Molecular phylogeny of moth flies (Diptera,Psychodidae, Psychodinae) revisited,with a revised tribal classification

Classification of Psychodinae has been a hotly contested topic in the taxonomic literature, with multiple mutually incompatible classifications proposed. Three main points of contention can be identified: (i) the validity of Maruinini Enderlein as a tribe‐level taxon and whether it forms a monophyletic group; (ii) the placement of subtribe Trichopsychodina Ježek – specifically whether it belongs with Psychoda Latreille in Psychodini or with Paramormia Enderlein and Telmatoscopus Eaton in Paramormiini Enderlein or Mormiini Enderlein; and (iii) whether Mormia Enderlein is more closely related to Brunettia Annandale or Paramormia Enderlein and Telmatoscopus Eaton. In the present paper, these questions are investigated using a molecular phylogeny of sequences compiled from all previous molecular phylogenies relevant to Psychodinae, as well as some hitherto unpublished sequences. The resulting matrix comprised 5406 base pairs from six markers for 32 taxa, and when analysed using Bayesian inference it yielded a well‐resolved tree which was unambiguous for all previously contentious points: Maruinini sensu lato (including Setomimini) was resolved as a valid taxon, Trichopsychodina is rendered paraphyletic by Psychodini, and Mormia is not closely related to Brunettia , but instead closer to Telmatoscopus and Paramormia . A revised tribal classification of Psychodinae is proposed, recognizing the tribes Psychodini, Brunettiini, Maruinini and Pericomaini as well as 17 unplaced genera.     

A phylogeny of Lophocoleaceae-Plagiochilaceae-Brevianthaceae and a revised classification of Plagiochilaceae

The Lophocoleaceae-Plagiochilaceae-Brevianthaceae clade is a largely terrestrial, subcosmopolitan lineage of jungermannialean leafy liverworts that may include significantly more than 1000 species. Here we present the most comprehensively sampled phylogeny available to date based on the nuclear ribosomal internal transcribed spacer region and the chloroplast markers rbcL and rps4 of 372 accessions. Brevianthaceae (consisting of Brevianthus and Tetracymbaliella) form a sister relationship with Lophocoleaceae; this lineage is in turn sister to Plagiochilaceae. Plagiochila is resolved monophyletic subsequent to exclusion of Plagiochila radiculosa; this species is placed in a new genus Cryptoplagiochila. Chiastocaulon and a polyphyletic Acrochila nest in Plagiochilion; these three genera are united under Chiastocaulon to include the Plagiochilaceae species with dominating or exclusively ventral branching. The generic classification of the Lophocoleaceae is still unresolved. We discuss alternative approaches to obtain strictly monophyletic genera by visualizing their consistence with the obtained consensus topology. The presented phylogeny will serve as a basis for follow-up studies including several thousand accessions. These studies will enable revision of current hypotheses on species diversity and distribution of Lophocoleaceae-Plagiochilaceae-Brevianthaceae and allow for a reconstruction of their evolution in time and space.     

Molecular phylogeny of Mugilidae fishes revised

Systematics derived from morphological characters often does not correspond with the evolutionary processes underlying the divergence within a group of organisms. In the family Mugilidae (Teleostei) morphological similarities have resulted in inconsistencies between taxonomy and phylogeny among its species, and particularly for the genera Mugil, Liza and Chelon where both intrageneric and intergeneric phylogenetic clarifications are needed. To address these issues, the direct sequencing of the mitochondrial region that encodes Phenylalanine (69 bp), 12S rRNA (842 bp), cytochrome c oxidase subunit I (651 bp) and cytochrome b (702 bp) was carried out. The data reveal that Mugil platanus and Mugil liza represent a continuum of a single species, closely related to but distinct from Mugil cephalus which itself appears to comprise a grouping of multiple and closely related species. This species complex was genetically distinct from Mugil curema, which, based on three clearly diverged species identified in this study along the Atlantic coast of the Americas, requires extensive taxonomic revision throughout its world-wide distribution. Unlike the monophyly supported within Mugil, relationships within Liza are paraphyletic, and a taxonomic revision of the genera Liza, Chelon and Oedalechilus is needed.     

DNA phylogeny supports revised classification of Salmothymus obtusirostris

Salmothymus obtusirostris (soft-muzzled trout) is endemic to the South Adriatic drainage. Owing to its unusual appearance, which resembles both trout and grayling, it has been initially classified as a separate genus. However, this classification is ambiguous and has never been firmly established. We have studied mtDNA (control region and cytochrome b gene) and nuclear DNA (a part of LDH C*1 gene) variation between soft-muzzled trout from the upper part of the River Neretva, Bosnia and Herzegovina, and other salmonid representatives in order to examine how the current classification is congruent with molecular data. On the basis of sequence identity of mtDNA control region among several genera (i.e. Salmo , Oncorhynchus , Salvelinus , Acantholingua , Brachymystax , Thymallus and Coregonus ) a close relationship between Salmothymus , Salmo and Acantholingua was established. Phylogenetic analysis on a combined data set of mitochondrial and nuclear DNA, supported by 100% bootstraping, indicated that S. obtusirostris and A. ohridana are sister taxa which exhibit a closer relationship to S. trutta than to S. salar . This finding refutes the current classification, which recognizes S. obtusirostris as separate genus, and instead suggests its reclassification on the species level as Salmo obtusirostris .  © 2002 The Linnean Society of London, Biological Journal of the Linnean Society , 2002, 77 , 399–411.     

A large-scale phylogeny of Amphibia including over 2800 species, and a revised classification of extant frogs, salamanders, and caecilians

The extant amphibians are one of the most diverse radiations of terrestrial vertebrates (>6800 species). Despite much recent focus on their conservation, diversification, and systematics, no previous phylogeny for the group has contained more than 522 species. However, numerous studies with limited taxon sampling have generated large amounts of partially overlapping sequence data for many species. Here, we combine these data and produce a novel estimate of extant amphibian phylogeny, containing 2871 species (∼40% of the known extant species) from 432 genera (∼85% of the ∼500 currently recognized extant genera). Each sampled species contains up to 12,712 bp from 12 genes (three mitochondrial, nine nuclear), with an average of 2563 bp per species. This data set provides strong support for many groups recognized in previous studies, but it also suggests non-monophyly for several currently recognized families, particularly in hyloid frogs (e.g., Ceratophryidae, Cycloramphidae, Leptodactylidae, Strabomantidae). To correct these and other problems, we provide a revised classification of extant amphibians for taxa traditionally delimited at the family and subfamily levels. This new taxonomy includes several families not recognized in current classifications (e.g., Alsodidae, Batrachylidae, Rhinodermatidae, Odontophrynidae, Telmatobiidae), but which are strongly supported and important for avoiding non-monophyly of current families. Finally, this study provides further evidence that the supermatrix approach provides an effective strategy for inferring large-scale phylogenies using the combined results of previous studies, despite many taxa having extensive missing data.     

Molecular phylogeny and the higher classification of eutherian mammals

Reconstructing the evolutionary relationships among the orders of eutherian mammals constitutes a formidable phylogenetic task. It entails the identification of a single true phylogenetic tree out of 10(12)-10(28) possible ones. For almost half a century, the field of mammalian Phylogeny has been dominated by a pessimistic view, according to which the great burst of mammalian radiations more than 65 million years ago has rendered the ordinal phylogeny of mammals insolvable. In the last few years, this pessimism has started to dissipate as several superordinal relationships were identified through the use of molecular data. DNA and protein sequences have the potential to supply millions of phyloge netically useful characters, and therefore, the Phylogeny of the orders of mammals may be resolved into a consistently bifurcating tree in the not-sodistant future.     

A revised classification of the Sphacelariales (Phaeophyceae) inferred from a psbC and rbcL based phylogeny

Phylogenetic relationships within the brown algal order Sphacelariales and with its sister group were investigated using chloroplast-encoded psbC and rbcL DNA sequences. A pilot study with 21 non-sphacelarialeans, representing nine orders (and some incertae sedis taxa), showed a strongly supported monophyly of the Sphacelariales with its sister taxa Phaeostrophion irregulare, Bodanella lauterborni and Heribaudiella fluviatilis. These three taxa were selected as outgroup for further analyses including DNA sequences of 30 sphacelarialean specimens representing all but two of the recognized genera (Phloiocaulon and Ptilopogon were not sampled). Bayesian Inference and Maximum Likelihood trees showed some incongruence with Maximum Parsimony trees. Trees based on rbcL showed some incongruence with trees based on psbC and combined alignments. Phylogenetic results were used as the basis for a newly proposed classification of the Sphacelariales that reflects evolutionary history. The Sphacelariales is subdivided into four families: Cladostephaceae (monotypic), Sphacelariaceae, Stypocaulaceae, and a newly created monotypic family Sphacelodermaceae to incorporate Sphaceloderma caespitula, comb. nov. (former Sphacelaria caespitula). Sphacelaria radicans is transferred to a newly created genus Protohalopteris and classified in the Stypocaulaceae, which also contains the two unsampled genera Phloiocaulon and Ptilopogon as well as the genus Halopteris. The genera Stypocaulon and monotypic Alethocladus were merged with Halopteris. The Sphacelariaceae were subdivided into six genera including Sphacelaria (consisting only of the former subgenus Propagulifera) and the monotypic Sphacella. Herpodiscus durvillaeae, Sphacelaria pulvinata and the Sphacelaria subgenera Bracteata and Reinkea were merged in an emended Herpodiscus. A new genus Sphacelorbus was created for Sphacelaria nana. Battersia was reinstated for Sphacelaria mirabilis and the subgenus Pseudochaetopteris, except for Sphacelaria plumosa for which Chaetopteris was reinstated.     

A multilocus phylogeny of Asian noodlefishes Salangidae (Teleostei: Osmeriformes) with a revised classification of the family

A group of small and transparent Asian noodlefishes (Osmeriformes: Salangidae) are commercially important fishery species, however, interrelationships among these fishes remain unresolved in previous studies using mitochondrial markers. We re-examine phylogenetic relationships of Salangidae by including complete taxon sampling, based on seven nuclear loci and one mitochondrial gene using a multilocus coalescence-based species-tree method. Our results show a well-resolved phylogeny of Salangidae that does not agree with previous hypotheses. The topology test suggests that our hypothesis represents the most likely phylogeny. Using the inferred species-tree as criterion, we recombine the rank of subfamilies and genera in the Salangidae, and erect a new genus Neosalangichthys. Our revised classification of Salangidae is well supported by reinterpreting previously proposed diagnostic characters. Finally, re-defined synapomorphic characters are used to erect a key to the genera of Salangidae.     

Molecular phylogeny and proposed classification of the simian picornaviruses.

The simian picornaviruses were isolated from various primate tissues during the development of general tissue culture methods in the 1950s to 1970s or from specimens derived from primates used in biomedical research. Twenty simian picornavirus serotypes are recognized, and all are presently classified within the Enterovirus genus. To determine the phylogenetic relationships among all of the simian picornaviruses and to evaluate their classification, we have determined complete VP1 sequences for 19 of the 20 serotypes. Phylogenetic analysis showed that A13, SV19, SV26, SV35, SV43, and SV46 are members of human enterovirus species A, a group that contains enterovirus 71 and 11 of the coxsackie A viruses. SA5 is a member of human enterovirus species B, which contains the echoviruses, coxsackie B viruses, coxsackievirus A9, and enterovirus 69. SV6, N125, and N203 are related to one another and, more distantly, to species A human enteroviruses, but could not be definitely assigned to a species. SV4 and SV28 are closely related to one another and to A-2 plaque virus, but distinct from other enteroviruses, suggesting that these simian viruses are members of a new enterovirus species. SV2, SV16, SV18, SV42, SV44, SV45, and SV49 are related to one another but distinct from viruses in all other picornavirus genera, suggesting that they may comprise a previously unknown genus in Picornaviridae. Several simian virus VP1 sequences (N125 and N203; SV4 and SV28; SV19, SV26, and SV35; SV18 and SV44; SV16, SV42, and SV45) are greater than 75% identical to one another (and/or greater than 85% amino acid identity), suggesting that the true number of distinct serotypes among the viruses surveyed is less than 20.     

Molecular evolution and phylogeny of the atpB-rbcL spacer of chloroplast DNA in the true mosses.

The nucleotide variation of a noncoding region between the atpB and rbcL genes of the chloroplast genome was used to estimate the phylogeny of 11 species of true mosses (subclass Bryidae). The A+T rich (82.6%) spacer sequence is conserved with 48% of bases showing no variation between the ingroup and outgroup. Rooted at liverworts, Marchantia and Bazzania, the monophyly of true mosses was supported cladistically and statistically. A nonparametric Wilcoxon Signed-Ranks test Ts statistic for testing the taxonomic congruence showed no significant differences between gene trees and organism trees as well as between parsimony trees and neighbor-joining trees. The reconstructed phylogeny based on the atpB-rbcL spacer sequences indicated the validity of the division of acrocarpous and pleurocarpous mosses. The size of the chloroplast spacer in mosses fits into an evolutionary trend of increasing spacer length from liverworts through ferns to seed plants. According to the relative rate tests, the hypothesis of a molecular clock was supported in all species except for Thuidium, which evolved relatively fast. The evolutionary rate of the chloroplast DNA spacer in mosses was estimated to be (1.12 +/- 0.019) x 10(-10) nucleotides per site per year, which is close to the nonsynonymous substitution rates of the rbcL gene in the vascular plants. The constrained molecular evolution (total nucleotide substitutions, K approximately 0.0248) of the chloroplast DNA spacer is consistent with the slow evolution in morphological traits of mosses. Based on the calibrated evolutionary rate, the time of the divergence of true mosses was estimated to have been as early as 220 million years ago.     

A molecular phylogeny of the groupers of the subfamily Epinephelinae (Serranidae) with a revised classification of the Epinephelini

The phylogenetic relationships among the fishes in the perciform tribe Epinephelini (Serranidae) have long been poorly understood, in large part because of the numerous taxa that must be considered and the large, circumtropical distribution of the group. In this study, genetic data from two nuclear (Tmo-4C4 and histone H3) and two mitochondrial (16S and 12S) genes were gathered from 155 serranid and acanthomorph species as a means of developing a phylogenetic hypothesis using both maximum-likelihood and -parsimony criteria. The maximum-parsimony analysis recovered 675 most parsimonious trees of length 5703 steps (CI = 0.2523, HI = 0.7477, RI = 0.6582), and the maximum-likelihood analysis recovered 1 tree at −lnLikelihood = 28279.58341. These phylogenetic hypotheses are discussed in light of previous morphological evidence to evaluate the evolutionary history of the group and their implications for the currently recognized taxonomy. Our results question the monophyly of the Serranidae, as well as the genera Cephalopholis, Epinephelus, and Mycteroperca as currently defined. The Serranidae is monophyletic only with the exclusion of the genera Acanthistius and Niphon. We propose a revised classification of the tribe Epinephelini that reflects the hypothesized shared ancestry of the group and recognizes 11 genera: Alphestes, Cephalopholis, Dermatolepis, Epinephelus, Gonioplectrus, Hyporthodus (which is resurrected for 11 species of deep-bodied groupers), Mycteroperca (including 7 species heretofore allocated to Epinephelus), Plectropomus, Saloptia, Triso, and Variola.     

Genome analysis,phylogeny, and classification

The implications of genome analysis for evolutionary theory and systematics are treated. The precise relationship between the theoretical and operational definitions of chromosome homology is shown to be uncertain. It is pointed out that genera defined by genome analysis may be either monophyletic or non-monophyletic, and that the genus is not a basic unit of evolution. Characters obtained by genome analysis may be useful in a phylogenetic context, provided they are treated as all other characters.