Synapomorphic Characters Research Articles

DNA barcoding of Palaearctic Ulidiidae (Diptera: Tephritoidea): morphology, DNA evolution, and Markov codon models

Here, for the first time, we report a barcoding survey of the dipterian family Ulidiidae (with two subfamilies Ulidiinae and Otitinae) coupled with morphology. To date, this is the first comprehensive analysis of the family that relies on molecular data. To reconstruct probable higher-level phylogenetic relationships between the genera of Ulidiidae, we exploited maximum likelihood and Bayesian inference, and additionally, we utilized a modern Markov model of codon substitutions for protein-coding genes coupled with the maximum likelihood approach to establish more realistic evolutionary scenarios connecting Ulidiinae and Otitinae. Though we found morphological synapomorphic characters that clearly distinguish two groups of genera, formerly relating to two subfamilies, the monophyly of the clade Otitinae was not firmly supported by molecular phylogenetic reconstructions. The subfamily Ulidiinae was recovered as the basal likely paraphyletic group with high reliability. Overall, our results suggest the inclusion of the genera Homalocephala and Seioptera into the tribe Seiopterini (Otitinae). Three genera of Ulidiinae (Physiphora, Timia, Ulidia), eight genera of Otitinae (Ceroxys, Herina, Melieria, Myennis, Otites, Pseudotephritis, Seioptera, Tetanops), and the genus of Homalocephala with still unconfirmed systematic status were included in the analysis. On all phylogenetic trees obtained in our survey, there is a clear tendency of clustering at the genus level with separation of (Physiphora + (Timia + Ulidia)) (Ulidiinae) and (Otitinae + Homalocephala). The genus Homalocephala takes basal or subbasal position relatively to Otitinae. Phylogenetic reconstruction based on Markov models of codon evolution provided a good resolution for our limited dataset.

Chemosystematics in the Opiliones (Arachnida): a comment on the evolutionary history of alkylphenols and benzoquinones in the scent gland secretions of Laniatores.

Large prosomal scent glands constitute a major synapomorphic character of the arachnid order Opiliones. These glands produce a variety of chemicals very specific to opilionid taxa of different taxonomic levels, and thus represent a model system to investigate the evolutionary traits in exocrine secretion chemistry across a phylogenetically old group of animals. The chemically best-studied opilionid group is certainly Laniatores, and currently available chemical data allow first hypotheses linking the phylogeny of this group to the evolution of major chemical classes of secretion chemistry. Such hypotheses are essential to decide upon a best-fitting explanation of the distribution of scent-gland secretion compounds across extant laniatorean taxa, and hence represent a key toward a well-founded opilionid chemosystematics.

On the phylogeny of Ischyroceridae (Amphipoda, Senticaudata, Corophiida), with the description of a new genus and eight new species from deep-sea Brazilian waters

The family Ischyroceridae is analysed herein by cladistic methods based on morphological characters, using both PAUP 4.0b and TNT. The data matrix of 41 characters × 32 terminal taxa was constructed using DELTA. Based on the results, we comment on the phylogenetic relationships of certain genera and their synapomorphic characters, also discussing the phylogenetic position of Myersius gen. nov., which appeared as the sister group of Bathyphotis. In addition, Pseudischyrocerus crenatipes is removed to Bathyphotis, for which a new diagnosis is provided. A taxonomic study with the Ischyroceridae collected on the continental slope (depth, 700–2000 m) in the Campos Basin (20.5–24°S, 40–41°W) was also performed. Samples were collected in November–December 2002 and July–August 2003 using a box core device. As a result, a new genus and eight new species are described: Bonnierella campensis sp. nov., Bonnierella laurensi sp. nov., Myersius denticaudatus gen. et sp. nov., Notopoma lowryi sp. nov., Notopoma teresae sp. nov., Pseudericthonius bousfieldi sp. nov., Pseudericthonius concavus sp. nov., and Pseudischyrocerus caecus sp. nov. The genus Bonnierella is recorded for the first time from Brazilian waters, and the subspecies Bonnierella linearis linearis and Bonnierella linearis californica are elevated to species rank. Keys to the genera of Ischyroceridae used in the cladistic analysis and the world species of Notopoma are given. © 2014 The Linnean Society of London

Phylogenetic Relationships and Evolution in <I>Dudleya</I> (Crassulaceae)

Dudleya (Crassulaceae) is a genus of succulent perennials endemic to western North America. Interspecific relationships within Dudleya have been difficult to discern due to a lack of synapomorphic characters for the genus or subgenera, highly variable morphologies within species, and extensive polyploidy. Here we present the first molecular phylogeny of diploid members of the genus using sequences from nrDNA and cpDNA. We cloned ITS alleles from six known polyploid individuals to determine their evolutionary origin. We have been able to resolve four clades within Dudleya, but many relationships are still uncertain. Our analyses support the monophyly of the genus and show that Dudleya is more closely related to North American Sedum species of the Sedoideae subfamily than to members of its currently circumscribed subfamily, the Echeverioideae. The current subgeneric distinctions within Dudleya are polyphyletic and should be revised in future taxonomic treatments. We tested the monophyly of several highly variable species and found that D. virens, D. cymosa, and D. abramsii are polyphyletic. The ITS alleles from polyploid taxa were not variable enough to resolve polyploid origins.

Recircumscription of Begonia sect. Baryandra (Begoniaceae): evidence from molecular data

BackgroundBegonia sect. Diploclinium is a ‘dust-bin’ section for species retaining pleisiomorphic characters and lacking novel synapomorphic characters used to delimit other Asian sections in Begonia. Part of this large and polymorphous section is transferred to Begonia sect. Baryandra in a move towards a more natural classification for the genus.ResultsPhylogenetic analysis of nuclear ribosomal ITS DNA sequences show a strongly supported monophyletic group containing Philippine and Bornean species previously in Begonia sect. Diploclinium, and the type of Begonia sect. Baryandra, B. oxysperma. This clade forms the basis for the now much-expanded Begonia sect. Baryandra, which as defined here contains 49 species and has its centre of diversity in the Philippines.ConclusionsA natural classification for a much expanded Begonia sect. Baryandra has been provided. This paper highlights the feasibility of moving towards a natural classification of Asian Begonia step by step as information comes to light through building upon previous framework phylogenies with denser sampling.Electronic supplementary materialThe online version of this article (doi:10.1186/1999-3110-54-38) contains supplementary material, which is available to authorized users.

A new genus of cardinalfish (Apogonidae: Percomorpha), redescription of Archamia and resemblances and relationships with Kurtus (Kurtidae: Percomorpha).

Archamia is restricted to a single species, A. bleekeri. A recently described genus, Kurtamia, a reference to a suggested relationship with the enigmatic Kurtus, is the junior synonym of Archamia. Kurtamia bykhovskyi is a junior synonym of A. bleekeri. Archamia is redescribed using osteological, color pattern, pore and free neuromast patterns supplementing those characters used in other publications noting clear differences between A. bleekeri and all other species formerly in that genus. The new genus Taeniamia, type species Archamia leai contains the remaining species. Osteology, color patterns and lateralis characters are reviewed for Taeniamia leai and other species. Species placed in Taeniamia have two broadly different color patterns: 1) yellow, orange, red or dark bars with or without a dark basicaudal spot, and 2) yellow or dark midline stripe with another stripe above the lateral line, lacking bars. These color patterns suggest two lineages exist within Taeniamia. New species combinations are: Taeniamia ateania, T. biguttata, T. bilineata, T. buruensis, T. dispilus, T. flavofasciata, T. fucata, T. kagoshimana, T. leai, T. lineolata, T. macroptera, T. melasma, T. mozambiquensis, T. pallida, and T. zosterophora. Archamia and Taeniamia are sister genera. A diagnosis is provided for the Apogonidae: one or two anal spines, first spine small, supernumerary in position, second spine or first anal fin-ray (only Paxton) in serial association with first distal and proximal-middle radials; first segmented anal ray branched; males mouth brood fertilized eggs; swim bladder simple without anterior or posterior modifications, a dorsal oval and ventral gas glands; free neuromasts on head, body and caudal fin. Characters of Holapogon were used to help identify common plesiomorphic characters for the Apogonidae, elsewhere among percoids using the Centropomidae and information for basal Percomorpha. A table of basal characters and derived changes is provided for the Apogonidae. Characters for two species Kurtus indicus and K. gulliveri are described and examined in a search for morphological synapomorphies with Archamia, Taeniamia, Holapogon and other apogonids. A diagnosis is provided for the Kurtidae: highly modified ribs, anterior dorsal spines individually fused with all radials of the pterygiophore complex, medially fused pterosphenoids, gill rakers on second branchial arch, tooth plates between each gill raker, serrated curved extension of the male's supraoccipital crest, tiny cycloid scales on head and body, very short pored lateral-line scales and free neuromast patterns on the head and body. The second epibranchial articulating with third pharyngobranchial and radial ridges simple or bifid filaments around the micropyle of the egg related to egg ball organization are supported as possible non-exclusive synapomorphic characters for kurtids and apogonids. Parental care of eggs has not been demonstrated for Kurtus indicus, an estuarine/coastal marine species. Kurtids share foramina in the lateral lower part of each caudal vertebra with carangine species, some ephippids, some leiognathids, some priacanthids and scatophagids and share tiny cycloid scales with carangoids: possible synapomorphies or independently derived features.

The importance of molecular dating analyses for inferring Hawaiian biogeographical history: a case study with bark lice (Psocidae: Ptycta)

AbstractAimThe use of intuitive or explicit biogeographical reconstruction techniques to estimate the timing of species radiations on the Hawaiian Islands, while often incorporating evidence on the timing of island formation, may be misleading if the effects of extinction are overlooked. Using phylogenies of the bark louse genus Ptycta (Psocidae), we compared results from biogeographical character mapping with those from molecular dating analyses. These results were used to evaluate the ‘progression model’, which predicts an oldest‐to‐youngest pattern of island colonization.LocationThe main Hawaiian Islands (Kauai, Oahu, Maui, Lanai, Molokai and Hawaii).MethodsWith a data set including 101 Hawaiian Ptycta specimens and 18 outgroup species, we constructed molecular phylogenies based on sequences of the nuclear gene wingless and mitochondrial genes 12S, 16S and cytochrome c oxidase subunit I (COI). Maximum‐likelihood, maximum‐parsimony and Bayesian phylogenetic analyses were used. We used beast to estimate a time‐calibrated tree under a relaxed clock model.ResultsOur analyses suggested a single colonization event, followed by extensive movement of Ptycta among islands and species radiations within and between islands. This monophyletic radiation is composed of two well‐supported clades that are also supported by two synapomorphic characters of the male genitalia.Main conclusionsVery different biogeographical patterns are inferred by molecular dating versus approaches based on character mapping. Simple biogeographical reconstruction over the molecular phylogeny supports a pattern of youngest‐to‐oldest island colonization, the reverse of that predicted by the ‘progression model’, and implies that this radiation could be as young as the most recent islands of Maui (1.4 Ma) or Hawaii (0.5 Ma). Molecular dating, however, infers a pattern consistent with oldest‐to‐youngest island colonization, and suggests a lineage age of 7.1 Ma. Extinction on the oldest island of Kauai may account for the differences in results between the two analyses.

The systematic significance of floral morphology, nectaries, and nectar concentration in epiphytic cacti of tribes Hylocereeae and Rhipsalideae (Cactaceae)

A long-standing interest in cactus taxonomy has existed since the Linnaean generation, but an appreciation of the reproductive biology of cacti started early in the 1900s. Numerous studies indicate that plant reproductive traits provide valuable systematic information. Despite the extensive reproductive versatility and specializations in breeding systems coupled with the striking floral shapes, the reproductive biology of the Cactaceae has been investigated in approximately 10% of its species. Hence, the systematic value of architectural design and organization of internal floral parts has remained virtually unexplored in the family. This study represents the most extensive survey of flower and nectary morphology in the Cactaceae focusing on tribes Hylocereeae and Rhipsalideae (subfamily Cactoideae). Our objectives were (1) to conduct comparative morphological analyses of flowers and floral nectaries and (2) to compare nectar solute concentration in these two tribes consisting of holo- and semi-epiphytic species. Flower morphology, nectary types, and sugar concentration of nectar have strong taxonomic implications at the tribal, generic and specific levels. Foremost, three types of nectaries were found, namely chamber nectary (with the open and diffuse subtypes), furrow nectary (including the holder nectary subtype), and annular nectary. All Hylocereeae species possess chamber nectaries, in which the nectarial tissue has both trichomes and stomata. The Rhipsalideae are distinguished by two kinds of floral nectaries: furrow and annular, both nectary types with stomata only. The annular nectary type characterizes the genus Rhipsalis. Nectar concentration is another significant taxonomic indicator separating the Hylocereeae and Rhipsalideae and establishing trends linked to nectar sugar concentration and amount of nectar production in relation to flower size. There is an inverse relationship between flower size and amount of nectar production in the smaller Rhipsalideae flowers, in which nectar concentration is more than two-fold higher despite the smaller volume of nectar produced when compared to the large Hylocereeae flowers. Variability of nectary morphology and nectar concentration was also evaluated as potential synapomorphic characters in recent phylogenies of these tribes. In conclusion, our data provide strong evidence of the systematic value of floral nectaries and nectar sugar concentration in the Cactaceae, particularly at different taxonomic levels in the Hylocereeae and Rhipsalideae.

Evolutionary Implications of Synapomorphic Wing-Molt Sequences among Falcons (Falconiformes) and Parrots (Psittaciformes)

Abstract. I examined over 4500 specimens to investigate the evolutionary significance of molt sequences as related to systematic relationships of falcons and parrots. Nodes of molt among the medial primaries (p4–p6) and at s5 among the secondaries, followed by bidirectional replacement from the node within each tract, was confirmed for most or all taxonomic groupings of both falcons and parrots, with the exception of the Kakapo or Owl Parrot (Strigops habroptila), which appears to replace its remiges in sequences similar to those of most other birds. Initiation of primary molt varies between p4 and p5 in falcons and between p5 and p6 in parrots, including within species, suggesting that the node's position may be fluid within a defined area along the alar tract. The coincidence and consistency of these molt sequences in parrots and falcons but in no other order of birds suggests that molt sequence may be a synapomorphic (shared) character state, supporting recent molecular evidence that the Falconiformes ...

Weevils of the Yixian Formation, China (Coleoptera: Curculionoidea): phylogenetic considerations and comparison with other Mesozoic faunas

The weevil fauna of the Yixian Formation, north-eastern China, is described and compared with other deposits of similar age and older. The fauna contains fossil groups that appear to be basal curculionoids, representing a mixture of taxa belonging to extant lineages and possibly extinct stem-groups. It contrasts particularly with Mesozoic curculionoids described from the Karatau site in southern Kazakhstan and El Montsec, Spain, the Yixian being quite different from the former due to its younger age. Although diagnoses are provided and characters are discussed, much of the taxonomy is considered tentative pending a full cladistic analysis and outline of diagnostic, synapomorphic characters. Most prior accounts have suffered from a reliance on the literature, which is grossly erroneous in many cases, rather than direct examination of fossil type material, and this has led to biased interpretations. Taxonomic changes made are: Leptocar Liu & Ren, 2007 is considered to be a junior synonym of Cretonanophyes Zherikhin, 1977; Cretonanophyes punctatus Liu & Ren, 2007, and Cretonanophyes zherikhini Liu & Ren, 2006 are resurrected as combinations; Leptocar polychaetus Liu & Ren, 2007 is regarded as a junior synonym of C. zherikhini Liu & Ren, 2006; Cretonanophyes rugosithorax Gratshev & Zherikhin, 2000a is resurrected as a combination; Montsecanomalus (Rugosocar) Legalov, 2009a is considered a junior synonym of Cretonanophyes Zherikhin, 1977; Chinabrenthorrhinus Legalov, 2009a is a junior synonym of Chinocimberis Legalov, 2009b; and Chinocimberis longidigitus (Ren, 1995) is a new combination. Abrocar concavus sp. nov. and A. relicinus sp. nov. are described. http://zoobank.org/urn:lsid:zoobank.org:pub:ED652610-3AF7-41BA-847F-CCC839C798EA

Phylogenetic Abnalysis of Malaysian Pineapples Cultivars Based on the DNA Sequence of the Internal Transcribed Spacer Region

The phylogenetic study was conducted to determine the phylogenetic status and evolutionary relationships among the nine commercial pineapple cultivars using sequences of the internal transcribed spacer (ITS) region. Genomic DNA was extracted, and the ITS region was amplified and sequenced. Parsimony analysis revealed that Malaysian cultivars could be classified into two major groups based on the ITS region. The first group comprised of the cultivars Sarawak Green Local, Gandul, and N36 whereas the second group consisted of the cultivars Josapine, Yankee, Morris Bentanggur, Morris Gajah, MD2 and MD2/T. Several combinations of synapomorphic characters (leaf and fruit) support this classification system, suggesting the ITS region has the ability to determine the phylogenetic status and relationships of pineapple cultivars. Since each group has its own similar genetic pattern and presumably certain specific biochemical properties, the relationships of pineapple cultivars revealed in the phylogenetic tree can be used as a basis for successful hybridizations to generate new pineapple cultivars.

A comprehensive molecular phylogeny of the <I>Mortierellales</I> (<I>Mortierellomycotina</I>) based on nuclear ribosomal DNA

The basal fungal order Mortierellales constitutes one of the largest orders in the basal lineages. This group consists of one family and six genera. Most species are saprobic soil inhabiting fungi with the ability of diverse biotransformations or the accumulation of unsaturated fatty acids, making them attractive for biotechnological applications. Only few studies exist aiming at the revelation of the evolutionary relationships of this interesting fungal group. This study includes the largest dataset of LSU and ITS sequences for more than 400 specimens containing 63 type or reference strains. Based on a LSU phylogram, fungal groups were defined and evaluated using ITS sequences and morphological features. Traditional morphology-based classification schemes were rejected, because the morphology of the Mortierellales seems to depend on culture conditions, a fact, which makes the identification of synapomorphic characters tedious. This study belongs to the most comprehensive molecular phylogenetic analyses for the Mortierellales up to date and reveals unresolved species and species complexes.

Phylogeny of Polycnemoideae (Amaranthaceae): Implications for biogeography, character evolution and taxonomy

AbstractPolycnemoideae is a poorly studied subfamily of the Amaranthaceae/Chenopodiaceae alliance which contains ca. 13 rare species in three disjunctly distributed genera. We present the results of a dated molecular phylogeny and a survey of morphology, micromorphology and stem anatomy revealing the phylogenetic relationships and historical biogeography of the subfamily as well as its morphological evolution. The results are converted into a new classification of the group. The divergence of Polycnemoideae from Amaranthaceae s. str. dates back to the Eocene and the oldest split in the subfamily separated a Northern Hemisphere lineage (Polycnemum) and a predominantly Southern Hemisphere lineage (Nitrophila, Hemichroa, Surreya gen. nov.) around the Eocene/Oligocene boundary. There is some evidence for a southern connection via Antarctica in the ancestor of the Nitrophila/Hemichroa/Surreya clade. The amphitropical genus Nitrophila likely originated in South America and reached North America via long–distance dispersal. Genera of Polycnemoideae diversified during the Miocene and Pliocene. They are species–poor and appear relictual. The morphological and micromorphological survey revealed a number of useful diagnostic characters which permit a clear definition of all four genera and 13 species recognized here. Hemichroa in its traditional circumscription lacks diagnostic characters. Hemichroa pentandra is much more similar to Nitrophila and shares a number of symplesiomorphies with it, while H. diandra and H. mesembryanthema, which form a highly supported clade, show several clear synapomorphic characters. Therefore the latter two species are here described within a new genus, Surreya R. Masson & G. Kadereit.

Molecular evidence for taxonomy of Rhacophorus appendiculatus and Kurixalus species from northern Vietnam, with comments on systematics of Kurixalus and Gracixalus (Anura: Rhacophoridae)

Abstract Phylogeny of Rhacophoridae is constructed using two mitochondrial (12S rRNA and 16S rRNA) and two nuclear (tyrosinase and Rag-1) genes in an attempt to test for the taxonomic status of Rhacophorus appendiculatus and Kurixalus species from Tam Dao. All phylogenetic analyses demonstrate that specimens from Tam Dao are nested in Kurixalus bisacculus , indicating that they belong to K. bisacculus . R. appendiculatus is closer to genus Kurixalus than to other genera with strong support values. In combination with morphological evidence, it is suggested that R. appendiculatus should be placed in Kurixalus . Kurixalus verrucosus is not related to Kurixalus appendiculatus and it is the sister taxon to the clade of K. bisacculus and Kurixalus odontotarsus , which rejects that K. verrucosus is a synonym of K. appendiculatus . The genus Kurixalus needs redefinition by clear synapomorphic characters, and generic status of Kurixalus ananjevae deserves further examination.

A review of the <I>Ustilago-Sporisorium-Macalpinomyces</I> complex

The fungal genera Ustilago, Sporisorium and Macalpinomyces represent an unresolved complex. Taxa within the complex often possess characters that occur in more than one genus, creating uncertainty for species placement. Previous studies have indicated that the genera cannot be separated based on morphology alone. Here we chronologically review the history of the Ustilago-Sporisorium-Macalpinomyces complex, argue for its resolution and suggest methods to accomplish a stable taxonomy. A combined molecular and morphological approach is required to identify synapomorphic characters that underpin a new classification. Ustilago, Sporisorium and Macalpinomyces require explicit re-description and new genera, based on monophyletic groups, are needed to accommodate taxa that no longer fit the emended descriptions. A resolved classification will end the taxonomic confusion that surrounds generic placement of these smut fungi.

Profundulus kreiseri, a new species of Profundulidae (Teleostei, Cyprinodontiformes) from northwestern Honduras

A new species of Profundulus, Profundulus kreiseri (Cyprinodontiformes: Profundulidae), is described from the Chamelecón and Ulúa Rivers in the northwestern Honduran highlands. Based on a phylogenetic analysis using cytochrome b and the presence of synapomorphic characters (dark humeral spot, a scaled preorbital region and between 32-34 vertebrae), this new species is placed in the subgenus Profundulus, which also includes Profundulus (Profundulus) oaxacae, Profundulus (Profundulus) punctatus and Profundulus (Profundulus) guatemalensis. Profundulus kreiseri can be distinguished from other members of the subgenus Profundulus by having less than half of its caudal fin densely scaled. Profundulus kreiseri can further be differentiated from Profundulus (Profundulus) oaxacae and Profundulus (Profundulus) punctatus by the absence of rows of dark spots on its flanks. The new species can further be differentiated from Profundulus (Profundulus) guatemalensis by the presence of fewer caudal- and pectoral-fin rays. The new species is distinguished from congeners of the profundulid subgenus Tlaloc (viz., Profundulus (Tlaloc) hildebrandi, Profundulus (Tlaloc) labialis, Profundulus (Tlaloc) candalarius and Profundulus (Tlaloc) portillorum) by having a scaled preorbital region and a dark humeral spot. Profundulus kreiseri and Profundulus portillorum are the only two species of Profundulus that are endemic to the region south of the Motagua River drainage in southern Guatemala and northwestern Honduras.

Australia's oldest Anseriform fossil: a quadrate from the Early Eocene Tingamarra Fauna

Abstract: A partial quadrate (essentially the otic part) from the nonmarine, earliest Eocene (54.6 Ma) Tingamarra Local Fauna in Queensland, Australia, has been identified as the oldest Australian anseriform fossil. The Tingamarra quadrate shows a combination of plesiomorphic anseriform characters with a unique synapomorphic character complex of the Anhimidae (screamers), which today are endemic to South America. In concert with the basal position of the Anhimidae among the crown‐group anseriforms, this set of characters suggests a stem group of the Anhimidae, raising a possibility of the Transantarctic migration of stem anhimids to South America. The quadrate morphology supports palaeognathous rather than recently claimed anhimid relationships of the Dromornithidae and identifies Sylviornis as an anseriform rather than a galliform.

The spinal cord supports of vertebrae in the crown‐group salamanders (Caudata, Urodela)

The development of spinal cord supports (bony thickenings which extend into the vertebral canal of vertebrae) in primitive (Salamandrella keyserlingii) and derived (Lissotriton vulgaris) salamanders were described. The spinal cord supports develop as the protuberances of periostal bone of the neural arches in the anteroproximal part of the septal collagenous fibers which connect a transverse myoseptum with the notochord and spinal cord, in the septal bundle inside the vertebral canal. Spinal cord supports were also found in some teleostean (Salmo salar, Oncorhynchus mykiss) and dipnoan (Protopterus sp.) fishes. The absence of the spinal cord supports in vertebrates with cartilaginous vertebrae (lampreys, chondrichthyan, and chondrostean fishes) corresponds to the fact that the spinal cord supports are bone structures. The absence of the spinal cord supports in frogs correlates with the lack of the well developed septal bundles inside the vertebral canal. The spinal cord supports are, presumably, a synapomorphic character for salamanders which originated independently of those observed in teleostean and dipnoan fishes.

A method for measuring support for synapomorphy using character state distributions on phylogenetic trees

Synapomorphies are fundamental to phylogenetic systematics as they offer empirical evidence of monophyletic groups. However, no method exists to directly measure synapomorphy. Here, we propose a method that quantifies synapomorphy using the pattern of character state distribution over a cladogram separately for each character and for each clade. We define a fully synapomorphic character state as one shared by all of a clade’s terminal taxa and at the same time completely absent from all terminal taxa outside that clade. The extent to which this condition is met corresponds to the support for the character state being synapomorphic or, in short, support for synapomorphy. It is calculated as the probability of randomly selecting, by multi-stage sampling following the topology of the tree, two terminals from inside a clade sharing the same character state and one terminal from outside the clade bearing a different character state. The method is independent of tree inference and free of transformational assumptions, and so can be applied to any tree and used for any type of discrete character. By measuring synapomorphy, the method offers a potential tool for determining diagnostic character states for taxa on different hierarchical levels, for evaluating alternative systems of character coding, and for evaluating clade support. We show how the method differs from ancestral character state reconstruction methods and goodness-of-fit indices. We demonstrate the behaviour of our method with several hypothetical scenarios and its potential use with two real-life examples.

Betaproteobacterial symbionts of the ciliate Euplotes: origin and tangled evolutionary path of an obligate microbial association

The Polynucleobacter-Euplotes association is an obligatory symbiotic system between a monophyletic group of ciliate species belonging to the genus Euplotes and bacteria of the species Polynucleobacter necessarius (Betaproteobacteria). Both organisms are unable to survive independently. Several studies revealed the existence of free-living populations of Polynucleobacter bacteria which are phylogenetically closely related to the endosymbiotic ones, but never share associations with Euplotes in the natural environment. Hence, following the most parsimonious explanation on the origin of the association, this symbiosis should represent a synapomorphic character for the hosts' clade. Nevertheless, phylogenetic analyses performed on an increased number of strains here presented suggest that Euplotes species, during their evolution, recruited Polynucleobacter bacteria as symbionts more than once. Moreover, in three cases, we observed different bacteria as obligate symbionts. These symbionts are the first characterized representatives of a phylogenetic lineage branching in a basal position with respect to the genus Polynucleobacter. The hypothesis that the original obligate symbionts belonged to this newly discovered clade and that, only subsequently, in most cases they have been replaced by Polynucleobacter bacteria recruited from the environment is proposed and discussed. The evolutionary path of this association seems anyway to have been more complex than so far supposed.