Phylogenetic relationships of thorny catfishes (Siluriformes: Doradidae) inferred from molecular and morphological data

Doradidae is a putatively monophyletic group of South American freshwater catfishes containing 30 extant genera and 72 valid species. Only one study to date has attempted to estimate phylogenetic relationships among doradids. This morphological analysis partitioned species into two basal genera ( Wertheimeria and Francisodoras ) and a crown group of three subfamilies (Platydoradinae, Astrodoradinae and Doradinae) whose relationships were unresolved. No subsequent work has been done to resolve the subfamilial trichotomy or to assess whether postulated intergeneric relationships are accurate. We address this problem with complete sequences (2.5 kilobases, kb) of mitochondrial 12S and 16S rRNA genes and partial (1.3 kb) sequences of the nuclear elongation factor-1 alpha (EF1α) gene from representatives of 23 doradid genera (43 species) and 13 outgroups from additional siluriform families. Phylogenetic analysis of these data yields strong support for the monophyly of Doradidae and Astrodoradinae (as well as other relationships), but otherwise shows significant conflict with morphological results. A partial re-examination of published morphological data indicates that many characters may have been incorrectly polarized and many taxa have incorrect state assignments. Our results provide a framework for ongoing efforts to describe the species-level diversity of this poorly understood neotropical family.  © 2004 The Linnean Society of London, Zoological Journal of the Linnean Society , 2004, 140 , 551–575.     

Phylogenetic placement of Yunnanopilia (Opiliaceae) inferred from molecular and morphological data

Yunnanopilia longistaminea (W.Z. Li) C.Y. Wu & D.Z. Li, which is a controversial species in Opiliaceae, is treated as a variety of Champereia manillana (Blume) Merrill in the Flora of China and morphological analysis has produced conflicting results regarding its affinity to Melientha and Champereia. To determine the systematic position of Yunnanopilia in Opiliaceae, we selected two nuclear regions (internal transcribed spacer [ITS4‐ITS5] and 18S rDNA) and four chloroplast regions (rbcL, matK, psbA‐trnH, and trnS‐trnG) to test the phylogenetics of the family Opiliaceae using maximum likelihood and Bayesian inference analysis. Morphological characteristics were also examined to clarify the similarities and differences among Y. longistaminea and two closely related species. Agonandra was located at the basal position in the family Opiliaceae; in the large clade including other remaining genera, two main clades were clearly identified and correlated with inflorescence morphological characteristics. All samples of Y. longistaminea formed a clade. Yunnanopilia, Melientha, and Champereia were more closely related than other genera of Opiliaceae. Yunnanopilia longistaminea was sister to M. suavis Pierre and was more closely related to M. suavis than to C. manillana. Morphological analysis also showed that differences in the inflorescences and flowers between Y. longistaminea and M. suavis were substantial enough to warrant the retention of Y. longistaminea in its current genus. Thus, we suggest that the monotypic Yunnanopilia be treated as a distinct genus and that the name Y. longistaminea should be adopted.     

Morphology of the gas bladder in bumblebee catfishes (Siluriformes,Pseudopimelodidae)

The gross morphology of the gas bladder is described and compared for representatives of all valid genera of Pseudopimelodidae (Siluriformes). Cephalosilurus albomarginatus and species of Batrochoglanis, and Microglanis have the most basic form: a large, cordiform gas bladder with a simple internal T‐shaped septum. Cephalosilurus apurensis, C. fowleri, and C. nigricauda also have a large, cordiform gas bladder, but they have well‐developed trabeculae associated with the internal T‐shaped septum, and a pair of well‐developed constrictor muscles inserted on the external wall; the latter feature is present in most species of Pimelodidae, but absent in all other catfishes. The monotypic Lophiosilurus alexandri also has well‐developed constrictor muscles, and its gas bladder is moderately sized. The species of Pseudopimelodus and Cruciglanis have a diminutive gas bladder partially divided into two lateral sacs without internal communication, and lack constrictor muscles. The parapophysis of the fourth vertebra is a wide and long shelf connected to the dorsal surface of the gas bladder in most pseudopimelodid genera. However, in the species of Pseudopimelodus and Cruciglanis the parapophysis of the fourth vertebra is shorter and has its anterior ramus folded back, partially covering the gas bladder anteroventrally; and the tympanic opening is smaller than in species of the other genera. Five phylogenetic characters are proposed based on the morphology of the gas bladder and associated structures in species of Pseudopimelodidae, and the evolution of those characters in the family is discussed. J. Morphol., 2011. © 2011 Wiley‐Liss, Inc.     

Comparative morphology of the gas bladder in driftwood catfishes (Siluriformes: Auchenipteridae)

The gross morphology of the gas bladder is described and illustrated for representatives of most species and all valid genera of the Auchenipteridae (Siluriformes). Although, a simple cordiform gas bladder is present in some species of the family, others are characterized by their distinctive gas‐bladder shape and diverticula disposition. An acute posterior end of the gas bladder characterizes Centromochlus heckelii and C. macracanthus, and is variably present in specimens of Auchenipterus. Tocantinsia piresi and Asterophysus batrachus have distinctive gas bladders differing in number of diverticula (two or many). The two species of Trachycorystes are diagnosed based on their gas bladder morphology: T. menezesi has a simple cordiform bladder, whereas T. trachycorystes has a pair of lateral diverticulum and, usually, a well‐developed terminal diverticulum. Species of Auchenipterichthys are characterized by having a secondary bladder with simple chamber. Short or elongate and divergent terminal diverticula are exclusive to most cis‐andine species of Trachelyopterus. Tetranematichthys and trans‐andine species of Trachelyopterus share a well‐developed secondary chamber or terminal diverticula ventrally or dorsally connected to the posterior chambers. The small‐sized species of Ageneiosus have well‐developed gas bladders with a pair of posterior diverticula, whereas large‐sized species have a reduced gas bladder with tunica externa varying from non‐, partially, or completely ossified. Eight phylogenetic characters are proposed based on the morphology of the gas bladder and associated structures in species of Auchenipteridae, and the evolution of those characters in the family discussed. J. Morphol., 2012. © 2012 Wiley Periodicals, Inc.     

A molecular assessment of species diversity in Tympanopleura and Ageneiosus catfishes (Auchenipteridae: Siluriformes)

In order to test the congruence of genetic data to the morphologically defined Neotropical catfish genera Tympanopleura and Ageneiosus and explore species diversity, we generated 17 DNA barcodes from five of six species of Tympanopleura and 12 of 13 species of Ageneiosus. To discriminate limits between species, an automatic barcode gap discovery (ABGD), a generalised mixed yule-coalescent model (GYMC) and fixed distance thresholds Kimura two-parameter (K2P; 3%) were used to discriminate putative species limits from the DNA barcodes. The ABGD, GMYC and K2P methods agreed by each generating 13 clusters: six in Tympanopleura (five nominal plus one undescribed species) and seven in Ageneiosus. These clusters corresponded broadly to the described species, except in the case of the Ageneiosus ucayalensis group (A. akamai, A. dentatus, A. intrusus, A. ucayalensis, A. uranophthalmus and A. vittatus). Haplotype sharing and low divergences may have prevented molecular methods from distinguishing these species. We hypothesise that this is the result of a recent radiation of a sympatric species group distributed throughout the Amazon Basin. One putative new species of Tympanopleura was also supported by the molecular data. These results taken together highlight the utility of molecular methods such as DNA barcoding in understanding patterns of diversification across large geographic areas and in recognising overlooked diversity.     

The taxonomy and diversity of Platerodrilus (Coleoptera,Lycidae) inferred from molecular data and morphology of adults and larvae

The Oriental neotenic net-winged beetles attracted attention of biologists due to conspicuous large-bodied females; nevertheless phylogenetic relationships remain contentious and only a few species are known in both the fully metamorphosed males and neotenic females. The phylogenetic analyses and morphology of larvae and adults provide data for investigation of relationships and species delineation. Platrilus Kazantsev, 2009, Platerodriloplesius Wittmer, 1944, and Falsocalochromus Pic, 1942 are synonymized to Platerodrilus Pic, 1921. Platrilus hirtus (Wittmer, 1938) and Pl. crassicornis (Pic, 1923) are transferred to Platerodrilus Pic, 1921. Platerodrilus hoiseni Wong, 1996 is proposed as a junior subjective synonym of Falsocalochromus ruficollis Pic, 1942. Platerodrilus is divided in three species-groups: P. paradoxus, P. major, and P. sinuatus groups defined based on the shape of genitalia and molecular phylogeny. The following species are described: Platerodrilus foliaceussp. n., P. wongisp. n. (P. paradoxus group); P. ngisp. n., P. wittmeri (P. major group), P. ijenensissp. n., P. luteussp. n., P. maninjauensissp. n., P. montanussp. n., P. palawanensissp. n., P. ranauensissp. n., P. sibayakensissp. n., P. sinabungensissp. n., P. talamauensissp. n., and P. tujuhensissp. n. (P. sinuatus group). P. korinchiana robinsoni Blair, 1928 is elevated to the species rank as P. robinsoni Blair, 1928, stat. n. The conspecific semaphoronts are identified using molecular phylogeny for P. foliaceussp. n., P. tujuhensissp. n., P. montanussp. n., P. maninjauensissp. n.; additional female larvae are assigned to the species-groups. Diagnostic characters are illustrated and keys are provided for P. paradoxus and P. major groups.     

Intergeneric phylogenetic relationships in catfishes of the Loricariinae (Siluriformes: Loricariidae), with the description of Fonchiiloricaria nanodon: a new genus and species from Peru

Recent investigations in the upper Río Huallaga in Peru revealed the presence of an intriguing species of the Loricariinae. To characterize and place this species within the evolutionary tree of the subfamily, a molecular phylogeny of this group was inferred based on the 12S and 16S mitochondrial genes and the nuclear gene F-reticulon4. The phylogeny indicated that this distinctive species was a member of the subtribe Loricariina. Given its phylogenetic placement, and its unusual morphology, this species is described as a new genus and new species of Loricariinae: Fonchiiloricaria nanodon. This new taxon is diagnosed by usually possessing one to three premaxillary teeth that are greatly reduced; lips with globular papillae on the surface; the distal margin of lower lip bearing short, triangular filaments; the premaxilla greatly reduced; the abdomen completely covered by plates, with the plates between lateral abdominal plates small and rhombic; a caudal fin with 14 rays; the orbital notch absent; five lateral series of plates; dorsal-fin spinelet absent; preanal plate present, large and solid, and of irregular, polygonal shape, the caudal peduncle becoming more compressed posteriorly for the last seven to 10 plates.     

Chromosomal diversification in the flightless Western Mediterranean bushcricket genus Odontura (Orthoptera: Tettigoniidae: Phaneropterinae) inferred from molecular data

We used molecular characters to infer the phylogenetic position of the Western Mediterranean bushcricket genus Odontura and to trace its high karyotype diversity. Analysis of 1391 base pairs of two mitochondrial genes (COI and ND1) and one nuclear sequence (ITS2) was conducted. Phylogenetic topologies were estimated using maximum parsimony, maximum likelihood and likelihood‐based Bayesian inference. The genus Odontura is a phylogenetic outlier in respect of all other European Phaneropterinae genera and has been proposed to have originated from a hitherto unknown ancestor. Our results support the monophyly of the genus Odontura and the recognition of two subgenera: Odontura and Odonturella. We found that both Sicilian taxa of the subgenus Odontura have a completely identical morphology and song patterns. Combining these results, we proposed that both should be treated as subspecies: O. (Odontura) stenoxypha stenoxypha and O. (O.) st. arcuata. Bioacoustic data also proved to support independent markers, with song characteristics reflecting the molecular topology. Mapping the karyotypic characters onto the phylogenetic tree allows a reconstruction of the directions and transitional stages of chromosome differentiation. The number of autosomes within the genus Odontura ranges from 26 to 30. In addition to the ancestral X0 sex determination mechanism, neo‐XY and neo‐X₁X₂Y sex chromosomes have evolved independently.     

Phylogenetic origin of Beckmannia （Poaceae） inferred from molecular evidence

The phylogenetic origin of Beckmannia remains unknown. The genus has been placed within the Chlorideae, Aveneae （Agrostideae）, Poeae, or treated as an isolate lineage, Beckmanniinae. In the present study, we used nuclear internal transcribed spacer （ITS） and chloroplast trnL-F sequences to examine the phylogenetic relationship between Beckmannia and those genera that have assumed to be related. On the basis of the results of our studies, the following conclusions could be drawn： （i） Beckmannia and Alopecurus are sister groups with high support; and （ii） Beckmannia and Alopecurus are nested in the Poeae clade with high support. The results of our analysis suggest that Beckmannia should be placed in Poeae.     

Phylogenetic relationships in the Niviventer-Chiromyscus complex (Rodentia,Muridae) inferred from molecular data,with description of a new species

Based on molecular data for mitochondrial (Cyt b, COI) and nuclear (IRBP, GHR) genes, and morphological examinations of museum specimens, we examined diversity, species boundaries, and relationships within and between the murine genera Chiromyscus and Niviventer. Phylogenetic patterns recovered demonstrate that Niviventer sensu lato is not monophyletic but instead includes Chiromyscus chiropus, the only previously recognized species of Chiropus. To maintain the genera Niviventer and Chiropus as monophyletic lineages, the scope and definition of the genus Chiromyscus is revised to include at least three distinct species: Chiromyscus chiropus (the type species of Chiromyscus), Chiromyscus langbianis (previously regarded as a species of Niviventer), and a new species, described in this paper under the name Chiromyscus thomasi sp. n.     

DNA barcoding of genus Toxoptera Koch (Hemiptera: Aphididae): Identification and molecular phylogeny inferred from mitochondrial COI sequences

Abstract Identification of aphid species is always difficult due to the shortage of easily distinguishable morphological characters. Aphid genus Toxoptera consists of species with similar morphology and similar to Aphis in most morphological characters except the stridulatory apparatus. DNA barcodes with 1 145 bp sequences of partial mitochondrial cytochrome‐coxidase I (COI) genes were used for accurate identification of Toxoptera. Results indicated mean intraspecific sequence divergences were 1.33%, whereas mean interspecific divergences were greater at 8.29% (0.13% and 7.79% if T. aurantii 3 and T. aurantii 4 are cryptic species). Sixteen samples were distinguished to four species correctly by COI barcodes, which implied that DNA barcoding was successful in discrimination of aphid species with similar morphology. Phylogenetic relationships among species of this genus were tested based on this portion of COI sequences. Four species of Toxoptera assembled a clade with low support in maximum‐parsimony (MP) analysis, maximum‐likelihood (ML) analysis and Bayesian phylogenetic trees, the genus Toxoptera was not monophyletic, and there were two sister groups, such as T. citricidus and T. victoriae, and two clades of T. aurantii which probably presented cryptic species in the genus.     

Systematic revision of the formerly monotypic genus Tanganikallabes (Siluriformes: Clariidae)

The monotypic genus Tanganikallabes, endemic to Lake Tanganyika, is a poorly known member of the family Clariidae. Examination of 142 specimens housed in museum collections has revealed the presence of at least two additional species in this genus. Tanganikallabes alboperca sp. nov. is distinguished from all congeners by the length of its pelvic fins, the presence of a depigmented vertical bar on the opercular margin, and a combination of additional morphometric (pectoral spine length, preanal length, body depth at anus) and meristic (dorsal and anal fin ray counts) characters. Tanganikallabes stewarti sp. nov. is distinguished from other Tanganikallabes species by having a relatively shorter, incomplete lateral line, and shallow body depth at the anus, as well as shorter prepelvic and preanal lengths, and a longer anal fin with a higher number of fin rays. Several morphological characters, as well as genetic data from cytochrome b (mitochondrial DNA) and 18S–ITS1–5.8S–ITS2–28S (ribosomal DNA), indicate that Tanganikallabes constitutes a monophyletic group within the Clariidae and support the recognition of additional species diversity. The monophyly of Tanganikallabes, coupled with the geographical isolation of this group to a single lake satisfy the requirements for its classification as a true species flock, the latest to be described from Lake Tanganyika. © 2012 The Linnean Society of London, Zoological Journal of the Linnean Society, 2012, 165 , 121–142.     

Multigene phylogeny reveals convergent evolution in small interstitial catfishes from the Amazon and Atlantic forests (Siluriformes: Trichomycteridae)

Interstitial trichomycterid catfishes of the Glanapteryginae and Sarcoglanidinae with uncommon morphology have been known for long time from taxa endemic to the Amazon. In most recent decades, two genera, Listrura and Microcambeva, respectively, placed in Glanapteryginae and Sarcoglanidinae on the basis of morphological characters, have been described from the Atlantic Forest of eastern South America, about 1,500 km from the area inhabited by those Amazon taxa. Herein, we first test the phylogenetic positioning of Listrura and Microcambeva using a multigene data set, including two nuclear and three mitochondrial genes for nine species of Listrura and Microcambeva and 11 species representing all closely related subfamilies (TSVSG-clade), as well as five used as outgroups. The phylogenetic analyses generated a robust tree with high support values in all nodes, where monophyly of Glanapteryginae and Sarcoglanidinae is refuted. In contrast, Listrura and Microcambeva form a highly supported clade, herein formally described as a new subfamily, sister to a clade containing taxa representing the Glanapteryginae, Sarcoglanidinae, Stegophilinae, Tridentinae and Vandelliinae. This study also indicates that Microcambeva and Listrura exhibit divergent evolutionary trends in ecological and morphological attributes. Species of Microcambeva inhabit patches of loose sand and possess morphological traits that were convergently acquired by Amazon sand-dwelling sarcoglanidines, including loss of body pigmentation and long maxilla. Species of Listrura live burrowed inside small stretches of dense leaf litter and have morphological traits that were convergently acquired by Amazon glanapterygines inhabiting leaf litter bottom rivers, including elongate body, with numerous vertebrae and loss or reduction of all fins.     

Phylogeography of Balkan wall lizard (Podarcis taurica) and its relatives inferred from mitochondrial DNA sequences

Wall lizards of the genus Podarcis (Sauria, Lacertidae) comprise 17 currently recognized species in southern Europe, where they are the predominant reptile group. The taxonomy of Podarcis is complex and unstable. Based on DNA sequence data the species of Podarcis falls into four main groups that have substantial geographical conherence (western island group, southwestern group, Italian group and Balkan group). The Balkan species are divided in two subgroups: the subgroup of Podarcis taurica (P. taurica, P. milensis, P. gaigeae and perhaps P. melisellensis), and the subgroup of Podarcis erhardii (P. erhardii and P. peloponnesiaca). We addressed the question of phylogenetic relations among the species of the P. taurica subgroup encountered in Greece, as they can be inferred from partial mtDNA (cyt b and 16S) sequences. Our data support the monophyly of P. taurica subgroup and suggest that P. gaigeae, P. milensis and P. melisellensis form a clade, which thereinafter connects to P. taurica. Within the previous clade, P. gaigeae is more closely related to P. milensis than to P. melisellensis. However, the specimens of P. taurica were subdivided in two different groups. The first one includes the specimens from northeastern Greece, and the other group includes the specimens from the rest of continental Greece and Ionian islands. Because the molecular clock of the cyt b and 16 rRNA genes was not rejected in our model test, it is possible to estimate times of speciation events. Based on the splitting of the island of Crete from Peloponnisos [c. 5 million years ago (Ma)], the evolutionary rate for the cyt b is 1.55% per million years (Myr) and for the 16S rRNA is 0.46% per Myr. These results suggest that the evolutionary history of P. taurica in Greece is more complex than a single evolutionary invasion. The data analysed, stress the need for a reconsideration of the evolutionary history of Greek Podarcis species and help overcome difficulties that classical taxonomy has encountered at both the species level.     

Phylogenetic relationships of the Clavelinidae and Pycnoclavellidae (Ascidiacea) inferred from mtDNA data

Abstract. The phylogenetic relationships within the Order Aplousobranchiata (Ascidiacea) are largely unexplored. In this work, we study the phylogenetic status of the genera Clavelina and Pycnoclavella. Traditionally, both genera had been included in the family Clavelinidae, until the new family Pycnoclavellidae was defined, removing the genus Pycnoclavella from Clavelinidae. Not all authors accept the validity of Clavelina and Pycnoclavella as distinct genera, let alone their belonging to different families. In addition, the assignment of species to these genera, as well as to the genus Archidistoma , has been controversial. We analyzed sequences of the mitochondrial gene cytochrome c oxidase subunit I belonging to ten species of Pycnoclavella (including several formerly assigned to Archidistoma and Clavelina ), 11 species of Clavelinidae, and ten species of other aplousobranch genera belonging to seven families, plus two outgroups. Two different tree construction methods (maximum likelihood and Bayesian inference) showed similar results. Pycnoclavella and Clavelina appeared in distinct clades but formed a monophyletic group relative to representatives of the main families of the order Aplousobranchiata. Our phylogenetic results indicate that both genera are valid but should be included within a single family, with the name Clavelinidae having precedence. The monotypic clavelinid genus Nephtheis branches in our trees within the clade of the genus Clavelina. Our results also confirm that some forms assigned to Archidistoma and Clavelina have been misplaced and belong to the genus Pycnoclavella. Pycnoclavella martae n.sp. is described.     

New data from an enigmatic phylum: evidence from molecular sequence data supports a sister-group relationship between Loricifera and Nematomorpha

Loricifera is one of the most recently discovered animal phyla. So far, the group has been considered closely related to Kinorhyncha and Priapulida, and assigned to the ecdysozoan clade Cycloneuralia. Using Bayesian inference, we present the first phylogeny that includes 18S rRNA and Histone 3 sequences from two species of Loricifera. Intriguingly, we find support for a sister-group relationship between Loricifera and Nematomorpha. Such relationship has not been suggested previously and the results imply that a revision of our conception of early ecdysozoan evolution is required. Additionally, the data suggest that evolution through progenesis (sexual maturation of larvae) may have played an important role among the ancestral cycloneuralians.     

Delineation of Chondrus (Gigartinales, Florideophyceae) in China and the origin of C. crispus inferred from molecular data

Complete nuclear ribosomal DNA (nrDNA) internal transcribed spacer (ITS) sequences were obtained for 18 Chondrus populations collected at 15 sites from eight countries worldwide. Pairwise comparisons with the multiple alignment revealed that intraspecific divergences of ITS sequences ranged from 0.3 to 1.8% in C. crispus Stackhouse (except for the entity SVLH from France) and from 0.0 to 0.6% in C. ocellatus Holmes, whereas interspecific divergences in Chondrus varied from 1.4 to 5.0%. Three phylogenetic methods (neighbour joining, maximum parsimony and maximum likelihood) confirmed three main lineages: the North Atlantic lineage containing entities of C. crispus from Canada, France, Germany, England, Portugal, Ireland and Wales; a second lineage comprising three species: C. sp. 1, C. armatus (Harvey) Yamada et Mikami, and C. pinnulatus (Harvey) Okamura from the Northern Pacific; and a third lineage containing just one species: C. ocellatus from the Northern Pacific. Chondrus yendoi Yamada et Mikami separated from other Chondrus species singly. nrDNA ITS data indicate that a previous assignment of C. sp. 2 to Mazzaella japonica (Mikami) Hommersand may be incorrect, and additional evidence is needed to resolve the generic placement of this entity. It is inferred from the nrDNA ITS data that three Chondrus species are presently known in China with two, C. ocellatus and C. nipponicus, in Qingdao and two, C. armatus and C. nipponicus, in Dalian. We hypothesize that the ancestor of North Atlantic C. crispus had a Pacific origin, and that the present distribution of C. crispus in the Atlantic Ocean correlates with a trans-Arctic dispersal and vicariance events associated with Pleistocene glaciation maxima.