast. WA P. leopardus forms a sister relationship with the EA P. leopardus-maculatus clade while WA P. maculatus is more basal and sister to the P. leopardus lineages, indicating mtDNA does not suffer from incomplete lineage sorting for these species. In contrast, one of three nuclear markers (locus 7-90TG) differentiated the species into two reciprocally monophyletic clades, with no evidence of hybridisation or ancestral polymorphism. The remaining two nuclear markers (2-22 and ETS-2) did not separate these two species, while distinguishing other plectropomid species, suggesting incomplete lineage sorting at these nuclear loci. These results together with coalescence analyses suggest that P. leopardus females have hybridised historically with P. maculatus males and that P. maculatus mitochondria were displaced through introgressive hybridisation and fixation in the P. maculatus founder population on the Great Barrier Reef. The contrasting regional patterns of mtDNA structure may be attributed to Quaternary sea-level changes and shelf width differences driving different reef configurations on each coast. These reef configurations have provided opportunities for local scale interaction and reproduction among species on the narrower EA continental shelves, but not on the broader WA continental shelves.

Untangling Long Branches: Identifying Conflicting Phylogenetic Signals Using Spectral Analysis, Neighbor-Net, and Consensus Networks

Long-branch attraction is a well-known source of systematic error that can mislead phylogenetic methods; it is frequently invoked post hoc, upon recovering a different tree from the one expected based on prior evidence. We demonstrate that methods that do not force the data onto a single tree, such as spectral analysis, Neighbor-Net, and consensus networks, can be used to detect conflicting signals within the data, including those caused by long-branch attraction. We illustrate this approach using a set of taxa from three unambiguously monophyletic families within the Pelecaniformes: the darters, the cormorants and shags, and the gannets and boobies. These three families are universally acknowledged as forming a monophyletic group, but the relationship between the families remains contentious. Using sequence data from three mitochondrial genes (12S, ATPase 6, and ATPase 8) we demonstrate that the relationship between these three families is difficult to resolve because they are separated by a short internal branch and there are conflicting signals due to long-branch attraction, which are confounded with nonhomogeneous sequence evolution across the different genes. Spectral analysis, Neighbor-Net, and consensus networks reveal conflicting signals regarding the placement of one of the darters, with support found for darter monophyly, but also support for a conflicting grouping with the outgroup, pelicans. Furthermore, parsimony and maximum-likelihood analyses produced different trees, with one of the two most parsimonious trees not supporting the monophyly of the darters. Monte Carlo simulations, however, were not sensitive enough to reveal long-branch attraction unless the branches are longer than those actually observed. These results indicate that spectral analysis, Neighbor-Net, and consensus networks offer a powerful approach to detecting and understanding the source of conflicting signals within phylogenetic data.

Wave energy and swimming performance shape coral reef fish assemblages

Physical factors often have an overriding influence on the distribution patterns of organisms, and can ultimately shape the long-term structure of communities. Although distribution patterns in sessile marine organisms have frequently been attributed to functional characteristics interacting with wave-induced water motion, similar evidence for mobile organisms is lacking. Links between fin morphology and swimming performance were examined in three diverse coral reef fish families from two major evolutionary lineages. Among-habitat variation in morphology and performance was directly compared with quantitative values of wave-induced water motion from seven coral reef habitats of different depth and wave exposure on the Great Barrier Reef. Fin morphology was strongly correlated with both field and experimental swimming speeds in all three families. The range of observed swimming speeds coincided closely with the magnitude of water velocities commonly found on coral reefs. Distribution patterns in all three families displayed highly congruent relationships between fin morphology and wave-induced water motion. Our findings indicate a general functional relationship between fin morphology and swimming performance in labriform-swimming fishes, and provide quantitative evidence that wave energy may directly influence the assemblage structure of coral reef fishes through interactions with morphology and swimming performance.

Should we be worried about long-branch attraction in real data sets? Investigations using metazoan 18S rDNA

Although long-branch attraction (LBA) is frequently cited as the cause of anomalous phylogenetic groupings, few examples of LBA involving real sequence data are known. We have found several cases of probable LBA by analyzing subsamples from an alignment of 18S rDNA sequences for 133 metazoans. In one example, maximum parsimony analysis of sequences from two rotifers, a ctenophore, and a polychaete annelid resulted in strong support for a tree grouping two "long-branch taxa" (a rotifer and the ctenophore). Maximum-likelihood analysis of the same sequences yielded strong support for a more biologically reasonable "rotifer monophyly" tree. Attempts to break up long branches for problematic subsamples through increased taxon sampling reduced, but did not eliminate, LBA problems. Exhaustive analyses of all quartets for a subset of 50 sequences were performed in order to compare the performance of maximum likelihood, equal-weights parsimony, and two additional variants of parsimony; these methods do differ substantially in their rates of failure to recover trees consistent with well established, but highly unresolved phylogenies. Power analyses using simulations suggest that some incorrect inferences by maximum parsimony are due to statistical inconsistency and that when estimates of central branch lengths for certain quartets are very low, maximum-likelihood analyses have difficulty recovering accepted phylogenies even with large amounts of data. These examples demonstrate that LBA problems can occur in real data sets, and they provide an opportunity to investigate causes of incorrect inferences.

Patterns of lineage diversification in the genus Naso (Acanthuridae)

The evolutionary history of the reef fish genus Naso (F. Acanthuridae) was examined using a complete species-level molecular phylogeny of all recognized (19) species based on three loci (one nuclear ETS2 and two mitochondrial 16S, cyt b). This study demonstrates that distinct foraging modes and specialized body shapes arose independently at different times in the evolutionary history of the genus. Members of the subgenus Axinurus, characterized by a scombriform morphology, caudal fin structure and pelagic foraging mode, were consistently placed basal to the remaining Naso species, suggesting that pelagic foraging is plesiomorphic and benthic foraging derived in this genus. We used a genus-level phylogeny (nuclear marker, ETS2), which included several taxa from all other acanthurid genera, to obtain a range of age estimates for the most recent common ancestor of the genus Naso. These age estimates (range of 52-43.3 MY) were then used to estimate divergence times (by nonparametric rate smoothing method) of the node giving rise to extant Naso species using the combined sequence data (from all loci). The reconstruction of the pattern of divergence of extant species indicates two sequences of events. The basal species characterized by pelagic foraging modes arose during the Eocene and Oligocene. Most of the remaining Naso species, including those characterized by benthic foraging, arose over a period of 20 MY during the Miocene. Diversification during this period was associated with major plate tectonic and glaciation events, resulting in changes in sea level, ocean temperature and productivity regimes. Regardless of the foraging mode exhibited, all species of Naso have a caudal propulsive unit similar to that observed in pelagic scombriform fishes, a legacy of the basal position of the subgenus Axinurus in the phylogeny of the genus.