Phylogeny of nereidids (Polychaeta, Nereididae) with paragnaths

A phylogenetic analysis was conducted of the Nereidinae — those members of the Nereididae (Polychaeta) with pharyngeal paragnaths. We had two objectives: to test the monophyly of currently accepted genera, subgenera and informal subgeneric groupings within the Nereidinae, and, if warranted, to propose a more natural classification of the Nereidinae. Parsimony analyses were undertaken, including 52 terminal taxa from all genera and informal groupings from the large heterogeneous genera Nereis , Ceratonereis , Neanthes and Perinereis . Analyses of a character set of 52 informative characters yielded more than 10 000 equally parsimonious trees with a length of 176 steps (consistency index [CI] = 0.34, retention index [RI] = 0.66). Reweighting three times resulted in 445 most parsimonious trees with length 54.62 (CI = 0.59, RI = 0.79). Many characters widely used in nereidid systematics were found to exhibit high levels of homoplasy. The most parsimonious trees could not be rooted such that the selected ingroup, 'Nereididae with paragnaths', was monophyletic, causing us to reject the monophyly of the Nereidinae as currently defined. The following genera were well supported by the parsimony analyses and are newly diagnosed: Alitta , Ceratonereis , Pseudonereis , Simplisetia , Solomononereis and Unanereis . Alitta succinea , Pseudonereis cortezi , Pseudonereis noodti and Pseudonereis pseudonoodti are proposed as new combinations. The parsimony analysis supported the monophyly of neither Composetia , Neanthes , Nereis and Perinereis nor of any new groupings of remaining species presently placed in those genera. It is these poorly supported genera that comprise most species of Nereididae.     

A phylogenetic analysis of higher-level gall wasp relationships (Hymenoptera: Cynipidae)

We present the most comprehensive analysis of higher-level relationships in gall wasps conducted thus far. The analysis was based on detailed study of the skeletal morphology of adults, resulting in 164 phylogenetically informative characters, complemented with a few biological characters. Thirty-seven cynipid species from thirty-one genera, including four genera of the apparently monophyletic Cynipini and almost all of the genera in the other tribes, were examined. The outgroup included exemplar species from three successively more distant cynipoid families: Figitidae (the sister group of the Cynipidae), Liopteridae and Ibaliidae. There was considerable homoplasy in the data, but many groupings in the shortest tree were nonetheless well supported, as indicated by bootstrap proportions and decay indices. Partitioning of the data suggested that the high level of homoplasy is characteristic of the Cynipidae and not the result of the amount of available phylogenetically conservative characters being exhausted. The analysis supported the monophyly of the Cynipini (oak gall wasps) which, together with the Rhoditini (the rose gall wasps), Eschatocerini and Pediaspidini formed a larger monophyletic group of gall inducers restricted to woody representatives of the eudicot subclass Rosidae. The inquilines (Synergini) were indicated to be monophyletic, whereas the Aylacini, primarily herb gall inducers, appeared as a paraphyletic assemblage of basal cynipid groups. The shortest tree suggests that the Cynipidae can be divided into three major lineages: one including the inquilines, the Aylacini genera associated with Rosaceae, and Liposthenes ; one consisting entirely of Aylacini genera, among them Aulacidea , Isocolus and Neaylax ; and one comprising the woody rosid gallers (the oak and rose gall wasps and allies), the Phanacis-Timaspis complex and the Aylacini genera associated with Papaveraceae.     

Molecular phylogeny,analysis of character evolution,and submersible collections enable a new classification of a diverse group of gobies (Teleostei: Gobiidae: Nes subgroup), including nine new species and four new genera

The Nes subgroup of the Gobiosomatini (Teleostei: Gobiiformes: Gobiidae) is an ecologically diverse clade of fishes endemic to the tropical western Atlantic and eastern Pacific oceans. It has been suggested that morphological characters in gobies tend to evolve via reduction and loss associated with miniaturization, and this, coupled with the parallel evolution of adaptations to similar microhabitats, may lead to homoplasy and ultimately obscure our ability to discern phylogenetic relationships using morphological characters alone. This may be particularly true for the Nes subgroup of gobies, where several genera that are diagnosed by ‘reductive characters’ have been shown to be polyphyletic. Here we present the most comprehensive phylogeny to date of the Nes subgroup using mitochondrial and nuclear sequence data. We then evaluate the congruence between the distribution of morphological characters and our molecular tree using maximum‐likelihood ancestral state reconstruction, and test for phylogenetic signal in characters using Pagel's λ tree transformations (Nature, 401 , 1999 and 877). Our results indicate that all of the characters previously used to diagnose genera of the Nes subgroup display some degree of homoplasy with respect to our molecular tree; however, many characters display considerable phylogenetic signal and thus may be useful in diagnosing genera when used in combination with other characters. We present a new classification for the group in which all genera are monophyletic and in most cases diagnosed by combinations of morphological characters. The new classification includes four new genera and nine new species described here, many of which were collected from rarely sampled deep Caribbean reefs using manned submersibles. The group now contains 38 species in the genera Carrigobius gen. nov., Chriolepis, Eleotrica, Gobulus, Gymneleotris, Nes, Paedovaricus gen. nov., Pinnichthys gen. nov., Psilotris, and Varicus. Lastly, we provide a key to all named species of the Nes subgroup along with photographs and illustrations to aid in identification.     

A preliminary cladistic investigation of relationships among the bumble bees (Hymenoptera, Apidae)

ABSTRACT. The cladistic method is used to classify sixty species of bumble bees by characters of the male genitalia selected for their functional importance. A system of three genera is recommended, preserving the holophyletic groups Mendacibombus Skorikov, Psithyrus Lepeletier and Bombus Latreille, with the retention of the named subgroups of Bombus in subgeneric status. A new subgenus Brachycephalibombus is recognized in order to avoid paraphyletic groupings. The phylogenetic interpretation of the cladogram is considered and biogeographic problems discussed.     

THE VALIDITY OF SOME GENERA OF LARKS (ALAUDIDAE)

The larks (Alaudidae) tend to be taxonomically arranged in a large number of small genera. There appear to be few characters which will separate the genera Alauda, Galerida and Lullula, and in recent times additional species have been placed in the first two genera without a reappraisal of the characters by which each genus is defined. Ten species are involved and originally these belonged to eight different genera. In this group of ten species of eight genera as at present, six morphological generic characters are examined separately: the length of the tenth primary in relation to the roundness of the wing, the length of the hind claw, the profile of the crest, the conspicuousness of the superciliary stripe, the thickness and taper of the bill, and the length of tertiaries and secondaries. All ten species show these characters, and the variation in any single character is fairly evenly graded through the group without marked discontinuity. The succession of species within the gradation varies from one character to another. It is not possible to find any group of characters which will subdivide the group of species. Little is known of the behaviour of the ten species but examination of song-flight suggests that such characters may also show a gradation without obvious subdivision. It is considered that the present data do not justify the retention of the present genera for these species, and that it would be preferable to group them under the earliest generic name, Alauda. The characters defining the Alauda group are listed and the relation of Chersophilus duponti to the group is discussed.     

Trees within trees: genes and species, molecules and morphology

The construction and interpretation of gene trees is fundamental in molecular systematics. If the gene is defined in a historical (coalescent) sense, there can be multiple gene trees within the single contiguous set of nucleotides, and attempts to construct a single tree for such a sequence must deal with homoplasy created by conflict among divergent histories. On a larger scale, incongruence is expected among gene tree topologies at different loci of individuals within sexually reproducing species, and it has been suggested that this discordance can be used to delimit species. A practical concern for such topological methods is that polymorphisms may be maintained through numerous cladogenic events; this polymorphism problem is less of a concern for nontopological approaches to species delimitation using molecular data. Although a central theoretical concern in molecular systematics is discordance between a given gene tree and the true "species tree," the primary empirical problem faced in reconstructing taxic phylogeny is incongruence among the trees inferred from different sequences. Linkage relationships limit character independence and thus have important implications for handling multiple data sets in phylogenetic analysis, particularly at the species level, where incongruence among different historically associated loci is expected. Gene trees can also be reconstructed for loci that influence phenotypic characters, but there is at best a tenuous relationship between phenotypic homoplasy and homoplasy in such gene trees. Nevertheless, expression patterns and orthology relationships of genes involved in the expression of phenotypes can in theory provide criteria for homology assessment of morphological characters.     

ESTIMATING CHARACTER WEIGHTS DURING TREE SEARCH

Abstract— A new method for weighting characters according to their homoplasy is proposed; the method is non-iterative and does not require independent estimations of weights. It is based on searching trees with maximum total fit, with character fits defined as a concave function of homoplasy. Then, when comparing trees, differences in steps occurring in characters which show more homoplasy on the trees are less influential. The reliability of the characters is estimated, during the analysis, as a logical implication of the trees being compared. The "fittest" trees imply that the characters are maximally reliable and, given character conflict, have fewer steps for the characters which fit the tree better. If other trees save steps in some characters, it will be at the expense of gaining them in characters with less homoplasy.     

Resolving evolutionary relationships in the lichen-forming genus Porpidia and related allies (Porpidiaceae, Ascomycota)

The lichen-forming genus Porpidia (Porpidiaceae, Ascomycota) provides excellent opportunities for evolutionary, reproductive, and ecological studies of crustose epilithic lichen symbioses. However, despite the fact that the genus itself seemed to be clearly delimited, the group was thought to be a hopeless case with regard to intrageneric relationships and species delimitations due to apparently rampant homoplasy throughout most character systems. Contrary to the situation for non-molecular data, a robust and generally well-resolved phylogeny was recovered based on DNA-sequence data. Separate and combined analyses of nuclear ribosomal RNA large subunit and nuclear beta-tubulin gene fragments were performed using maximum parsimony, maximum likelihood, and Bayesian approaches. Branch support was estimated using non-parametic bootstrapping and posterior probabilities, while monophyly of a priori defined groups was tested using posterior probabilities. The results reveal a highly supported "Porpidia sensu lato," however, Porpidia itself is not monophyletic. Several smaller genera of the Porpidiaceae and probably the large genus Lecidea (Lecideaceae) are nested within the group. Most taxa analyzed fall into one of four major subgroups within Porpidia s.l., though the basal relationships among these subgroups could not be supported. This phylogeny will make it possible to re-evaluate morphological and chemical characters in the group, and to conduct detailed studies of species delimitations within the monophyletic subgroups.     

Taxonomic classification of the reef coral family Mussidae (Cnidaria: Anthozoa: Scleractinia)

Molecular analyses are transforming our understanding of the evolution of scleractinian corals and conflict with traditional classification, which is based on skeletal morphology. A new classification system, which integrates molecular and morphological data, is essential for documenting patterns of biodiversity and establishing priorities for marine conservation, as well as providing the morphological characters needed for linking present‐day corals with fossil species. The present monograph is the first in a series whose goal is to develop such an integrated system. It addresses the taxonomic relationships of 55 Recent zooxanthellate genera (one new) in seven families (one new), which were previously assigned to the suborder Faviina (eight genera are transferred to incertae sedis). The present monograph has two objectives. First, we introduce the higher‐level classification system for the 46 genera whose relationships are clear. Second, we formally revise the taxonomy of those corals belonging to the newly discovered family‐level clade (restricted today to the western Atlantic and Caribbean regions); this revised family Mussidae consists of ten genera (one of which is new) and 26 species that were previously assigned to the ‘traditional’ families Faviidae and Mussidae. To guide in discovering morphologic characters diagnostic of higher‐level taxa, we mapped a total of 38 morphologic characters [19 macromorphology, eight micromorphology, 11 microstructure] onto a molecular tree consisting of 67 species [22 Indo‐Pacific and seven Atlantic species in the traditional family Faviidae; 13 Indo‐Pacific and ten Atlantic species in the traditional family Mussidae; 13 species in the traditional families Merulinidae (5), Pectiniidae (7), and Trachyphylliidae (1); two Atlantic species of traditional Montastraea], and trace character histories using parsimony. To evaluate the overall effectiveness of morphological data in phylogeny reconstruction, we performed morphology‐based phylogenetic analyses using 27 (80 states) of the 38 characters, and compared morphological trees with molecular trees. The results of the ancestral state reconstructions revealed extensive homoplasy in almost all morphological characters. Family‐ and subfamily‐level molecular clades [previously identified as XVII?XXI] are best distinguished on the basis of the shapes of septal teeth and corresponding microstructure. The newly revised family Mussidae (XXI) has septal teeth with regular pointed tips (a symplesiomorphy) and a stout blocky appearance. It has two subfamilies, Mussinae and Faviinae. The subfamily Mussinae is distinguished by spine‐shaped teeth and widely spaced costoseptal clusters of calcification centres. The subfamily Faviinae is distinguished by blocky, pointed tricorne or paddle‐shaped teeth with elliptical bases, transverse structures such as carinae that cross the septal plane, and well‐developed aligned granules. Defining diagnostic characters for the broader data set is more challenging. In analyses of taxonomic subsets of the data set that were defined by clade, morphological phylogenetic analyses clearly distinguished the families Mussidae (XXI) and Lobophylliidae (XIX), as well as the two subfamilies of Mussidae (Mussinae, Faviinae), with one exception (Homophyllia australis). However, analyses of the entire 67‐species data set distinguished the family Lobophylliidae (XIX), but not the Merulinidae (XVII) and not the newly defined Mussidae (XXI), although the subfamily Mussinae was recovered as monophyletic. Some lower‐level relationships within the Merulinidae (XVII) agree with molecular results, but this particular family is especially problematic and requires additional molecular and morphological study. Future work including fossils will not only allow estimation of divergence times but also facilitate examination of the relationship between these divergences and changes in the environment and biogeography. Published 2012. This article is a U.S. Government work and is in the public domain in the USA. Zoological Journal of the Linnean Society, 2012, 166 , 465–529.     

A PRELIMINARY INVESTIGATION OF THE PHYLOGENETIC RELATIONSHIPS AMONG THE FRESHWATER,APICAL PORE FIELD-BEARING CYMBELLOID AND GOMPHONEMOID DIATOMS (BACILLARIOPHYCEAE)1

Relationships among the apical pore field-bearing diatom genera Brebissonia, Cymbella, Gomphonema, Gomphoneis, Didymosphenia, Gomphocymbella, and Reimeria and their close ally Encyonema were evaluated using cladistics. These biraphid genera are a polythetic group defined by chloroplast number and type, mode of sexual reproduction, valve orientation and presence of apical pore fields. Character states of valve as well as non-siliceous features were described and then polarized using the outgroup method, with the naviculoid genera Anomoeoneis and Placoneis serving as outgroups. The cladistic analysis suggests two groups of terminal taxa, corresponding to to a predominantly cymbelloid lineage and a gomphonemoid lineage. Didymosphenia, previously thought to be closely allied to gomphonemoid diatoms, is shown to be more closely related to Cymbella. Gomphonema appears to be without distinguishing characteristics. Relationships of the other genera are described. The systematic position of small, doubly-punctate Gomphonema species is discussed.     

Homoplasious character combinations and generic delimitation: a case study from the Indo-Pacific arecoid palms (Arecaceae: Areceae)

The complex distributions of morphological character states in the Indo-Pacific palm tribe Areceae (Arecaceae; Arecoideae) are potentially challenging for the delimitation of its genera. In the first exhaustive sampling of all 65 genera of the Areceae, we examined relationships of two of the tribe's most problematic genera, Heterospathe and Rhopaloblaste, using portions of the low-copy nuclear genes phosphoribulokinase (PRK) and RNA-polymerase II subunit B (RPB2). Both genera fell within a highly supported clade comprising all Areceae genera, but are clearly unrelated. Rhopaloblaste was strongly supported as monophyletic and is most closely related to Indian Ocean genera. Heterospathe was resolved with strong support within a clade of western Pacific genera, but with the monotypic Alsmithia nested within it. Ptychosperma micranthum, which has previously been included in both Heterospathe and Rhopaloblaste, is excluded from these and from Ptychosperma, supporting its recent placement in a new genus Dransfieldia. Morphological comparisons indicate that the crownshaft is putatively synapomorphic for the Areceae with numerous reversals within the clade and some independent origins elsewhere. The putative diagnostic characters of Heterospathe show high levels of homoplasy, and the genus can only be distinguished by a suite of characters, whereas Rhopaloblaste is more clearly defined. Our results have implications not only for the two genera in focus, but have also been influential for the new classification of the Areceae.     

Morphology,molecules and the phylogeny of Characidae (Teleostei,Characiformes)

This is the most comprehensive phylogenetic analysis of the Characidae to date and the first large-scale hypothesis of the family, combining myriad morphological data with molecular information. A total of 520 morphological characters were analysed herein, of which 98 are newly defined. Among the analysed taxa, 259 species were coded by examining specimens, three fossil species were coded from the literature, one species was coded almost completely from published figures, 122 were partially coded from the literature, and 88 were analysed exclusively from molecular data. The total number of species in the analysed dataset is 473. Analyses were made by parsimony under equal and extended implied weighting with a broad range of parameters. The final hypothesis was selected using a stability criterion that chooses among the most parsimonious trees of all searches. It was found by weighting molecular characters with the average homoplasy of entire partitions (markers). The resulting hypothesis is congruent with previous molecular-based phylogenies of the family. The Characidae are monophyletic, with four main clades: the Spintherobolinae new subfamily; an expanded Stethaprioninae including the Grundulini, Gymnocharacini, Rhoadsiini and Stethaprionini; the Stevardiinae; and a clade composed of the Aphyocharacinae, Characinae, Cheirodontinae, Exodontinae and Tetragonopterinae. Also, a stem Characidae was found, as formed by the Eocene–Oligocene genera †Bryconetes and †Paleotetra as successive sister groups of extant members of the family. A subfamilial classification is proposed, but deep changes in the systematics that are beyond the scope of this study are still needed to classify the Characidae into monophyletic genera.     

Weighting against homoplasy improves phylogenetic analysis of morphological data sets

The problem of character weighting in cladistic analysis is revisited. The finding that, in large molecular data sets, removal of third positions (with more homoplasy) decreases the number of well supported groups has been interpreted by some authors as indicating that weighting methods are unjustified. Two arguments against that interpretation are advanced. Characters that collectively determine few well‐supported groups may be highly reliable when taken individually (as shown by specific examples), so that inferring greater reliability for sets of characters that lead to an increase in jackknife frequencies may not always be warranted. But even if changes in jackknife frequencies can be used to infer reliability, we demonstrate that jackknife frequencies in large molecular data sets are actually improved when downweighting characters according to their homoplasy but using properly rescaled functions (instead of the very strong standard functions, or the extreme of inclusion/exclusion); this further weakens the argument that downweighting homoplastic characters is undesirable. Last, we show that downweighting characters according to their homoplasy (using standard homoplasy‐weighting methods) on 70 morphological data sets (with 50–170 taxa), produces clear increases in jackknife frequencies. The results obtained under homoplasy weighting also appear more stable than results under equal weights: adding either taxa or characters, when weighting against homoplasy, produced results more similar to original analyses (i.e., with larger numbers of groups that continue being supported after addition of taxa or characters), with similar or lower error rates (i.e., proportion of groups recovered that subsequently turn out to be incorrect). Therefore, the same argument that had been advanced against homoplasy weighting in the case of large molecular data sets is an argument in favor of such weighting in the case of morphological data sets. © The Willi Hennig Society 2008.     

The phylogeny of the Rosaceae

KALKMAN, C., 1988. The phylogemy of the Rosaceae. A phylogenetic (cladistic) analysis of Rosaceae (excluding Chrysobalanaceae and Neuradaceae) is presented, based on the postulated direction of evolution in 14 morphological characters. Tribes or smaller groups, considered to be holophyletic, are taken as operational units. Three possible cladograms, made by hand, are presented and discussed. One of them is, within the limits of the method, selected as the most plausible image of real history, but this cladogram is not fully resolved and contains much homoplasy. Also presented is a fourth cladogram, produced by computer (CAFCA program); it is of about the same quality.
It is not justified to base drastic alterations in current classification on the weak phylogenetic hypothesis. For the time being it seems better not to recognize any subfamilies, but only a number of tribes.
It is hypothesized that the family originated in West Gondwana. A diagram is presented in which the most plausible cladogram is combined with the present distribution, clarifying the postulated routes of migration.
The sistergroup of Rosaceae is far from evident. The Cunoniaceae are considered to be the most plausible choice.     

Suprageneric systematics of flea beetles (Chrysomelidae: Alticinae) inferred from multilocus sequence data

Recent phylogenetic studies of flea beetles (Alticinae) based on morphological or molecular data have focused on the relationship and possible paraphyly with respect to the closely related Galerucinae, while the supra-generic classification mainly dates back to the 19th century. Here, phylogenetic analysis was performed on DNA sequences for two mitochondrial (rrnL and cox1) and two nuclear (SSU and LSU rRNA) genes from 158 genera and 165 species that cover most suprageneric groups of flea beetles proposed in the older literature. Various alignment strategies and tree search methods were used to test the stability of major clades. Besides confirmation of the placement of several alticine lineages within Galerucinae, a preliminary framework for classification of the main alticine clades was obtained. It is proposed to recognize 18 groups of genera based on well-supported nodes. These include the Altica, Amphimela, Aphthona, Blepharida, Chabria, Chaetocnema, Dibolia, Disonycha, Griva, Lactica, Longitarsus, Manobia, Monoplatus, Nisotra, Oedionychis, Pentamesa, Phygasia and Pseudodera groups. These groups provide a novel perspective to the existing classification. The analysis of 14 morphological characters used in the traditional classification of Alticinae and Galerucinae revealed high levels of homoplasy with respect to the DNA-based tree, but significant hierarchical structure in most of them. Even if not unique to any particular group of genera, these traits largely corroborate the groupings established with DNA sequences.     

Phylogenetic relationships among Heliconiinae genera based on morphology (Lepidoptera: Nymphalidae)

Abstract.  Phylogenetic relationships among Heliconiinae genera are proposed based on early-stage and adult morphology. Parsimony analyses of forty-nine species in twenty-nine genera indicate that Heliconiinae can be divided into four main groups: (1) Pardopsis , Acraea and Actinote ; (2) Cethosia plus Neotropical genera; (3) Oriental genera and (4) fritillaries. Analyses of adult characters suggested that Oriental genera form a monophyletic group, whereas those of adult plus early-stage characters artificially split this group into three separate lineages. Our character set does not contain enough phylogenetic information to resolve relationships among fritillary genera with confidence, and further studies of this group are needed. The classification of the Heliconiinae is revised based on our results.