Previous Morphological Hypotheses Research Articles

Revision and cladistic analysis of Psalistops Simon, 1889, Trichopelma Simon, 1888 and Cyrtogrammomma Pocock, 1895 (Araneae: Theraphosidae) based on a cladistic analysis of relationships of Theraphosidae, Barychelidae and Paratropididae

The genera Psalistops Simon, 1889, Trichopelma, Simon, 1888 and Cyrtogrammomma Pocock, 1895 are revised and included in cladistics analyses including almost all species of these genera. In order to test previous morphological hypotheses on the relationships of Barychelidae, Paratropididae and Theraphosidae and because of the controversial taxonomic position of Psalistops and Trichopelma, a set of terminal taxa representing all subfamilies of Paratropididae (Paratropidinae, Glabropelmatinae), Barychelidae (Barychelinae, Sasoninae, Trichopelmatinae) and most theraphosid subfamilies were included, as well as a diplurid, a nemesiid, and a pycnothelid, the later used to root the cladogram. The matrix with 66 terminal taxa, 2 continuous and 93 discrete characters was analysed with TNT 1.5. We found that Trichopelmatinae is not a monophyletic group, and Psalistops is transferred to Theraphosidae, as well as the barychelid genus Cyrtogrammomma and the paratropidid genus Melloina Brignoli. Cyrtogrammomma was retrieved as the sister group of Trichopelma, and Melloina as the sister group of Holothele Karsch. Psalistops was retrieved as the sister group of Reichlingia Rudloff, and the clade with these two genera is the most basal in Theraphosidae. Barychelidae was found to be monophyletic and the sister group of Theraphosidae. Paratropididae was retrieved as the sister group of Barychelidae + Theraphosidae. The relationship and possible synapomorphies of the three families are herein discussed. This is the first time since Raven (1985) that representatives of all barychelid (Barychelinae, Sasoninae, Trichopelmatinae), paratropidid (Paratropidinae, Glabropelmatinae) and most theraphosid subfamilies have been included in a morphological cladistic analysis. Psalistops comprises two species, P. melanopygius Simon, 1889 (type species) and P. colombianus sp. nov. Psalistops montigena Simon, 1889, P. tigrinus Simon, 1889 and P. zonatus Simon, 1889 are synonymized with P. melanopygius Simon, 1889. Psalistops fulvus Bryant, 1948, P. hispaniolensis Wunderlich, 1988 (fossil), P. maculosus Bryant, 1948, P. venadensis Valerio, 1986 and P. steini (Simon, 1889) are transferred to Trichopelma. Psalistops gasci Maréchal, 1996 is transferred to Hapalopus Ausserer (Theraphosidae); P. opifex (Simon, 1889) and P. solitarius (Simon, 1889) are transferred to Schismatothele Karsch, 1879 (Theraphosidae). Schismatothele solitarius (Simon, 1889) n. comb. is synonymized with Schismatothele lineata Karsch, 1879, n. syn. Psalistops nigrifemuratus Mello-Leitão, 1939 is probably a nemesiid or pycnothelid, and herein considered as nomen dubium in Pycnothelidae. Trichopelma comprises 22 species: Trichopelma nitidum Simon, 1888 (type species), T. coenobita (Simon, 1889), T. steini (Simon, 1889), T. affine (Simon, 1892), T. cubanum (Simon, 1903), T. maculatum (Banks, 1906), T. zebra (Petrunkevitch, 1925), T. banksia Özdikmen & Demir, 2012, T. insulanum (Petrunkevitch, 1926), T. fulvus (Bryant, 1948) n. comb., T. laselva Valerio, 1986, T. venadensis (Valerio, 1986) n. comb., T. huffi sp. nov., T. gabrieli sp. nov., T. tostoi sp. nov., T. goloboffi sp. nov., T. juventud sp. nov., T. laurae sp. nov., T.bimini sp. nov., T. loui sp. nov., T. platnicki sp. nov., and T. hispaniolensis Wunderlich, 1988 n. comb. (fossil). Trichopelma maculosus (Bryant, 1948) n. comb. is synonymized with P. fulvus Bryant, 1948; T. corozalis (Petrunkevitch, 1929) is synonymized with T. insulanum (Petrunkevitch, 1926). Trichopelma astutum Simon, 1889 is transferred to Euthycaelus Simon, 1889, and T. maddeni Esposito & Agnarsson, 2014 to Holothele Karsch, 1879 (Theraphosidae). Trichopelma flavicomum Simon, 1891 is transferred to Neodiplothele (Barychelidae, Sasoninae). The species T. illetabile Simon, 1888, T. spinosum (Franganillo, 1926), T. scopulatum (Fischel, 1927) and T. eucubanum Özdikmen & Demir, 2012 are considered as nomina dubia. Cyrtogrammomma comprises two species: C. monticola Pocock, 1895 (type species) and C. raveni sp. nov.

Juvenile morphology: A clue to the origins of the most mysterious of mysticetes?

The origin of the pygmy right whale (Caperea marginata) has long been one of the most vexing conundrums of marine mammal evolution. The extremely disparate skeletal structure of Caperea and a patchy fossil record have left morphology and molecules at odds: whereas most morphological analyses ally Caperea with right whales (Balaenidae), most molecular studies instead suggest a close relationship with rorquals (Balaenopteridae) and grey whales (Eschrichtiidae). The morphological evidence supporting a Caperea-balaenid clade consists of several shared features of the skull and mandible, as traditionally observed in adult individuals. Here, we show that at least two of these features, the ascending process of the maxilla and the coronoid process, arise from substantially different precursors early during ontogeny and therefore likely do not represent genuine synapomorphies. Both of these juvenile morphologies have adult counterparts in the fossil record, thus indicating that the ontogenetic variation in the living species may be a genuine reflection of differing ancestral states. This new evidence contradicts previous morphological hypotheses on the origins of Caperea and may help to reconcile morphological and molecular evidence.

AFLPs support deep relationships among darters (Percidae: Etheostomatinae) consistent with morphological hypotheses

Recent attention has focused on the efficacy of amplified fragment length polymorphisms (AFLPs) for resolving deep evolutionary relationships. Here we show that AFLPs provide resolution of deep relationships within the family Percidae that are more consistent with previous morphological hypotheses than are relationships proposed by previous molecular analyses. Despite in silico predictions, we were able to resolve relatively ancient divergences, estimated at >25 MA. We show that the most distantly related species share the fewest fragments, but suggest that large data sets and extensive taxon sampling are sufficient to overcome this obstacle of the AFLP technique for deep divergences. We compare genetic distances estimated from mitochondrial DNA with those from AFLPs and contrast traditional PAUP(*) Nei-Li AFLP genetic distances with a recently proposed method utilizing the Dice equation with constraining nucleotides.

Monophyly and interrelationships of Snook and Barramundi (Centropomidae sensu Greenwood) and five new markers for fish phylogenetics

Centropomidae as defined by Greenwood (1976) is composed of three genera: Centropomus, Lates, and Psammoperca. But composition and monophyly of this family have been challenged in subsequent morphological studies. In some classifications, Ambassis, Siniperca and Glaucosoma were added to the Centropomidae. In other studies, Lates+Psammoperca were excluded, restricting the family to Centropomus. Recent analyses of DNA sequences did not solve the controversy, mainly due to limited taxonomic or character sampling. The present study is based on DNA sequence data from thirteen genes (one mitochondrial and twelve nuclear markers) for 57taxa, representative of all relevant species. Five of the nuclear markers are new for fish phylogenetic studies. The monophyly of Centropomidae sensu Greenwood was supported by both maximum likelihood and Bayesian analyses of a concatenated data set (12,888bp aligned). No support was found for previous morphological hypotheses suggesting that ambassids are closely allied to the Centropomidae. Putative affinities between centropomids and Glaucosoma, Niphon, or Siniperca were strongly rejected by topology tests. In agreement with previous molecular hypotheses, our results place Centropomidae within a group of fishes that includes carangoids (e.g., jacks, remoras, dolphinfish, roosterfish, and cobia), flatfishes, barracudas, archerfishes, billfishes, moonfish, and threadfins. The phylogeny for the extant Centropomidae is ((Lates, Psammoperca), Centropomus).

Molecular phylogeny of acariform mites (Acari, Arachnida): Strong conflict between phylogenetic signal and long-branch attraction artifacts

Acariformes (one of the two main lineages of Acari) represent an exceptionally diverse group of Arachnida. We performed first comprehensive phylogenetic analysis of Acariformes using sequence data from the nuclear small subunit rRNA gene (18S rDNA) and the mitochondrial cytochrome c oxidase subunit I (COI, amino acids). Our analyses confirm the monophyly of Acariformes and recognize two orders within Acariformes: Sarcoptiformes, consisting of Endeostigmata and Oribatida+Astigmata, and Trombidiformes. The data revealed the origin of Astigmata within Oribatida with the desmonomatan superfamily Crotonioidea as the source of astigmatan radiation and the sexual family Hermanniidae as the sister group, which generally supports previous morphological hypotheses. These results were found despite the strong conflict between long-branch attraction (LBA) artifacts and phylogenetic signal. It is likely that the conflict resulted from differences in the substitution rates among acariform lineages, especially comparing slowly evolving Oribatida with rapidly evolving Astigmata. The use of likelihood methods considered more resistant to LBA only slightly decreased the chance of falling into the LBA trap; the probability of recovering the origin of Astigmata within Desmonomata differs only by about 10% from that of having the long branched Astigmata and Trombidiformes either connected directly or shifted to deep parts of the tree due to outgroup attraction. Molecular dating using the rate-smoothing method PATHd8 shows that Acariformes originated c. 435 MYA and were probably among the earliest arthropods invading terrestrial habitats in late Silurian or the Lower Devonian, when the first vascular plants are thought to have arisen. Our analyses did not support the monophyly of Acari because we recovered clades Acariformes-Solifugae and Parasitiformes-Pseudoscorpionida. However, a formal revision of arachnid classification that would reflect these results must await future analyses.

Toward reconstructing the evolution of advanced moths and butterflies (Lepidoptera: Ditrysia): an initial molecular study

BackgroundIn the mega-diverse insect order Lepidoptera (butterflies and moths; 165,000 described species), deeper relationships are little understood within the clade Ditrysia, to which 98% of the species belong. To begin addressing this problem, we tested the ability of five protein-coding nuclear genes (6.7 kb total), and character subsets therein, to resolve relationships among 123 species representing 27 (of 33) superfamilies and 55 (of 100) families of Ditrysia under maximum likelihood analysis.ResultsOur trees show broad concordance with previous morphological hypotheses of ditrysian phylogeny, although most relationships among superfamilies are weakly supported. There are also notable surprises, such as a consistently closer relationship of Pyraloidea than of butterflies to most Macrolepidoptera. Monophyly is significantly rejected by one or more character sets for the putative clades Macrolepidoptera as currently defined (P < 0.05) and Macrolepidoptera excluding Noctuoidea and Bombycoidea sensu lato (P ≤ 0.005), and nearly so for the superfamily Drepanoidea as currently defined (P < 0.08). Superfamilies are typically recovered or nearly so, but usually without strong support. Relationships within superfamilies and families, however, are often robustly resolved. We provide some of the first strong molecular evidence on deeper splits within Pyraloidea, Tortricoidea, Geometroidea, Noctuoidea and others.Separate analyses of mostly synonymous versus non-synonymous character sets revealed notable differences (though not strong conflict), including a marked influence of compositional heterogeneity on apparent signal in the third codon position (nt3). As available model partitioning methods cannot correct for this variation, we assessed overall phylogeny resolution through separate examination of trees from each character set. Exploration of "tree space" with GARLI, using grid computing, showed that hundreds of searches are typically needed to find the best-feasible phylogeny estimate for these data.ConclusionOur results (a) corroborate the broad outlines of the current working phylogenetic hypothesis for Ditrysia, (b) demonstrate that some prominent features of that hypothesis, including the position of the butterflies, need revision, and (c) resolve the majority of family and subfamily relationships within superfamilies as thus far sampled. Much further gene and taxon sampling will be needed, however, to strongly resolve individual deeper nodes.

On the molecular phylogeny of sponges (Porifera)*

In the past decade molecular genetic markers have been introduced for research on the evolution and systematics of sponges. Historically, sponges have been difficult to classify due to lack of complex characters with the result that hypothesised phylogenetic relationships for various sponge taxa have changed rapidly over the past few years. Here, we summarize the current status of systematic and phylogenetic hypotheses proposed for sponges. We discuss the relationships among the three classes, Calcarea (calcareous sponges), Hexactinellida (glass sponges) and Demospongiae, as well as those among the members within each class. While molecular phylogenies of hexactinellids corroborate previous morphological hypotheses, phylogenetic hypotheses based on rDNA sequence analyses in Calcarea largely conflict with the previous, typological classifications. Many demosponge taxa have only recently been shown to be para– or polyphyletic and thus their new clades and other phylogenetic relationships have only now begun to be tested using current molecular approaches.

Phylogenetic incongruence between nuclear and mitochondrial markers in the Asian colobines and the evolution of the langurs and leaf monkeys

Evidence of incongruence between mitochondrial and nuclear gene trees is now becoming documented with increasing frequency. Among the Old World monkeys, this discordance has been well demonstrated in the Cercopithecinae, but has not yet been investigated in the Colobinae. The mitochondrial relationships between the colobine genera have recently been clarified and cluster Presbytis and Trachypithecus as sister taxa to the exclusion of Semnopithecus. This is incongruent with previous morphological hypotheses that suggest the latter two are sister taxa, and perhaps even congeneric. In addition to analyzing a previously published 10,896 bp mitochondrial dataset, we sequenced and analyzed a 4297 bp fragment of the X-chromosome in order to test the competing mitochondrial and morphological phylogenetic hypotheses. The results from the mitochondrial dataset again support a Presbytis + Trachypithecus group while the X-chromosomal dataset supported a Semnopithecus + Trachypithecus group. A Shimodaira–Hasegawa test performed on both datasets indicates that the mitochondrial and X-chromosomal trees are significantly better at explaining their respective datasets than alternative topologies ( p < 0.05). We suggest that differential lineage sorting or ancient hybridization may be the cause of this strong discordance between the mitochondrial and X-chromosomal markers in these taxa.

Molecular phylogeny of the stromateoid fishes (Teleostei: Perciformes) inferred from mitochondrial DNA sequences and compared with morphology-based hypotheses

The phylogenetic relationships among 21 species of stromateoid fishes, representing five families and 13 genera, were reconstructed using 3263 bp of mitochondrial DNA sequences, including the posterior half of the 16S rRNA and entire COI and Cytb genes. The resultant molecular phylogenies were compared with previous phylogenetic hypotheses inferred from morphological characters. Molecular phylogenetic trees were constructed using the maximum parsimony, maximum likelihood, and Bayesian methods. All three methods resulted in well-resolved trees with most nodes being supported by moderate to high support values. In contrast to previous morphological analyses, which resulted in non-monophyly of Centrolophidae, all three methods utilized for the present molecular analyses supported the monophyly of Centrolophidae, as well as the reciprocal monophyly of the other stromateoid families, previous morphological hypotheses being rejected by the Templeton and Shimodaira–Hasegawa tests. In addition, the three methods indicated a sister-group relationship between Ariommatidae and Nomeidae. The position of Tetragonuridae was, however, incongruent between the MP method and the ML and Bayesian methods, being placed in the most basal position of Stromateoidei in the former, but occupying a sister relationship to Stromateidae in the latter. Comparison of the molecular phylogenies to previous morphological hypotheses suggested that evolutionary changes in morphological characters have not occurred equally among the stromateoid lineages, the evolution of the centrolophids not having been accompanied by appreciable morphological changes, whereas other stromateoids have undergone considerable morphological changes during their evolutionary history. The molecular phylogenies also shed some light on the evolutionary pattern of the pharyngeal sac, two of the four types of sac corresponding to two main lineages of Stromateoidei. Some taxonomic implications were also discussed.

A molecular analysis of the interrelationships of tetraodontiform fishes (Acanthomorpha: Tetraodontiformes)

Tetraodontiform fishes (e.g., triggerfishes, boxfishes, pufferfishes, and giant ocean sunfishes) have long been recognized as a monophyletic group. Morphological analyses have resulted in conflicting hypotheses of relationships among the tetraodontiform families. Molecular data from the single-copy nuclear gene RAG1 and from two mitochondrial ribosomal genes, 12S and 16S, were used to test these morphology-based hypotheses. Total evidence (RAG1 + 12S + 16S), RAG1-only, and mitochondrial-only analyses were performed using both maximum parsimony and Bayesian criteria. Total evidence and RAG1-only analyses recover a monophyletic Tetraodontiformes. However, the relationships recovered within the order differ, and none completely conform to previous hypotheses. Analysis of mitochondrial data alone fails to recover a monophyletic Tetraodontiformes and therefore does not support any of the morphology-based topologies. The RAG1 data appear to give the best estimate of tetraodontiform phylogeny, resulting in many strongly supported nodes and showing a high degree of congruence between both parsimony and Bayesian analyses. All analyses recover every tetraodontiform family for which more than one representative is included as a strongly supported monophyletic group. Balistidae and Monacanthidae are recovered as sister groups with robust support in every analysis, and all analyses except the Bayesian analyses of the mitochondrial data alone recover a strongly supported sister-group relationship between Tetraodontidae and Diodontidae. Many of the intrafamilial relationships recovered from the molecular data presented here corroborate previous morphological hypotheses.

Phylogeny and behaviour of the Gollumiellinae, a new subfamily of the ant‐parasitic Eucharitidae (Hymenoptera: Chalcidoidea)

Abstract. Gollumiellinae is proposed as a new subfamily for the Indo‐Pacific genera Gollumiella Hedqvist and Anorasema Bouc̆ek based on analyses of three ribosomal transcript gene regions (28S‐D2 and ‐D3, and 18S‐E23; 1262 aligned base pairs) sequenced for twenty‐eight genera and fifty‐four species of Eucharitidae, and twelve genera and nineteen species of Pteromalidae (Pteromalinae) and Perilampidae (Chrysolampinae and Perilampinae). Gollumiella and Anorasema have been treated as either a monophyletic or paraphyletic group within the Eucharitini (Hymenoptera: Eucharitidae). The monophyly of the Eucharitidae and a sister‐group relationship between Gollumiellinae and Oraseminae + Eucharitinae are supported strongly in parsimony and Bayesian analyses. The molecular phylogeny contradicts previous morphological hypotheses, in which Gollumiella and Anorasema are within Eucharitini. The strength of the molecular hypothesis is explored through evaluations of data alignments that are eye optimized, clustal‐x aligned, eye optimized but with gaps coded as a fifth base, and eye optimized and combined with morphological data. The oviposition behaviour and host associations of G. longipetiolata on tree ferns (Cyathea latebrosa, Cyatheaceae), and the morphology of the planidium and pupa are newly described. Eggs are deposited vertically, with the base anchored into the leaf or petiolar surface. Unlike other Eucharitidae, the eggs are not stalked, but rather tipped with a secretion that may act as an attractant for their ant host, Paratrechina sp. (Formicidae: Formicinae). Various morphological character state optimizations and their implications for convergent morphology, behaviour and host associations are discussed. All results using gene regions treated separately or combined with the morphological data reach the same conclusion: Anorasema + Gollumiella form the sister group of Oraseminae + Eucharitinae, and thus deserve subfamily status. This suggests that very distinct traits such as the fusion of the pronotum and prepectus in adults and the fusion of the first two tergites of the planidia are convergent apomorphies. Molecular data, when strongly supported, can provide new information to unravel convergent from synapomorphic changes, resulting in more robust hypotheses of relationship.

First molecular evidence for reassessing phylogenetic affinities between genets (Genetta) and the enigmatic genet‐like taxa Osbornictis, Poiana and Prionodon (Carnivora, Viverridae)

Gaubert, P., Tranier, M., Delmas, A.‐S., Colyn, M. &amp; Veron, G. (2004). First molecular evidence for reassessing phylogenetic affinities between genets (Genetta) and the enigmatic genet‐like taxa Osbornictis, Poiana and Prionodon (Carnivora, Viverridae). —Zoologica Scripta, 33, 117–129.The subfamily Viverrinae is a composite group of carnivores comprising the large and plantigrade terrestrial civets (Civettictis, Viverricula and Viverra) and the slender and generally more arboreal genets and genet‐like taxa (Genetta, Prionodon, Poiana, Osbornictis), both having Asiatic and African representatives. The problematic phylogenetic relationships between genets and genet‐like taxa are addressed for the first time from a molecular perspective through complete cytochrome b gene sequences. We used a large taxonomic sample set including some very rare and crucial species such as Osbornictis piscivora, Poiana richardsonii (museum specimen material) and Genetta johnstoni. The results from parsimony, distance and maximum likelihood analyses do not support the monophyly of the Viverrinae and contradict previous morphological hypotheses. The Asiatic linsangs (Prionodon spp.) are excluded from the Viverrinae and represent either a basal Feliformia or Viverridae. The other genet‐like taxa constitute a strongly supported monophyletic African group, in which the African linsang (represented by Poiana richardsonii) is a sister group to the genets. The aquatic genet Osbornictis piscivora is included within the latter clade, and the genus Osbornictis should be considered a junior synonym of Genetta. African and Asiatic terrestrial civets are monophyletic, but their phylogenetic affinities with the genet‐like clade are inconclusive using our data set. On the basis of our molecular results, morphological convergences and adaptations to peculiar habitats and ways of life within genets and genet‐like taxa are discussed.

Phylogenetic relationships of Pestalotiopsis and allied genera inferred from ribosomal DNA sequences and morphological characters

The taxonomy of the coelomycetous fungus Pestalotiopsis and other closely related genera based on morphological characters has been equivocal. To gain insight in the phylogenetic relationships of Pestalotiopsis and its allies, part of the large subunit (28S) ribosomal DNA region was examined and compared with existing morphological information. Phylogenetic analyses were conducted using parsimony, distance, and likelihood criteria. Results of the analyses showed that Bartalinia, Pestalotiopsis, Seimatosporium, and Seiridium represent distinct monophyletic groups with high bootstrap support. However, Truncatella species are paraphyletic with Bartalinia, sharing a common ancestor. Pestalotia species sequenced clustered together with Pestalotiopsis. These genera should be recognized as distinct natural groups except for Monochaetia and Discosia, which need to be further resolved. Tree topologies are generally in concordance with previous morphological hypotheses, most notably the placement of all Pestalotia species, except the type P. pezizoides, in Pestalotiopsis. Well-supported clades corresponding to groupings based on conidial morphology were resolved and the relative importance of morphological characters for generic delimitation is discussed. Molecular data also provide further evidence to support the association of these coelomycetes with the Amphisphaeriaceae.

PHYLOGENETIC POSITION OF THE FRESHWATER ANOMURAN FAMILY AEGLIDAE

Abstract We sequenced approximately 2,000 nucleotides of the 18S ribosomal DNA gene to test previous morphological hypotheses concerning family and superfamily relationships within the Anomura. Twelve new sequences from the superfamilies Galatheoidea, Paguroidea, Hippoidea (all Anomura), and Callianassoidea (Thalassinidea) were generated, and these were combined with three previously published sequences from GenBank to estimate phylogenetic relationships among these taxa. Our results show a clear separation of the Aeglidae from the other galatheoid families, which form a sister group with the Paguroidea. Within the Galatheoidea, chirostylids and porcellanids are sister groups. Hippoidea was revealed as the most basal taxon within the anomurans.

Evaluation of Relationships within the Endemic Hawaiian Platynini (Coleoptera: Carabidae) Based on Molecular and Morphological Evidence

Relationships among 69 species of Hawaiian Platynini, a monophyletic beetle radiation, was investigated based on evidence from five data partitions, comprising mitochondrial and nuclear DNA sequences (cytochrome oxidase II, 624 bp; cytochrome b, 783 bp; 28S rDNA, 668 bp; wingless; 441 bp) and morphology (206 features of external and internal anatomy). Results from individual and combined data analyses generally support the monophyly of three putative divisions within Platynini in Hawaii: Division 0 (Colpocaccus species group), Division 1 (Blackburnia species group), and Division 2 (Metromenus species group). However, relationships within and among these three divisions differ from previous morphological hypotheses. An extensive series of sensitivity analyses was performed to assess robustness of recovered clades under a variety of weighted parsimony conditions. Sensitivity analyses support the monophyly of Divisions 0 and 1, but were equivocal for the monophyly of Division 2. A phylogeny based on combined data suggests at least four independent losses/reductions of platynine flight wings. The combined analysis provides corroboration for biogeographic hypotheses, including (1) colonization of Kauai by Hawaiian Platynini with subsequent dispersal and colonization along the island chain from Oahu to Maui Nui to Hawaii Island and (2) incongruent area relationships among Eastern Molokai, West Maui, and Haleakala for two species triplets.

The Phylogenetic Relationships of the Suborder Acanthuroidei (Teleostei: Perciformes) Based on Molecular and Morphological Evidence

Fragments of 12S and 16S mitochondrial DNA genes were sequenced for 14 acanthuroid taxa (representing all six families) and seven outgroup taxa. The combined data set contained 1399 bp after removal of all ambiguously aligned positions. Examination of site saturation indicated that loop regions of both genes are saturated for transitions, which led to a weighted parsimony analysis of the data set. The resulting tree topology generally agreed with previous morphological hypotheses, most notably placing the Luvaridae within the Acanthuroidei, but it also differed in several areas. The putative sister group of Acanthuroidei,Drepane,was recovered within the suborder, and the sister group of the family Acanthuridae,Zanclus,was likewise recovered within the family. Morphological characters were included to produce a combined data set of 1585 characters for 14 acanthuroid taxa and a single outgroup taxon. An analysis of the same 15 taxa was performed with only the DNA data for comparison. The total-evidence analysis supports the monophyly of the Acanthuridae. A parametric bootstrap suggests the possibility that the paraphyly of Acanthuridae indicated by the molecular analyses is the result of long-branch attraction. The disagreement between molecular and morphological data on the relationships of the basal acanthuroids and its putative sister taxon is unresolved.

Multilocus phylogeny of cichlid fishes (Pisces: Perciformes): evolutionary comparison of microsatellite and single-copy nuclear loci.

Among vertebrates, cichlid fishes are the paradigmatic example of adaptive radiation and ecological specialization. In turn, molecular genetic studies of cichlids have focused primarily on more recently diverged groups. Here, we present an evolutionary hypothesis of the major lineages of cichlid fishes based on DNA sequence data from two nuclear loci. One marker, Tmo-4C4, is a single-copy locus containing a region of amino acid similarity to the muscle protein TITIN. Flanking sequence from a second, microsatellite, locus Tmo-M27, shows similarity to mammalian RAS guanine nucleotide-releasing factor. We compare and combine data from these loci to evaluate phylogenetic performance. In separate and combined analyses, the sequence data support and clarify previous morphological hypotheses of cichlid major-group relationships. Indian and Malagasy cichlids form a basal, paraphyletic group. Neotropical cichlids are the sister clade to an African assemblage composed of the paraphyletic west and Pan-African lineages and a group of east African rift lake taxa. We use a consensus phylogeny of the Cichlidae to trace evolutionary changes in the microsatellite repeat motif at Tmo-M27. Analysis reveals that the repeat region was nearly lost in the ancestor to cichlids and then amplified extensively in African taxa. Results demonstrate that the two new DNA markers could be widely applied in perciform systematics. Furthermore, the comparative approach can unveil mutational dynamics of simple-sequence repeat loci over long periods of fish evolution. Simple-sequence repeat regions are increasingly being found in introns of important regulatory genes. We address issues involving their function and suggest caution in making assumptions of strict neutrality.