Morphological characterization of infra‐generic lineages in Deparia (Athyriaceae: Polypodiales)

Deparia, including the previously recognized genera Lunathyrium, Dryoathyrium (=Parathyrium), Athyriopsis, Triblemma, and Dictyodroma, is a fern genus comprising about 70 species in Athyriaceae. In this study, we inferred a robust Deparia phylogeny based on a comprehensive taxon sampling (~81% of species) that captures the morphological diversity displayed in the genus. All Deparia species formed a highly supported monophyletic group. Within Deparia, seven major clades were identified, and most of them were characterized by inferring synapomorphies using 14 morphological characters including leaf architecture, petiole base, rhizome type, soral characters, spore perine, and leaf indument. These results provided the morphological basis for an infra‐generic taxonomic revision of Deparia.     

Reconciling taxonomy and phylogeny in the bristleworm family Eunicidae (polychaete,Annelida)

Eunicid annelids inhabit diverse marine habitats worldwide, have ecological and economic importance and have been pictured in the news as giant predator worms. They compose a traditional stable taxon recently supported as monophyletic but characterized by plesiomorphies. Most genera within the family have been recovered as paraphyletic in previous studies. We present a phylogenetic hypothesis for eunicid based on molecular (COI, 16S rDNA, 18S rDNA) and morphological data (213 characters), including an explicit attempt to account for serial homology. Eunicidae as well as monophyletic genera Marphysa sensu stricto and Lysidice is redefined based on synapomorphies. Nematonereis is synonymized to Lysidice. Leodice and Nicidion are resurrected to name monophyletic groups including species previously included in Eunice and Marphysa sensu lato. Traditional diagnostic characters such as the absence/presence of peristomial cirri, lateral antennae and branchiae are homoplasies and not informative at the generic level. Different coding of traditional characters (i.e. articulation of prostomial appendages) and novel characters of prostomial features and regionalization of the body support the monophyly of the family and genera level clades. Thus, the phylogenetic hypothesis presented here and the evolution of characters provided background information for taxonomic changes yielding evolutionary meaningful classification and diagnoses for the family and genera.     

Phylogeny of Australasian venomous snakes (Colubroidea, Elapidae, Hydrophiinae) based on phenotypic and molecular evidence

Scanlon, John D. & Lee, Michael S. Y. (2004). Phylogeny of Australasian venomous snakes (Colubroidea, Elapidae, Hydrophiinae) based on phenotypic and molecular evidence. — Zoologica Scripta , 33 , 335–366.
Phylogenetic relationships among Hydrophiinae (Australasian and marine elapid snakes) are inferred using 87 characters from external, skeletal, hemipenial and internal anatomy, ecology, and chromosomes as well as available sequences of two mitochondrial genes (cytochrome b and 16S rRNA). Parsimony analysis of the combined data retrieves many widely accepted clades; while observed bootstrap or branch (Bremer) support for these is often weak, most have never been corroborated previously by a rigorous numerical analysis. Sea kraits ( Laticauda ) and Solomon Islands elapids are basal to the remaining hydrophiines (Australian terrestrial forms and hydrophiin sea snakes). The latter clade includes three main lineages: a large-bodied oviparous lineage, a small-bodied oviparous lineage, and a viviparous lineage (which also includes the hydrophiin sea snakes, strongly reaffirmed as monophyletic). While the Solomons retain a relictual fauna, New Guinea has less endemism and has been invaded multiple times by Australian lineages, so there is no clear 'stepping stone' pattern supporting a northern (Asian, rather than Gondwanan) biogeographical origin.     

Morphology agrees with molecular data: phylogenetic affinities of Euptychiina butterflies (Nymphalidae: Satyrinae)

Euptychiina is the most species‐rich subtribe of Neotropical Satyrinae, with over 450 known species in 47 genera (14 monotypic). Here, we use morphological characters to examine the phylogenetic relationships within Euptychiina. Taxonomic sampling included 105 species representing the majority of the genera, as well as five outgroups. A total of 103 characters were obtained: 45 from wing pattern, 48 from genitalia and 10 from wing venation. The data matrix was analysed using maximum parsimony under both equal and extended implied weights. Euptychiina was recovered as monophyletic with ten monophyletic genera, contrasting previous DNA sequence‐based phylogenies that did not recover the monophyly of the group. In agreement with sequence‐based hypotheses, however, three main clades were recognized: the ‘Megisto clade’ with six monophyletic and three polyphyletic genera, the ‘Taygetis clade’ with nine genera of which three were monophyletic, and the ‘Pareuptyhia clade’ with four monophyletic and two polyphyletic genera. This is the first morphology‐based phylogenetic hypothesis for Euptychiina and the results will be used to complement molecular data in a combined analysis and to provide critical synapomorphies for clades and genera in this taxonomically confused group.     

Phylogenetic relationships of toads of the Rhinella granulosa group (Anura: Bufonidae): a molecular perspective with comments on hybridization and introgression

The Rhinella granulosa group consists of 13 species of toads distributed throughout open areas of South America and Panama. In this paper we perform a phylogenetic analysis considering all but one species of the group, employing five nuclear and four mitochondrial genes, for up to 7910 bp per specimen. Separate phylogenetic analyses under direct optimization (DO) of nuclear and mitochondrial sequences recovered the R. granulosa group as monophyletic and revealed topological incongruence that can be explained mainly by multiple events of hybridization and introgression, both mitochondrial and nuclear. The DO combined analysis, after the exclusion of putatively introgressed or heterozygous genomes, resulted in a phylogenetic hypothesis for the R. granulosa group in which most of the species are recovered as monophyletic, but with interspecific relationships poorly supported. The optimization of morphological (adult and larval), chromosomal, and behavioural characters resulted in 12 putative phenotypic synapomorphies for this species group and some other synapomorphies for internal clades. Our results indicate the need for additional population genetic studies on R. dorbignyi and R. fernandezae to corroborate the taxonomic status of both taxa. Finally, we discuss biological and genetic characteristics of Bufonidae, as possible explanations for the common occurrence of hybridization and introgression observed in some lineages of this family.     

Phylogeny of the tribe Empoascini (Hemiptera: Cicadellidae: Typhlocybinae) based on morphological characteristics,with reclassification of the Empoasca generic group

A morphology‐based phylogenetic analysis of the tribe Empoascini (Hemiptera: Cicadellidae: Typhlocybinae) is presented for 58 of 83 formerly recognized genera based on 99 morphological characters of adults. The results support excluding the New World Beamerana generic group from Empoascini. The remaining genera of Empoascini were recovered as a monophyletic sister group of Dikraneurini. Previously recognized tribes Jorumini and Helionini are derived from within Empoascini and are considered synonyms of the latter tribe. Three previously recognized informal generic groups, the Empoasca group, Alebroides group and Usharia group were paraphyletic but the Ficiana group was recovered as monophyletic based on five synapomorphies. Genera previously placed in the Alebroides group represent at least six independent lineages, indicating that the hind wing character separating this group from the Empoasca group (CuA and MP veins free) is highly homoplasious. Empoasca (sensu lato) is also paraphyletic. Thus, twelve previously recognized subgenera of Empoasca are elevated to genus status and five species groups of Empoasca from the New World are recognized as separate new genera. Sikkimasca Dworakowska, 1993 is treated as synonym of Marolda Dworakowska, 1977 based on the phylogeny. Biogeographic analysis suggests that Empoascini most likely first evolved in the Oriental region and spread to other biogeographic realms more recently by multiple independent invasions.     

The recognition of ancestors

The recognition of ancestors is problematic using cladistic logic alone because monophyletic groups (clades) are defined by shared derived characters (synapomorphies) which their ancestors must have lacked. Nevertheless, ancestors possess three key attributes. They belong within a larger, paraphyletic group. They will be morphologically most similar to their immediate descendants, and they evolved before any and all of their descendants. Recognition of ancestors requires both morphological and stratigraphic data and, in practice, the task is to reduce the size of the paraphyletic group within which the ancestor must lie. All ancestor‐descendant relationships are phylogenetic hypotheses. Despite the legendary incompleteness of the fossil record, testing the validity of available data is far more difficult for character analysis than for stratigraphy.     

A multiple‐gene phylogeny reveals polyphyly among eastern North American Aphaenogaster species (Hymenoptera: Formicidae)

Twenty‐three Aphaenogaster species (Hymenoptera: Formicidae) occur in North America. While morphology and ecology define most species, the species limits of a group in the Eastern United States are unclear. In particular, the morphological and behavioural characters of A. carolinensis, A. picea and A. rudis overlap. These observations suggest that these three species are not monophyletic. We therefore tested the monophyly of Aphaenogaster in the context of molecular phylogenetic analyses. We used DNA data from five genes: CO1, CAD, EF1αF2, long‐wavelength rhodopsin and wingless, to reconstruct phylogenies for 44 Aphaenogaster and outgroup species. In the resulting trees, reconstructed using parsimony and Bayesian inference, species boundaries associated with well‐supported monophyletic clades of individuals in most of the 23 North American Aphaenogaster collected from multiple locations. However, some clades were unresolved, and both A. picea and A. rudis were not monophyletic. Although this may indicate that clades of multiple species represent fewer but morphologically varied species, given the short branch lengths, the lack of resolution may reflect the fact that these ants have recently radiated, and a lack of gene lineage sorting explains the non‐monophyly of species. Additional biological information concerning pre‐ and postmating barriers is needed before a complete revision of species boundaries for Aphaenogaster.     

A phylogenetic analysis of morphological and molecular characters of Boraginaceae: evolutionary relationships,taxonomy, and patterns of character evolution

The angiosperm family Boraginaceae includes ca. 1600 species distributed among ca. 110 genera. Some floral features are constant within the family, but many vegetative, floral, pollen, and nutlet traits vary. Utilizing 224 species of Boraginaceae and related taxa, five matrices were constructed with various combinations of morphological characters, three chloroplast DNA regions, and one nuclear ribosomal DNA region. Phylogenetic analyses were conducted for these matrices, and patterns of character evolution were examined. Boraginaceae is resolved as monophyletic, with Wellstedia as its sister. Codon is sister to Boraginaceae + Wellstedia. Although most of the investigated morphological characters have a low consistency index, particular character states are synapomorphies for large clades in each of the tribes of the family. In Boraginaceae, the breeding system heterostyly evolved at least 12 times, which is the largest number of origins resolved in any family; therefore Boraginaceae can serve as a model for the evolution and development of heterostyly. Nutlet ornamentation is most diverse in Cynoglosseae and Trichodesmeae, while pollen and floral features are most variable in Boragineae and Lithospermeae. Phylogenetic relationships and patterns of character evolution identified in the present study set the stage for future work creating an updated taxonomic system of Boraginaceae.     

Phylogeny and placement of Boganiidae (Coleoptera,Cucujoidea) with a review of Australian and New Caledonian taxa

A phylogeny of the cucujoid family Boganiidae (Coleoptera) is inferred for the first time based on a parsimony analysis of 102 morphological characters (70 adult and 32 larval). The analysis resulted in a monophyletic Boganiidae divided into two main clades, Boganiinae and Paracucujinae, each supported by a series of synapomorphies. The Boganiinae genera recovered were Afroboganium Endrödy‐Younga & Crowson and Boganium Sen Gupta & Crowson, whereas Paracucujinae includes Paracucujus Sen Gupta & Crowson, Metacucujus Endrödy‐Younga & Crowson, Athertonium Crowson and the New Caledonian Dzumacium caledonicum gen.n. , sp.n. New specimen data and biological information for the Australian taxa are summarized with overviews on biogeography and comments on the fossil Jurassic Parandrexis Martynov (Parandrexidae). Two new species of Boganium, primarily from the Australian mallee are described: B. malleense sp.n. and B. medioflavum sp.n . Boganium malleense is recorded from flowers of Eucalyptus gracilis F. (Myrtaceae). Adults and larvae of Paracucujus rostratus Sen Gupta & Crowson are redescribed. Athertonium parvum Crowson is redescribed and Athertonium williamsi sp.n. is described from coastal New South Wales. Several host records for Athertonium are also presented.     

A phylogenetic analysis of relationships among genera of Conopidae (Diptera) based on molecular and morphological data

Members of the family Conopidae (Diptera) have been the focus of little targeted phylogenetic research. The most comprehensive test of phylogenetic support for the present subfamily classification of Conopidae is presented here using 66 specimens, including 59 species of Conopidae and seven outgroup taxa. Relationships among subfamily clades are also explored. A total of 6824 bp of DNA sequence data from five gene regions (12S ribosomal DNA, cytochrome c oxidase subunit I, cytochrome b, 28S ribosomal DNA and alanyl‐tRNA synthetase) are combined with 111 morphological characters in a combined analysis using both parsimony and Bayesian methods. Parsimony analysis recovers three shortest trees. Bayesian analysis recovers a nearly identical tree. Five monophyletic subfamilies of Conopidae are recovered. The rarely acknowledged Zodioninae is restored, including the genera Zodion and Parazodion. The genus Sicus is removed from Myopinae. Morphological synapomorphies are discussed for each subfamily and inter‐subfamily clade, including a comprehensive review of the character interpretaions of previous authors. Included are detailed comparative illustrations of male and female genitalia of representatives of all five subfamilies with new morphological interpretation.     

Phylogenetic reconstruction of Chirita and allies (Gesneriaceae) with taxonomic treatments

Abstract Chirita D. Don, a large genus in the subfamily Cyrtandroideae of Gesneriaceae, has been the subject of much debate whether it is a natural group or not. In addition, the highly heterogeneous Chirita has also been very problematic with regard to delimitation and subdivision. Here we used the nrDNA internal transcribed spacer and cpDNA trnL‐F for molecular phylogenetic analaysis, combined with morphological data. Our results suggest that Chirita is an artificial, polyphyletic genus. The most important character that defines Chirita, the dorso‐ventrally oblique and bilamellar stigma, has evolved convergently in different clades of diandrous Cyrtandroideae. Chirita sensu stricto only includes the species of Chirita sect. Chirita, whereas Chirita sect. Microchirita is an independent clade located at the basal node of the phylogenetic tree. Chirita sect. Liebigia is closely related to Didymocarpus with an entire stigma unlike other species of Chirita. The species of Chirita sect. Gibbosaccus, Chiritopsis, Primulina, and Wentsaiboea form a monophyletic group that is sister to a strongly supported clade comprising four monotypic genera Paralagarosolen, Calcareoboea, Petrocodon, and Tengia. We further analyzed the morphological evolution of Chirita and identified a series of morphological synapomorphies for the monophyletic groups revealed herein, and thereby provide a taxonomic treatment in this study.     

Molecular taxonomy and phylogeny of the Geodiidae (Porifera, Demospongiae, Astrophorida) – combining phylogenetic and Linnaean classification

Cárdenas, P., Rapp, H. T., Schander, C. & Tendal, O. S. (2009). Molecular taxonomy and phylogeny of the Geodiidae (Porifera, Demospongiae, Astrophorida) – combining phylogenetic and Linnaean classification.—Zoologica Scripta, 39, 89–106. According to the fossil records, the Geodiidae represents one of the oldest families of demosponges (Phylum Porifera). There are approximately 220 described extant species, geographically and bathymetrically widely distributed around the world. Species of this family all share a two-layered cortex with ball-shaped spicules called ‘sterrasters’ in the endocortex. However, molecular studies have questioned the monophyly of the group. Moreover, the evolutionary history and the intrafamily relationships of the Geodiidae are not fully resolved. Using a partial sequence of the cytochrome c oxidase subunit 1 (COI) gene and a partial sequence of the 28S rDNA gene (D1–D2 domains), we present the first molecular phylogeny focusing on this group. The congruent results from the two gene fragments suggest that (i) the Geodiidae is monophyletic, (ii) the Erylinae/Geodinae subdivision sensu Sollas, 1888 is valid and that (iii) Isops and Sidonops are junior synonyms of Geodia. The synonymization of Isops and Sidonops implies that the oscule/pore morphology as a diagnostic character should be abandoned. Geodia hentscheli nom. nov. has been given for Geodia mesotriaena ( Hentschel, 1929 ). This study served as the basis for a revised phylogenetic classification of the Geodiidae. Well-supported clades led to the establishment of clade names following the PhyloCode. The Geodinae clade is strongly supported and notably composed of Depressiogeodia, Cydonium and Geodia. A morphological synapomorphy of Geodinae is the presence of euasters in the ectocortex. The Erylinae (Erylus, Penares, Caminus and Pachymatisma) form a strongly supported monophyletic group with three morphological synapomorphies: (i) loss of anatriaenes and protriaenes, (ii) microrhabds (or spherules) in the ectocortex and (iii) short-shafted triaenes. The Erylus monophyly is ambiguous. Erylus species are distributed in three well-supported clades. Finally, spicule homology in the cortex of the Geodiidae is discussed.     

Phylogeny,evolutionary morphology,and hemipenis descriptions of the Middle American jumping pitvipers (Serpentes: Crotalinae: Atropoides)

The jumping pitvipers, genus Atropoides, occur at low to middle elevations throughout Middle America. Recent molecular phylogenetic analyses have included all six species of Atropoides, but only two studies have found Atropoides to be monophyletic and questions persist about relationships within the A. nummifer complex. In this study, our phylogenetic analyses of morphological data provide strong support for the monophyly of Atropoides and recover relationships within the genus that are mostly congruent with those of recent molecular studies, further supporting the evolutionary and biogeographic hypotheses proposed in those studies. Our analyses find support for a sister relationship between A. picadoi and the other Atropoides species and an A. occiduus–A. indomitus clade sister to an A. nummifer–A. mexicanus–A. olmec clade. Within the A. nummifer complex, we find A. mexicanus and A. olmec to be sister species to the exclusion of A. nummifer. We include morphological synapomorphies to support each clade within Atropoides and describe and illustrate the hemipenes of each species. In addition, we discuss the importance of morphological phylogenetics and the functionality and limitations of hemipenial data in systematics.     

Higher‐level phylogenetic affinities of the Neotropical genus Mastigodryas Amaral, 1934 (Serpentes: Colubridae), species‐group definition and description of a new genus for Mastigodryas bifossatus

Most Neotropical colubrid snakes belong to a single, well‐supported lineage. Relationships between the major constituents of this clade remain. Here, we explore the phylogenetic relationships of Mastigodryas and its affinities to other Neotropical colubrid genera by combining DNA and morphological data. Analyses demonstrate that the concatenation of multiple individuals into a single terminal can mask the detection of new taxa. Further, non‐random missing data and/or taxa in some empirical datasets can bias species tree analyses more than concatenation approaches. Our results place Mastigodryas in a strongly supported clade that includes Drymarchon, Rhinobothryum, Drymoluber, Simophis and Leptodrymus. Mastigodryas bifossatus is more closely related to species of Drymoluber and Simophis than to its congeners. Thus, we erect a new genus to accommodate it and recover a monophyletic Mastigodryas. We highlight the importance of the use of morphological characters to diagnose suprageneric clades by showing that some key external and hemipenial characteristics are phylogenetically informative.     

A New Marsupial from the Early Eocene Tingamarra Local Fauna of Murgon, Southeastern Queensland: A Prototypical Australian Marsupial?

Djarthia murgonensis, a new genus and species of marsupial from the early Eocene Tingamarra Local Fauna of Murgon in southeastern Queensland, is described on the basis of dental material. The combination of marsupial synapomorphies and symplesiomorphies present in D. murgonensis suggests phylogenetic placement within either Didelphidae or Australidelphia. Tarsal morphology, fundamental to the concepts of Ameridelphia and Australidelphia respectively, is not yet known for this taxon. Consequently, it cannot be assigned to either clade with confidence. If this taxon is australidelphian, it constitutes support for the hypothesis that the common ancestor of the Australian marsupial radiation was didelphoid-like in dental features. Some previous authors have contended that marsupial faunas of South America and Australia are manifestly distinct, excepting for the australidelphian affinity of South American microbiotheres. However, because tarsal anatomy is unknown in some generalized Australian fossil taxa, including D. murgonensis, and character analysis reveals that no synapomorphies of the dentition unequivocally define either Ameridelphia or Australidelphia to the exclusion of the other, we consider this interpretation to be premature. In short, available evidence neither supports nor refutes the argument of distinct South American and Australasian marsupial faunas. A further ramification is the need to reconsider the phylogenetic position of Ankotarinja tirarensis and Keeuna woodburnei. These central Australian fossil taxa might be referred to either Australidelphia or Ameridelphia, and it is recommended that both be treated as Marsupialia incertae sedis until further material comes to light.     

Phylogenetic reassessment and biogeography of the Ectateus generic group (Coleoptera: Tenebrionidae: Platynotina)

Owing to the reinterpretation of its morphological synapomorphies, the taxonomic composition of the Ectateus generic group had been ambiguous. The present study scrutinized all existing taxonomic concepts of the group based on a cladistic analysis of the adult morphology of all of the Afrotropical platynotoid Platynotina genera. The phylogenetic relationships were reconstructed using parsimony and Bayesian inference. The results show that all previous taxonomic concepts of the Ectateus generic group concerned paraphyletic entities. The cladistic analysis revealed the following synapomorphies for the taxon: (1) presence of basal indentations of the pronotal disc, (2) ratio of prothorax width to its maximal height > 6.0, and (3) ratio of maximal height of the prothorax to total height < 0.3. Moreover, phylogenetic studies revealed the existence of the Upembarus generic group, a sister‐taxon group to the Ectateus generic group, within the Afrotropical platynotoid Platynotina. Autapomorphic and synapomorphic character mapping show that several taxonomic and nomenclatural changes are needed to consider the particular generic‐level entities traditionally assigned to Afrotropical platynotoid Platynotina as monophyletic lineages. The following taxonomic and nomenclatural adjustments are made in this paper: P teroselinus gen. nov. is erected to accommodate a single species that was previously assigned to Zidalus: Pteroselinus insularis comb. nov. Additionally, the following synonymies are proposed: Anchophthalmops (= Platykochius syn. nov. ), Angolositus (= Aberlencus syn. nov. , = Platymedvedevia syn. nov. ), Glyptopteryx (= Microselinus syn. nov. , = Quadrideres syn. nov. , = Synquadrideres syn. nov. ). In addition, Kochogaster is lowered in rank and is treated as one of the subgenera of Anchophthalmus. Moreover, Pseudoselinus is treated as a subgenus of Upembarus. An identification key to all Afrotropical platynotoid Platynotina genera and subgenera is presented. Zoogeographical analyses revealed the following dispersal barriers for the Ectateus generic group: (1) the Sahara (northern barrier); (2) the dry ecosystems of Botswana, Namibia, and South Africa (southern barrier); and (3) the Congolian rainforests (internal distributional gap). The ancestor of the taxon probably originated in East African ecoregions that predominantly contained wattletrees (acacias) and Commiphora Jacq. Moreover, past climate changes seem to have had a great impact on the observed generic distribution. © 2015 The Linnean Society of London     

Phylogenetic relationships in the Marcetia alliance (Melastomeae,Melastomataceae) and implications for generic circumscription

The Marcetia alliance of Melastomataceae is an exclusively Neotropical group that includes at least 12 genera of mostly herbs and subshrubs, occurring in the cerrado of central Brazil and savannas of the Amazon region and Guayana highlands. This study aimed to test the monophyly of genera in the Marcetia alliance, evaluate their phylogenetic relationships and generic boundaries, and investigate morphological characters as potential synapomorphies for delimiting clades or genera. We used nuclear (ITS, ETS) and plastid (accD‐psaI, atpH‐atpF, trnS‐trnG) DNA sequences of 107 terminals in 12 genera from the alliance. Aciotis, Fritzschia, Marcetia and Siphanthera were shown to be monophyletic and supported by molecular and morphological characters. Other genera with variable morphology and wider distributions, such as Acisanthera, Comolia, Ernestia and Macairea, were recovered as paraphyletic or polyphyletic. Most morphological characters analysed were found to be homoplastic, but when combined they are potentially useful for the diagnosis of genera and infrageneric groups. This study represents a major step in understanding internal relationships and provides the basis for a revision of the generic classification in the Marcetia alliance.