Phylogenetic relationships of the Sparidae (Teleostei: Percoidei) and implications for convergent trophic evolution

A phylogenetic analysis of the majority of sparid genera and representatives of the sparoid families Centracanthidae, Lethrinidae and Nemipteridae is presented using 87 predominately osteological characters. The Sparidae constitute a monophyletic grouping, with the inclusion of the centracanthid Spicara smaris , which nests deep within the ingroup. The phylogeny was then used to investigate agreement with the most recent molecular study, taxonomic stability of subfamilial classification and the evolution of feeding strategies. Results show that the incongruence between morphological and molecular data appears largely to be an artifact of errors in rooting. However, there appears to be real and substantial conflict between the molecular tree and the morphological data, which is not attributable to the different positions of the least congruent taxa. The data support the molecular hypothesis that none of the subfamilial classification, based on dentition and trophic specialization, is monophyletic, and should be rejected pending further taxonomic revision. The phylogeny supports multiple independent origins of trophic types and it is suggested that the evolutionary plasticity of the oral teeth of sparids has been fundamental to the adaptive radiation of this family compared to their closest allies. ©2002 The Linnean Society of London, Biological Journal of the Linnean Society , 2002, 76 , 269–301.     

The Phylogeny of the Lophopidae and the Impact of Sexual Selection and Coevolutionary Sexual Conflict

A cladistic analysis of Lophopidae was performed, using 73 observed morphological characters and 41 taxa. This analysis involved 36 genera belonging to the Lophopidae family and 5 outgroups. For a better understanding of the selected characters some illustrations are provided. The most parsimonious cladograms obtained show that the Lophopidae cannot be considered as a monophyletic lineage unless two genera are withdrawn from this family: Hesticus Walker, 1862, and Silvanana Metcalf, 1947. The systematic position of these two genera remains uncertain. They cannot yet be included in another family of Fulgoromorpha. A cladistic analysis of each of the 19 remaining Fulgoromorphan families must be performed first. A new family could be created for these two genera, but not before we are sure that these two genera are in no way members of an existing family. The outgroup problem is discussed. The monophyletic lineage represented by the Lophopidae can be divided into four natural groups: Carriona⁺, Makota⁺, Sarebasa⁺, and Bisma⁺. When a cladistic analysis is completed using a data matrix without characters linked to females, the cladogram obtained presents a disrupted basal resolution. Female characters appear to bring a phylogenetic signal important basally in the evolution of the Lophopidae but also apically, directly between the relationships of some genera. A similar analysis, using a matrix without characters linked to males, provides a phylogeny disrupted between the groups that form the Lophopidae and in the basal resolution in these groups. The respective impacts of the genitalic characters are discussed in relation to sexual selection conflict.     

Phylogenetic relationships of some common Indo-Pacific snappers (Perciformes: Lutjanidae) based on mitochondrial DNA sequences, with comments on the taxonomic position of the Caesioninae

The phylogenetic relationships of 27 species of common Indo-Pacific snappers (Lutjanidae) were explored using the 16S ribosomal RNA and cytochrome b mitochondrial genes with minimum evolution, maximum parsimony, maximum likelihood and Bayesian inference analyses. Included were species representing four subfamilies, the Caesioninae, Etelinae, Paradicichthyinae, and Lutjaninae. Members of the closely related families Haemulidae, Lethrinidae, Nemipteridae and Sparidae, were included for outgroup comparisons and to explore the relationships between the Haemuloidea, Lutjanoidea and Sparoidea. Monophyly of the Lutjanidae was resolved. The Caesioninae was nested within the Lutjaninae, supporting the recent view that the Caesionidae should be treated as a synonym of the Lutjanidae. The subfamilies Etelinae and Paradicichthyinae were resolved as sister taxa to the remainder of the Lutjanidae, which corroborates previous cladistic analyses conducted to determine relationships of lutjanid subfamilies. Bayesian inference and maximum likelihood analyses suggest that Macolor is the sister taxon to the Caesioninae and may represent a transitional form between the Lutjaninae and Caesioninae. Three species of Western Atlantic lutjanids, Lutjanus campechanus, L. synagris, and Rhomboplites aurorubens, were included in the analyses to examine their relationships to Indo-Pacific species; they formed a well-supported clade nested within Pacific lutjanines suggesting that Atlantic species of Lutjaninae are derived from an Indo-Pacific lineage. Results of our molecular phylogenetic analyses are congruent with the general morphology and external colouration of the resolved groups of species of Lutjanus. The "black spot" complex containing L. fulviflamma, L. monostigma, and L. russelli was resolved with strong support, and had L. carponotatus nested within. The morphology of L. carponotatus suggests a close relationship to this group, and the lack of the black spot near the lateral line below the soft dorsal fin is possibly a secondary loss. As expected, the "blue-lined" species, L. kasmira and L. quinquelineatus, formed a strongly supported clade. Lutjanus bohar and L. gibbus, both distinctly red, long-lived fish that often accumulate large quantities of ciguatera toxin in their tissues, were resolved as sister taxa.     

A phylogeny of the fish family Sparidae (porgies) inferred from mitochondrial sequence data

The porgies (Sparidae) comprise a diverse group of neritic fishes with a broad geographic distribution. We used mitochondrial DNA sequences from partial 16S ribosomal RNA and cytochrome b genes to reconstruct the phylogenetic history of these fishes. Sequences from 38 sparid species, 10 species in outgroups closely related to sparids, seven basal percoid species, and a non-perciform outgroup species were analyzed with parsimony and maximum likelihood. The Sparidae were monophyletic with the inclusion of Spicara, which is currently placed in the Centracanthidae. The genera Spicara, Pagrus, and Pagellus, were not monophyletic indicating a need for revision. Two main sparid lineages were recovered in all analyses, but the previously proposed six sparid subfamilies (Boopsinae, Denticinae, Diplodinae, Pagellinae, Pagrinae, and Sparinae) were not monophyletic. This suggests that dentition and feeding modes, upon which these subfamilies are based, were independently derived multiple times within sparid fishes. There was no evidence from the 16S or combined analyses for a monophyletic Sparoidea.     

What do we know about chrysidoid (Hymenoptera) relationships?

The phylogeny of the superfamily Chrysidoidea is reviewed. Relationships among the families proposed by Carpenter (1986) were confirmed by Brothers & Carpenter (1993) . The status of knowledge of phylogenetic relationships within families is assessed. Cladistic analyses have been undertaken only within Plumariidae (by Roig-Alsina 1994 ; a manual analysis of genera), Chrysididae (by Kimsey & Bohart 1991 ; a manual analysis of subfamilies and tribes, and genera within subfamilies) and Bethylidae (by Sorg 1988 ; a manual analysis of subfamilies, and genus groups within three of these; and by Polaszek & Krombein 1994 ; a quantitative cladistic analysis of the genera of Bethylinae). These analyeses are critically evaluated, and the current classifications within all the families examined cladistically. Generic relationships are investigated within Scolebythidae and Embolemidae; subfamily relationships are investigated within Sclerogibbidae and Dryinidae.     

Notes on the position of the true freshwater crabs within the brachyrhynchan Eubrachyura (Crustacea: Decapoda: Brachyura)

Cladistic and phenetic relationships of 51 eubrachyuran crab genera, comprising 36 genera of marine crabs and 18 genera of true freshwater crabs from 7 families, were investigated using 121 parsimony-informative adult morphological characters. The data matrix was subjected to four different treatments: (1) a cladistic analysis with a combination of unordered and ordered characters, (2) a cladistic analysis with all characters unordered, (3) neighbour-joining, and (4) UPGMA phenetic analyses. The parsimony analysis conducted with a combination of ordered and unordered characters produced a set of hypotheses which supported monophyly of a Pseudothelphusidae+Potamoidea clade. Furthermore, exemplar genera of the Bythograeidae and Pinnotheridae formed an unresolved polytomy with the Pseudothelphusidae+Potamoidea group, the Thoracotremata. The trichodactylid freshwater crabs were positioned as the sister taxon of the basal portunoid Carcinus, but were unresolved relative to other portunoids and geryonids. Second, the parsimony analysis conducted with all characters unordered resulted in a [bythograeid, pseudothelphusid+potamoid, pinnotherid, thoracotreme] group with no hierarchical resolution, which in turn formed a polytomy with a goneplacid+portunoid clade and a polyphyletic Xanthoidea. And third, phenetic groupings of the eubrachyuran genera invariably placed the pseudothelphusids with the potamoids, and this clustered with a group containing the thoracotremes (either in whole or part). Support was thus found for morphological connections among the nontrichodactylid freshwater crabs, thoracotremes, bythograeids, and pinnotherids, and for the placement of the trichodactylids within the Portunoidea. These two latter findings (that used a range of genera from each family) are broadly congruent with a previous cladistic analysis of selected eubrachyuran familial groundpatterns that used a basal exemplar of each marine and freshwater crab family (Sternberg et al., 1999). However, it is clear that the large scale homoplasy identified here may nullify any reliable hypothesis of brachyrhynchan groupings at this stage.     

An annotated list of fish parasites (Isopoda, Copepoda, Monogenea, Digenea, Cestoda, Nematoda) collected from Snappers and Bream (Lutjanidae, Nemipteridae, Caesionidae) in New Caledonia confirms high parasite biodiversity on coral reef fish

ABSTRACT: BACKGROUND: Coral reefs are areas of maximum biodiversity, but the parasites of coral reef fishes, and especially their species richness, are not well known. Over an 8-year period, parasites were collected from 24 species of Lutjanidae, Nemipteridae and Caesionidae off New Caledonia, South Pacific. RESULTS: Host-parasite and parasite-host lists are provided, with a total of 207 host-parasite combinations and 58 parasite species identified at the species level, with 27 new host records. Results are presented for isopods, copepods, monogeneans, digeneans, cestodes and nematodes. When results are restricted to well-sampled reef fish species (sample size[THIN SPACE]>[THIN SPACE]30), the number of host-parasite combinations is 20[EN DASH]25 per fish species, and the number of parasites identified at the species level is 9[EN DASH]13 per fish species. Lutjanids include reef-associated fish and deeper sea fish from the outer slopes of the coral reef: fish from both milieus were compared. Surprisingly, parasite biodiversity was higher in deeper sea fish than in reef fish (host-parasite combinations: 12.50 vs 10.13, number of species per fish 3.75 vs 3.00); however, we identified four biases which diminish the validity of this comparison. Finally, these results and previously published results allow us to propose a generalization of parasite biodiversity for four major families of reef-associated fishes (Lutjanidae, Nemipteridae, Serranidae and Lethrinidae): well-sampled fish have a mean of 20 host-parasite combinations per fish species, and the number of parasites identified at the species level is 10 per fish species. CONCLUSIONS: Since all precautions have been taken to minimize taxon numbers, it is safe to affirm than the number of fish parasites is at least ten times the number of fish species in coral reefs, for species of similar size or larger than the species in the four families studied; this is a major improvement to our estimate of biodiversity in coral reefs. Our results suggest that extinction of a coral reef fish species would eventually result in the coextinction of at least ten species of parasites.     

A CLADISTIC ANALYSIS AMONG TRILOPHODONT GOMPHOTHERES (MAMMALIA, PROBOSCIDEA) WITH SPECIAL ATTENTION TO THE SOUTH AMERICAN GENERA

Abstract:  The trilophodont gomphothere group is a monophyletic group of genera separated from other proboscideans by one synapomorphy, the presence of trefoil-shaped wear patterns on the occlusal surfaces of their teeth. These wear patterns vary from being just a single trefoil, through double trefoils, to more complex combinations of trefoils. They are present in all of the genera studied here. Our cladistic analysis makes use of 12 genera as terminal taxa. It was performed using 43 cranial, dental and postcranial morphological characters. The polarity of characters was based on outgroup criteria using the genus Phiomia as the outgroup. All characters are considered to be unordered (34 are binary and nine are multistate). The present analysis leads us to reject the hypothesis that considered Rhynchotherium as a direct ancestor of South American gomphotheres and supports the hypothesis that Sinomastodon is the sister group of Cuvieronius and Stegomastodon. High congruence between the stratigraphical record and the phylogenetic hypothesis is observed.     

Classification of the family Plectonemertidae (Nemertea): a phenetic comparison

A phenetic classification based on overall morphological similarity between the species in the family Plectonemertidae (genera Plectonemertes, Campbellonemertes, Potamonemertes, Leptonemertes, Katechonemertes, Argonemertes, Anliponemertes, and Acteonemertes) was undertaken and the result compared with a cladistic and an evolutionary classification. Similarity between species was computed by Gower's general coefficient of similarity and various techniques were used to find patterns in the similarity matrix: single-linkage, average-linkage, and complete-linkage clustering, together with principal coordinate analysis. Although the explicit aim of phenetics is not to estimate the phylogeny, the classification based on overall similarity still portrays phylogeny better than an intuitive assessment of morphological similarity, as judged by the cladistic analysis. The classification does not support the previously proposed hypothesis that the two freshwater genera Campbellonemertes and Potamonemertes have descended from a terrestrial ancestor.     

Classification of the family Plectonemertidae (Nemertea): a phenetic comparison

A phenetic classification based on overall morphological similarity between the species in the family Plectonemertidae (genera Plectonemertes, Campbellonemertes, Potamonemertes, Leptonemertes, Katechonemertes, Argonemertes, Anliponemertes, and Acteonemertes ) was undertaken and the result compared with a cladistic and an evolutionary classification. Similarity between species was computed by Gower's general coefficient of similarity and various techniques were used to find patterns in the similarity matrix: single-linkage, average-linkage, and complete-linkage clustering, together with principal coordinate analysis. Although the explicit aim of phenetics is not to estimate the phylogeny, the classification based on overall similarity still portrays phylogeny better than an intuitive assessment of morphological similarity, as judged by the cladistic analysis. The classification does not support the previously proposed hypothesis that the two freshwater genera Campbellonemertes and Potamonemertes have descended from a terrestrial ancestor.     

Using critical path method to analyse the radiation of rudist bivalves

It has been suggested that certain families of rudist bivalves (superfamily Hippuritoidea) were 'preadapted' to inhabit different environments and radiated to fill them. This scenario was based on a hypothesis of a geometric constraint of shell growth, a differential increase in the number of rudist genera possessing uncoiled shells relative to those possessing spirogyrate (i.e. coiled) shells, and a speculative phylogeny. In this paper, these ideas are reformulated and tested by comparing a postulated sequence of structural changes, expressed according to critical path method of management theory, and phylogeny, inferred from cladistic analysis. The hypothesis of constraint is unfalsified, and the cladogram is consistent with a proliferation of rudists possessing uncoiled shells. The proliferation may be attributed to the origin of an invaginated ligament, which should be considered as a direct adaptation.     

A morphological phylogeny for four families of amblyceran lice (Phthiraptera: Amblycera: Menoponidae, Boopiidae, Laemobothriidae, Ricinidae)

The suborder Amblycera (Insecta: Phthiraptera) comprises seven recognized families of parasitic lice. Three of these families (the Menoponidae, Laemobothriidae and Ricinidae) are present on a wide range of avian hosts. The four remaining families are restricted to a small section of mammals (the Boopiidae are parasites of Australian and New Guinean marsupials, and the Gyropidae, Trimenoponidae and Abrocomophagidae parasitize South and Central American rodents). This study uses a morphological approach to examine the evolutionary relationships between the genera from four amblyceran families: the Menoponidae, Boopiidae, Laemobothriidae and Ricinidae. Genera are represented by exemplars and a total of 44 louse taxa and one outgroup taxon were included. A cladistic analysis of 147 unordered characters recovered six equally parsimonious trees. Bootstrap, jackknife and Bremer support analyses were undertaken to assess the level of support for each resolved node in the strict consensus topology. Strong support was found for deep branch relationships between the families and in some cases for supra-generic groupings within families. The clades present in the strict consensus tree are discussed with reference to supra-generic and interfamily relationships, character choice, morphological convergence and host distribution. This study is the first phylogeny presented solely for amblyceran genera.  © 2003 The Linnean Society of London, Zoological Journal of the Linnean Society , 2003, 138 , 39–82.     

Phylogenetic relationships of conifers inferred from partial 28S rRNA gene sequences

The conifers, which traditionally comprise seven families, are the largest and most diverse group of living gymnosperms. Efforts to systematize this diversity without a cladistic phylogenetic framework have often resulted in the segregation of certain genera and/or families from the conifers. In order to understand better the relationships between the families, we performed cladistic analyses using a new data set obtained from 28S rRNA gene sequences. These analyses strongly support the monophyly of conifers including Taxaceae. Within the conifers, the Pinaceae are the first to diverge, being the sister group of the rest of conifers. A recently discovered Australian genus Wollemia is confirmed to be a natural member of the Araucariaceae. The Taxaceae are nested within the conifer clade, being the most closely related to the Cephalotaxaceae. The Taxodiaceae and Cupressaceae together form a monophyletic group. Sciadopitys should be considered as constituting a separate family. These relationships are consistent with previous cladistic analyses of morphological and molecular (18S rRNA, rbcL) data. Furthermore, the well-supported clade linking the Araucariaceae and Podocarpaceae, which has not been previously reported, suggests that the common ancestor of these families, both having the greatest diversity in the Southern Hemisphere, inhabited Gondwanaland.     

Phylogeny and jaw evolution in Gnathostomulida, with a cladistic analysis of the genera

Sørensen, M. V. (2002). Phylogeny and jaw evolution in Gnathostomulida, with a cladistic analysis of the genera. — Zoologica Scripta, 31, 461–480.
The relationships between the genera in Gnathostomulida were investigated in a computerized cladistic analysis. The data matrix comprised 55 morphological characters of sensory structures, the reproductive systems, and the hard mouthparts. The cladistic analysis produced four almost identical most parsimonious trees. The four trees differed by having different topologies within the family Gnathostomulidae. Based on the obtained trees, the following was concluded: (1) Filospermoidea and Bursovaginoidea are both monophyletic; (2) Scleroperalia is paraphyletic; (3) all known families except Onychognathiidae (Sterrer 1972) are monophyletic; (4) Onychognathiidae emend. comprises the genera Nanognathia, Onychognathia, Rastrognathia, Valvognathia and Vampyrognathia ; (5) Paucidentulidae and Onychognathiidae emend. branch off in the lower part of Bursovaginoidea; (6) the following two clades are monophyletic and appear as sister groups: Problognathiidae−Gnathostomulidae−Austrognathiidae and Gnathostomariidae− Goannagnathia −Mesognathariidae−Clausognathiidae−Agnathiellidae. Based on the character optimization it was suggested that the gnathostomulid jaw evolved from a relatively simple ancestral jaw belonging to the compact type or the open lamellar type. The fused lamellar type evolved from the open lamellar type. The ancestral dentarium resembled the arc type and evolved along two different evolutionary paths into the basket type and the row type.     

Relationships of Fossil and Living Elasmobranchs

Preliminary cladistic analysis corroborates the hypothesis thatthe Elasmobranchii and the Holocephali are sister groups, andthat the Chondrichthyes are more closely related to the Teleostomi(Acanthodi plus Osteichthyes) than either is to the Placodermi.In regard to the Paleozoic and Mesozoic elasmobranchs, a theoryof relationships has been proposed for six better known genera(Xenacanthus, Denaea, Cladoselache, Hybodus, Ctenacanthus andPaleospinax) by evaluation of certain characters in the skull,postcranial axial skeleton, fin supports, and fins.     

Phylogeny of fossil and extant glypheid and litogastrid lobsters (Crustacea,Decapoda) as revealed by morphological characters

A phylogenetic analysis of a total of 31 species: 27 fossil species from seven families (Glypheidae, Litogastridae, Mecochiridae, Pemphicidae, Erymidae, Clytiopsidae, Chimaerastacidae), and four extant species from three families (Glypheidae, Nephropidae, Stenopodidae) is proposed. Most of the genera considered are coded exclusively based upon their type species and, as much as possible, based upon the type specimens. The cladistic analysis demonstrates that the glypheidean lobsters (infraorder Glypheidea) form a monophyletic group including two superfamilies: Glypheoidea and Pemphicoidea new status. Glypheoidea includes three families: Glypheidae, Mecochiridae and Litogastridae. Litogastridae is the sister group of the clade Glypheidae + Mecochiridae. Pemphicoidea includes a single family: Pemphicidae. A new classification of Glypheidea is proposed and currently known genera are rearranged based upon the phylogenetic analysis.     

Differences in recreationally targeted fishes between protected and fished areas of a coral reef marine park

Many comparisons have been made between sanctuary (no-fishing) and fished areas, where fishing pressure is exerted by artisanal or commercial fishers, but few have examined the effect of recreational fishing on fish assemblages in coral reef habitats. In this study, we compared assemblages of targeted fish from coral reef habitats in sanctuary (no-fishing) and recreationally fished zones of a marine protected area (MPA). Surface visual census (SVC) transects were conducted two times, at three regions, to compare the composition of predatory fish assemblages and the abundance, biomass, and size of the most commonly targeted fish. Baited remote underwater video (BRUV) was used to make relative counts of fish between zones. We also measured benthic cover and rugosity, which may influence fish assemblages. Analysis of similarity (ANOSIM) revealed significant differences in the composition of fish families/genera targeted by fishers (Lethrinidae, Lutjanidae, Haemulidae, Serranidae, and the genus Choerodon of the family Labridae) in terms of biomass (P<0.01) and abundance (P<0.05). The most consistent trends were recorded for biomass and this was supported by clustering of replicates in nonmetric multidimensional scaling (nMDS) ordinations. Similarity percentages (SIMPER) analysis indicated that the family Lethrinidae accounted for 73% (as abundance), and up to 69% (as biomass), of the dissimilarity between zones. Three-factor ANOVA highlighted significantly greater biomass, size, and abundance of legal-sized lethrinids (the most targeted family in the region) in sanctuary zones, but no differences in other families/genera. Results of BRUV supported SVC with greater relative counts of lethrinids (P<0.01) in sanctuaries, but no significant differences for other families. Cover of Acropora coral and hard substrate differed between zones at some regions but differences were inconsistent. There were no significant differences in algal cover or rugosity between zones. Given the inconsistency in benthic cover, the similarity of rugosity between zones, the consistently greater biomass of lethrinids in sanctuaries, and the abundance of large lethrinids in sanctuaries, the cessation of fishing in sanctuary zones appears responsible for observed differences in the populations of these fish. These results demonstrate that recreational fishing pressure may be sufficient to deplete fish populations below that of adjacent protected areas and that the effect of recreational fishing in coral reef habitats may be greater than previously thought.     

Primates and their pinworm parasites: the cameron hypothesis revisited

A morphologically based cladistic analysis of the Enterobiinae, which includes most of the Oxyuridae parasitic in Primates, allows a reevaluation of the Cameron's hypothesis of close coevolution with cospeciation between hosts and parasites. Each of the three genera separated in the Enterobiinae fits with one of the suborders defined in Primates: Lemuricola with the Strepsirhini, Trypanoxyuris with the Platyrrhini, and Enterobius with the Catarrhini. Inside each of the three main groups, the subdivisions observed in the parasite tree also fit with many of the subdivisions generally accepted within the Primate order. These results confirm the subgroups previously described in the subfamily and support Cameron's hypothesis in its aspect of association by descent. Although the classification of the Enterobiinae generally closely underlines the classification of Primates, several discordances also are observed. These are discussed case by case, with use of computed reconstruction scenarios. Given that the occurrences of the same pinworm species as a parasite for several congeneric host species is not the generalized pattern, and given that several occurrences also are observed in which the speciations of the parasites describe a more complex network, Cameron's hypothesis of a slower rhythm of speciation in the parasites can be considered partly refuted. The presence of two genera parasitic on squirrels in a family that contains primarily primate parasites also is discussed. The cladistic analysis does not support close relationships between the squirrel parasites and suggests an early separation from the Enterobiinae for the first (Xeroxyuris), and a tardy host-switching from the Platyrrhini to the squirrels for the second (Rodentoxyuris).