The phylogenetic relationships of lampridiform fishes (Teleostei: acanthomorpha), based on a total-evidence analysis of morphological and molecular data

We investigated the phylogenetic relationships among five species of lampridiform fishes, three basal outgroup species (two aulopiforms and one myctophiform), and two species of non-lampridiform acanthomorphs (Polymixia and Percopsis) using a combined parsimony analysis of morphological and molecular data. Morphological characters included 28 transformation series obtained from the literature. Molecular characters included 223 informative transformation series from an aligned 854-base pair fragment of 12S mtDNA and 139 informative transformation series from an aligned 561-base pair fragment of 16S mtDNA. A total-evidence analysis using the aulopiforms Synodus and Aulopus and the myctophiform Hygophum as outgroups corroborates the monophyly of Lampridiformes and unites Polymixia with Percopsis. Among the lampridiform fishes we examined, Metavelifer is basal, followed in ascending order by Lampris, Lophotus, Regalecus, and Trachipterus. This hypothesis is congruent with the most recent morphological analysis of the Lampridiformes and rejects a diphyletic origin of elongate body form within the clade. Analysis of a combined matrix of 12S and 16S mtDNA data yielded a phylogenetic hypothesis isomorphic with the total-evidence phylogeny. Analyses of partitioned DNA data sets reveals that single gene regions are poor predictors of the total-evidence phylogeny while combined analyses of both DNA data sets are good predictors of the total-evidence phylogeny.     

PHYLOGENETIC HYPOTHESES UNDER THE ASSUMPTION OF NEUTRAL QUANTITATIVE-GENETIC VARIATION

There are many situations in which the only available characters for reconstructing phylogenies are morphological. Those traits that are subject only to the forces of mutation and random genetic drift can be used to obtain unbiased estimates of phylogenetic relationships. However, the accurate recovery of a phylogeny from information on neutral characters requires the procurement of data for a large number of independent traits, individuals, and populations. Phylogenetic trees fit to data from more than five species will almost always contain topological errors, even with very large data sets. The population-genetic consequences of the neutral model are reviewed, and some statistical methods for testing whether the diversification of a phylogeny is compatible with such a model are outlined. The theory is then applied to a very large data set on cranial morphology in modern man. The results are consistent with the hypothesis that interracial differences in human skull dimensions are a simple consequence of random drift and mutation.     

Phylogenetic relationships of the carabid subfamily Harpalinae (Coleoptera) based on molecular sequence data

The carabid subfamily Harpalinae contains most of the species of carabid beetles. This subfamily, with over 19,000 species, radiated in the Cretaceous to yield a large clade that is diverse in morphological form and ecological habit. While there are several morphological, cytological, and chemical characters that unite most harpalines, the placement of some tribes within the subfamily remains controversial, as does the sister group relationships to this large group. In this study, DNA sequences from the 28S rDNA gene and the wingless nuclear protein-coding gene were collected from 52 carabid genera representing 31 harpaline tribes in addition to more than 21 carabid outgroup taxa to reconstruct the phylogeny of this group. Molecular sequence data from these genes, along with additional data from the 18S rDNA gene, were analyzed with a variety of phylogenetic analysis methods, separately for each gene and in a combined data approach. Results indicated that the subfamily Harpalinae is monophyletic with the enigmatic tribes of Morionini, Peleciini, and Pseudomorphini included within it. Brachinine bombardier beetles are closely related to Harpalinae as they form the sister group to harpalines or, in some analyses, are included within it or with austral psydrines. The austral psydrines are the sister group to Harpalinae+Brachinini clade in most analyses and austral psydrines+Brachinini+Harpalinae clade is strongly supported.     

Phylogenetic analyses of marine sponges within the order Verongida: a comparison of morphological and molecular data

Abstract. Because the taxonomy of marine sponges is based primarily on morphological characters that can display a high degree of phenotypic plasticity, current classifications may not always reflect evolutionary relationships. To assess phylogenetic relationships among sponges in the order Verongida, we examined 11 verongid species, representing six genera and four families. We compared the utility of morphological and molecular data in verongid sponge systematics by comparing a phylogeny constructed from a morphological character matrix with a phylogeny based on nuclear ribosomal DNA sequences. The morphological phylogeny was not well resolved below the ordinal level, likely hindered by the paucity of characters available for analysis, and the potential plasticity of these characters. The molecular phylogeny was well resolved and robust from the ordinal to the species level. We also examined the morphology of spongin fibers to assess their reliability in verongid sponge taxonomy. Fiber diameter and pith content were highly variable within and among species. Despite this variability, spongin fiber comparisons were useful at lower taxonomic levels (i.e., among congeneric species); however, these characters are potentially homoplasic at higher taxonomic levels (i.e., between families). Our molecular data provide good support for the current classification of verongid sponges, but suggest a re-examination and potential reclassification of the genera Aiolochroia and Pseudoceratina . The placements of these genera highlight two current issues in morphology-based sponge taxonomy: intermediate character states and undetermined character polarity.     

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.     

Why do morphological phylogenies vary in quality? An investigation based on the comparative history of lizard clades

Phylogenies based on morphology vary considerably in their quality: some are robust and explicit with little conflict in the data set, whereas others are far more tenuous, with much conflict and many possible alternatives. The main primary reasons for untrue or inexplicit morphological phylogenies are: not enough characters developed between branching points, uncertain character polarity, poorly differentiated character states, homoplasy caused by parallelism or reversal, and extinction, which may remove species entirely from consideration and can make originally conflicting data sets misleadingly compatible, increasing congruence at the expense of truth. Extinction differs from other confounding factors in not being apparent either in the data set or in subsequent analysis. One possibility is that variation in the quality of morphological phylogenies has resulted from exposure to different ecological situations. To investigate this, it is necessary to compare the histories of the clades concerned. In the case of explicit morphological phylogenies, ecological and behavioural data can be integrated with them and it may then be possible to decide whether morphological characters are likely to have been elicited by the environments through which the clade has passed. The credibility of such results depends not only on the phylogeny being robust but also on its detailed topology: a pectinate phylogeny will often allow more certain and more explicit statements to be made about historical events. In the case of poor phylogenies, it is not possible to produce detailed histories, but they can be compared with robust phylogenies in the range of ecological situations occupied, and whether they occupy novel situations in comparison with their outgroups. LeQuesne testing can give information about niche homoplasy, and it may also be possible to see if morphological features are functionally associated with ecological parameters, even if the direction of change is unknown. Examination of the robust and explicit phylogeny of the semaphore geckoes (Pristurus) suggests that its quality does stem from a variety of environmental factors. The group has progressed along an ecological continuum, passing through a series of increasingly severe niches that appear to have elicited many morphological changes. The fact that niches are progressively filled reduces the likelihood of species reinvading a previous one with related character reversal. Because the niches of advanced Pristurus are virtually unique within the Gekkonidae the morphological changes produced are also very rare and therefore easy to polarize. Ecological changes on the main stem of the phylogeny are abrupt and associated character states consequently well differentiated.(ABSTRACT TRUNCATED AT 400 WORDS)     

Molecular phylogeny of bony fishes,based on the amino acid sequence of the growth hormone

Bony fishes (Osteichthyes) comprise over 22,000 species, about half of all vertebrate species. In order to investigate the phylogenetic relationships within this vertebrate class, we have studied the only protein whose primary structure is known in a rather large (27) number of fish species belonging to seven orders—the growth hormone. The phylogeny obtained using the maximum parsimony method based on amino acid sequences represents the first molecular phylogeny of teleostean fishes based on an extensive set of data. This phylogeny agrees remarkably well with the generally accepted phylogeny based on morphological characters and paleontological data. Correspondence to: G. Bernardi     

The utility of morphological characters in gastropod phylogenetics: an example from the Calyptraeidae

Organismal taxonomy is often based on a single or a small number of morphological characters. When they are morphologically simple or known to be plastic, we may not have great confidence in the taxonomic conclusions of analyses based on these characters. For example, calyptraeid gastropod shells are well known for their simplicity and plasticity, and appear to be subject to frequent evolutionary convergences, but are nevertheless the basis for calyptraeid taxonomy. In a case like this, knowing how the pattern of relationships inferred from morphological features used in traditional taxonomy compares to the patterns of relationships inferred from other morphological characters or DNA sequence data would be useful. In this paper, I examine the relative utility of traditional taxonomic characters (shell characters), anatomical characters and molecular characters for reconstructing the phylogeny of calyptraeid gastropods. The results of an ILD test and comparisons of the recovered tree topologies suggest that there is conflict between the DNA sequence data and the morphological data. Very few of the nodes recovered by the morphological data were recovered by any other dataset. Despite this conflict, the inclusion of morphological data increased the resolution and support of nodes in the topology recovered from a combined dataset. The RIs and CIs of the morphological data on the best estimate topology were not any worse than these indices for the other datasets. This analysis demonstrates that although analyses can be misled by these convergences if morphological characters are used alone, these characters contribute significantly to the combined dataset.  © 2003 The Linnean Society of London . Biological Journal of the Linnean Society , 2003, 78 , 541–593.     

Molecular and morphological phylogenetics of weevils (coleoptera,curculionoidea): do niche shifts accompany diversification?

The main goals of this study were to provide a robust phylogeny for the families of the superfamily Curculionoidea, to discover relationships and major natural groups within the family Curculionidae, and to clarify the evolution of larval habits and host-plant associations in weevils to analyze their role in weevil diversification. Phylogenetic relationships among the weevils (Curculionoidea) were inferred from analysis of nucleotide sequences of 18S ribosomal DNA (rDNA; approximately 2,000 bases) and 115 morphological characters of larval and adult stages. A worldwide sample of 100 species was compiled to maximize representation of weevil morphological and ecological diversity. All families and the main subfamilies of Curculionoidea were represented. The family Curculionidae sensu lato was represented by about 80 species in 30 "subfamilies" of traditional classifications. Phylogenetic reconstruction was accomplished by parsimony analysis of separate and combined molecular and morphological data matrices and Bayesian analysis of the molecular data; tree topology support was evaluated. Results of the combined analysis of 18S rDNA and morphological data indicate that monophyly of and relationships among each of the weevil families are well supported with the topology ((Nemonychidae, Anthribidae) (Belidae (Attelabidae (Caridae (Brentidae, Curculionidae))))). Within the clade Curculionidae sensu lato, the basal positions are occupied by mostly monocot-associated taxa with the primitive type of male genitalia followed by the Curculionidae sensu stricto, which is made up of groups with the derived type of male genitalia. High support values were found for the monophyly of some distinct curculionid groups such as Dryophthorinae (several tribes represented) and Platypodinae (Tesserocerini plus Platypodini), among others. However, the subfamilial relationships in Curculionidae are unresolved or weakly supported. The phylogeny estimate based on combined 18S rDNA and morphological data suggests that diversification in weevils was accompanied by niche shifts in host-plant associations and larval habits. Pronounced conservatism is evident in larval feeding habits, particularly in the host tissue consumed. Multiple shifts to use of angiosperms in Curculionoidea were identified, each time associated with increases in weevil diversity and subsequent shifts back to gymnosperms, particularly in the Curculionidae.     

Relationships within the family Actiniidae (Cnidaria,Actiniaria) based on molecular characters

Current sea anemone systematics is based on relatively few morphological characters, and potentially could benefit from the use of molecular characters. In this paper, the phylogenetic relationships of 12 species from 6 genera in the family Actiniidae have been investigated using electrophoretically separated isozymes. A numerical cladistic analysis has produced an estimated phylogeny. The implications of this phylogeny for the taxonomic use of certain morphological characters are discussed.     

Assessing phylogenetic resolution among mitochondrial, nuclear, and morphological datasets in Nothonotus darters (Teleostei: Percidae)

External morphological characters are the basis of our understanding of diversity and species relationships in many darter clades. The past decade has seen the publication of many studies utilizing mtDNA sequence data to investigate darter phylogenetics, but only recently have nuclear genes been used to investigate darter relationships. Despite a long tradition of use in darter systematics few studies have examined the phylogenetic utility of external morphological characters in estimating relationships among species in darter clades. We present DNA sequence data from the mitochondrial cytochrome b (cytb) gene, the nuclear encoded S7 intron 1, and discretely coded external morphological characters for all 20 species in the darter clade Nothonotus. Bayesian phylogenetic analyses result in phylogenies that are in broad agreement with previous studies. The cytb gene tree is well resolved, while the nuclear S7 gene tree lacks phylogenetic resolution, node support, and is characterized by a lack of reciprocal monophyly for many of the Nothonotus species. The phylogenies resulting from analysis of the morphological dataset lack resolution, but nodes present are found in the cytb and S7 gene trees. The highest resolution and node support is found in the Bayesian combined data phylogeny. Based on our results we propose continued exploration of the phylogenetic utility of external morphological characters in other darter clades. Given the extensive lack of reciprocal monophyly of species observed in the S7 gene tree we predict that nuclear gene sequences may have limited utility in intraspecific phylogeographic studies of Nothonotus darters.     

The Phylogeny of the Gasterosteidae: Combining Behavioral and Morphological Data Sets

Genealogical relationships among the five genera of stickleback (Gasterosteidae: Smegmomorpha) fishes were reconstructed based upon 47 behavioral and 89 morphological characters. Phylogenetic systematic analysis of the combined data set produced a single MPT (consistency index of 82.54%) structured ( Spinachia ( Apeltes-((Pungitius + Culaea )( Gasterosteus aculeatus + G. wheatlandi )))). When analyzed separately, both behavioral and morphological data sets produced the same tree topology, although the consistency index (excluding uninformative characters) was higher for the behavioral (90.70%) than for the morphological (68.13%) characters. This total evidence analysis provides a highly robust estimate of phylogeny for the sticklebacks and reiterates the importance of discarding a priori biases about behavioral evolution when selecting characters for phylogenetic analysis.     

Using 18S rDNA to resolve diaptomid copepod (Copepoda: Calanoida: Diaptomidae) phylogeny: an example with the North American genera

The phylogenetic relationships among the numerous genera of diaptomid copepods remain elusive due to difficulties in obtaining sufficient numbers of phylogenetically informative morphological characters for cladistic analysis. Molecular phylogenetic techniques offer high potential to resolve phylogenetic relationships in the absence of sufficient morphological characters because of the ease in which many characters can be unambiguously coded. I present the first molecular phylogeny for diaptomid copepod genera using 18S rDNA. Specifically, I test Light’s (1939) hypothesis regarding the interrelationships among the North American diaptomid genera. The 18S phylogeny is remarkably consistent with Light’s hypothesis. The endemic North American genera represent a monophyletic group exclusive of the non-endemic genera. Moreover, his hypothesized basal genus for the North America genera, Hesperodiaptomus, is the basal genus in this analysis. However, his Leptodiaptomus group is not reciprocally monophyletic with his Hesperodiaptomus group, but is rather a derived member of the latter group. Finally, the genus Mastigodiaptomus is found to be more closely allied with the non-endemic genera, as Light suggested. This phylogeny contributes heavily to the understanding of phylogenetic relationships among North American diaptomids and has large implications for the systematics of diaptomids in general. The use of 18S rDNA sequences in phylogenetic analyses of diaptomid copepods can be used to confirm the monophyly of recognized genera, the interrelationships among genera, and subsequent biogeographic interpretation of the family’s diversification. The use of molecular data, such as 18S rDNA sequences, to test phylogenetic hypotheses based on a very limited number of morphological characters will be a particularly useful approach to phylogenetic analysis in this system.     

Phylogeny of the Oriental Drosophila melanogaster species group: a multilocus reconstruction

The melanogaster species group of Drosophila (subgenus Sophophora) has long been a favored model for evolutionary studies because of its morphological and ecological diversity and wide geographic distribution. However, phylogenetic relationships among species and subgroups within this lineage are not well understood. We reconstructed the phylogeny of 17 species representing 7 "oriental" species subgroups, which are especially closely related to D. melanogaster. We used DNA sequences of four nuclear and two mitochondrial loci in an attempt to obtain the best possible estimate of species phylogeny and to assess the extent and sources of remaining uncertainties. Comparison of trees derived from single-gene data sets allowed us to identify several strongly supported clades, which were also consistently seen in combined analyses. The relationships among these clades are less certain. The combined data set contains data partitions that are incongruent with each other. Trees reconstructed from the combined data set and from internally homogenous data sets consisting of three or four genes each differ at several deep nodes. The total data set tree is fully resolved and strongly supported at most nodes. Statistical tests indicated that this tree is compatible with all individual and combined data sets. Therefore, we accepted this tree as the most likely model of historical relationships. We compared the new molecular phylogeny to earlier estimates based on morphology and chromosome structure and discuss its taxonomic and evolutionary implications.     

The phylogeny ofActaea (Ranunculaceae): A biogeographical approach

Phylogenetic analyses of the genusActaea were performed using morphological, ecological and biogeographical characters. Using solely morphological characters, the relationships of the three identified species-groups remain uncertain. Close biogeographical examination and comparison of the areas with ecological peculiarities as well as climate data gave important insight into the phylogeny ofActaea and the whole tribe. Consequently, the obtained biogeographical data were used for phylogenetic reconstructions. Both, from the point of view of morphological and biogeographical data,A. pachypoda andA. asiatica are the most ancestral species. They grow on the east sides of the continents, mainly in broad-leaved forests. In West Eurasia the apomorphicA. spicata andA. acuminata occur under similar climatic and ecological conditions, but these species are adapted to another climate rhythm. The most advanced species (A. erythrocarpa, A. rubra) are to be found in the boreal forests where they are widely distributed. This biogeographical approach revealed that the evolution of the species led to a gradual widening and shifting of their ecological constitutions.     

The ecological tale of Gonyleptidae (Arachnida,Opiliones) evolution: phylogeny of a Neotropical lineage of armoured harvestmen using ecological,behavioural and chemical characters

The large Neotropical family Gonyleptidae comprises nearly 820 species divided into 16 subfamilies. The majority of publications on harvestman ecology, behaviour and scent gland secretion chemistry have focused on this family. We used the information available in the literature and combined it with an intensive search for ecological, behavioural and chemical data to infer the phylogeny of the Gonyleptidae. We included 28 species belonging to 14 of the 16 gonyleptid subfamilies in the ingroup and four species belonging to the families Cosmetidae, Stygnidae and Manaosbiidae in the outgroup. We performed the analyses using equally weighted characters and coded 63 characters comprising 153 states, which makes this the largest non‐morphological, non‐molecular phylogenetic data matrix published to date. We obtained five most parsimonious trees, and the strict consensus resulted in six collapsed nodes. The results show that the monophyly of Gonyleptidae is equivocal because Metasarcinae is placed at a basal polytomy with the outgroups Cosmetidae and Stygnidae. Gonyleptinae, Pachylinae and Progonyleptoidellinae are polyphyletic groups, but the remaining subfamilies are monophyletic and have several synapomorphies. Based on the resulting topology, we discuss the performance of ecological, behavioural and chemical characters, and map a selected set of characters to discuss their evolutionary patterns in the family.     

Phylogeny of Greya (Lepidoptera: Prodoxidae), based on nucleotide sequence variation in mitochondrial cytochrome oxidase I and II: congruence with morphological data

The phylogeny of Greya Busck (Lepidoptera: Prodoxidae) was inferred from nucleotide sequence variation across a 765-bp region in the cytochrome oxidase I and II genes of the mitochondrial genome. Most parsimonious relationships of 25 haplotypes from 16 Greya species and two outgroup genera (Tetragma and Prodoxus) showed substantial congruence with the species relationships indicated by morphological variation. Differences between mitochondrial and morphological trees were found primarily in the positions of two species, G. variabilis and G. pectinifera, and in the branching order of the three major species groups in the genus. Conflicts between the data sets were examined by comparing levels of homoplasy in characters supporting alternative hypotheses. The phylogeny of Greya species suggests that host-plant association at the family level and larval feeding mode are conservative characters. Transition/transversion ratios estimated by reconstruction of nucleotide substitutions on the phylogeny had a range of 2.0-9.3, when different subsets of the phylogeny were used. The decline of this ratio with the increase in maximum sequence divergence among taxa indicates that transitions are masked by transversions along deeper internodes or long branches of the phylogeny. Among transitions, substitutions of A-->G and T-->C outnumbered their reciprocal substitutions by 2-6 times, presumably because of the approximately 4:1 (77%) A+T-bias in nucleotide base composition. Of all transversions, 73%-80% were A<-->T substitutions, 85% of which occurred at third positions of codons; these estimates did not decrease with an increase in maximum sequence divergence of taxa included in the analysis. The high frequency of A<-->T substitutions is either a reflection or an explanation of the 92% A+T bias at third codon positions.      

Phylogeny of extant nephilid orb-weaving spiders (Araneae, Nephilidae): testing morphological and ethological homologies

The Pantropical spider clade Nephilidae is famous for its extreme sexual size dimorphism, for constructing the largest orb-webs known, and for unusual sexual behaviors, which include emasculation and extreme polygamy. We synthesize the available data for the genera Nephila , Nephilengys , Herennia and Clitaetra to produce the first species level phylogeny of the family. We score 231 characters (197 morphological, 34 behavioral) for 61 taxa: 32 of the 37 known nephilid species plus two Phonognatha and one Deliochus species, 10 tetragnathid outgroups, nine araneids, and one genus each of Nesticidae, Theridiidae, Theridiosomatidae, Linyphiidae, Pimoidae, Uloboridae and Deinopidae. Four most parsimonious trees resulted, among which successive weighting preferred one ingroup topology. Neither an analysis of an alternative data set based on different morphological interpretations, nor separate analyses of morphology and behavior are superior to the total evidence analysis, which we therefore propose as the working hypothesis of nephilid relationships, and the basis for classification. Ingroup generic relationships are ( Clitaetra ( Herennia ( Nephila , Nephilengys ))) . Deliochus and Phonognatha group with Araneidae rather than Nephilidae. Nephilidae is sister to all other araneoids ( contra most recent literature). Ethological data, although difficult to obtain and thus frequently missing for rare taxa, are phylogenetically informative. We explore the evolution of selected morphological and behavioral characters, discuss and redefine the homology of palpal sclerites, disprove semientelegyny in spiders, trace the newly interpreted evolution of the orb web, and show that nephilid genital morphologies coevolve with sexual behaviors and extreme sexual size dimorphism. Phylogenetic interpretations of behavior suggest new insights into spider biology and avenues for future research.
© The Willi Hennig Society 2007.