Geographical diversification of the genus Cicer (Leguminosae: Papilionoideae) inferred from molecular phylogenetic analyses of chloroplast and nuclear DNA sequences

Cicer L. (Leguminosae: Papilionoideae) consists of 42 species of herbaceous or semi-shrubby annuals and perennials distributed throughout the temperate zones of the Northern Hemisphere. The origin and geographical relationships of the genus are poorly understood. We studied the geographical diversification and phylogenetic relationships of Cicer using DNA sequence data sampled from two plastid regions, trnK / matK and trnS - trnG , and two nuclear regions, the internal transcribed spacer (ITS) and external transcribed spacer (ETS) regions of nuclear ribosomal DNA, from 30 species. The results from the phylogenetic analyses of combined nuclear and chloroplast sequence data revealed four well-supported geographical groups: a Middle Eastern group, a West-Central Asian group, an Aegean–Mediterranean group, and an African group. Age estimates for Cicer based on methods that do not assume a molecular clock (for example, penalized likelihood) demonstrate that the genus has a Mediterranean origin with considerable diversification in the Miocene/Pliocene epochs. Geological events, such as mountain orogenesis and environmental changes, are major factors for the dispersal of Cicer species. The early divergence of African species and their geographically distinct region in the genus suggest a broader distribution pattern of the genus in the past than at present.  © 2007 The Linnean Society of London, Botanical Journal of the Linnean Society, 2007, 154 , 175–186.     

Parmelina quercina (Parmeliaceae, Lecanorales) includes four phylogenetically supported morphospecies

Morphological and phylogenetic relationships of the worldwide Mediterranean lichen forming fungus, Parmelina quercina , have been studied. Specimens from western Europe, western North America and southern Australia were analysed using molecular data (nuITS rDNA, nuLSU rDNA and mtSSU rDNA) and selected morphological features (upper cortex maculae, scanning electron microscopy examination of the epicortex, ascospores and conidia shape and size, and amphithecial retrorse rhizines). The results conclusively reveal that: (1) there is not one single species but four separate species in the Mediterranean or sub Mediterranean areas of the world. Parmelina quercina and Parmelina carporrhizans (Euroasiatic species), Parmelina coleae sp. nov. (North America) and Parmelina elixia sp. nov. (Australia); (2) largely debated P. carporrhizans is not a synonym of P. quercina but supported as a valid species circumscribed to Macaronesic relict sites; (3) the geographical isolation of the Australian population is correlated with a large genetic distance; (4) morphological characters (ascospores and conidial variability and thallus epicortex) correlate with the phylogenetic hypothesis; (5) the new or revalidated species within Parmelina quercina are not cryptic species but morphologically recognizable taxa.  © 2007 The Linnean Society of London, Biological Journal of the Linnean Society , 2007, 91 , 455–467.     

Systematics of African lowland rainforest Praomys (Rodentia, Muridae) based on molecular and craniometrical data

Representatives of the genus Praomys occur throughout the African intertropical zone. It is unclear how many species this genus contains, nor do we know the exact distribution ranges and phylogenetic relationships of these taxa. Using molecular (16S rRNA gene sequencing) and morphological (multivariate craniometry) analyses we clarify the taxonomy and phylogenetic relationships among the Praomys occurring in Africa's lowland tropical rainforests. We studied most species known from this area, based on specimens collected in seven countries (Guinea, Ivory Coast, Cameroon, Central African Republic, Gabon, Congo Republic and Democratic Republic of Congo). In our study, Praomys appears to be monophyletic. Our results identify two species complexes: the jacksoni complex includes at least two species ( P. jacksoni and P. mutoni ) and the tullbergi complex contains at least four species ( P. tullbergi , P. rostratus , P. misonnei , P. petteri ). Although the 16S rRNA gene appears insufficient to resolve the phylogenetic relationships among all the members of the tullbergi species complex, it is suitable for the identification of most of the studied species, and its use has allowed us to redefine the geographical limits of several species.  © 2005 The Linnean Society of London, Zoological Journal of the Linnean Society , 2005, 145 , 539–553.     

Molecular phylogeny of the western Atlantic species of the genus Portunus (Crustacea, Brachyura, Portunidae)

The genus Portunus encompasses a comparatively large number of species distributed worldwide in temperate to tropical waters. Although much has been reported about the biology of selected species, taxonomic identification of several species is problematic on the basis of strictly adult morphology. Relationships among species of the genus are also poorly understood, and systematic review of the group is long overdue. Prior to the present study, there had been no comprehensive attempt to resolve taxonomic questions or determine evolutionary relationships within this genus on the basis of molecular genetics. Phylogenetic relationships among 14 putative species of Portunus from the Gulf of Mexico and other waters of the western Atlantic were examined using 16S sequences of the rRNA gene. The resultant molecularly based phylogeny disagrees in several respects with current morphologically based classification of Portunus from this geographical region. Of the 14 species generally recognized, only 12 appear to be valid. We recommend that P. vossi be hereafter regarded as a junior synonym of P. spinimanus and that P. bahamensis be regarded as a junior synonym of P. depressifrons . Our analysis suggests that western Atlantic members of the genus can be subdivided into at least three well-defined clades. Pending further molecular analyses with a large subset of species, it appears that the genus is not monophyletic and that it warrants further taxonomic revision.  © 2007 The Linnean Society of London, Zoological Journal of the Linnean Society , 2007, 150 , 211–220.     

The relationship of Sophora sect. Edwardsia (Fabaceae) to Sophora tomentosa, the type species of the genus Sophora, observed from DNA sequence data and morphological characters

Sophora tomentosa , the type species of the genus Sophora , is shown by phylogenetic analyses of rbc L and ITS sequence data to be sister to Sophora sect. Edwardsia . S. tomentosa and most of the species from sect. Edwardsia share hypogeal germination, exstipulate leaves, and terete filaments. These species have buoyant seeds, and are distributed by ocean currents throughout the pantropics ( S. tomentosa ) and around southern temperate oceanic islands (sect. Edwardsia ). S. tomentosa differs from the species of sect. Edwardsia by its frutescent growth habit, terminal elongate inflorescence and smooth-walled legume. S. macrocarpa is unusual in sect. Edwardsia as its leaves have stipules, the filaments are winged, and the legume is smooth-walled.  © 2004 The Linnean Society of London, Botanical Journal of the Linnean Society , 2004, 146 , 439–446.     

Chromosome number, karyotype, and taxonomic considerations on the enigmatic Sellocharis paradoxa Taubert (Leguminosae, Papilionoideae, Genisteae)

Until recently, Sellocharis paradoxa Taubert, the only species of this Genisteae genus, was known solely by the isotypes. Recent new collections in Rio Grande do Sul, southern Brazil, have enabled data on chromosome number and karyotype morphology to be obtained for the first time. S. paradoxa has 2 n  = 20 chromosomes, and a bimodal asymmetrical karyotype, composed of one pair of long ( c . 6.3 µm) metacentric, five pairs of shorter acrocentric, and four pairs of shorter telocentric chromosomes ranging from c . 3.7 to 2.7 µm. The chromosome number and karyotype morphology of S. paradoxa do not fit into the Genisteae pattern. Existing information is so far insufficient to answer evolutionary questions about its origin and phylogenetic relationships, but the uniqueness of this taxon, first indicated by its peculiar leaf arrangement, and now supported by its uncommon karyological constitution, strongly suggests that the suprageneric taxonomic position of S. paradoxa should be re-evaluated.  © 2007 The Linnean Society of London, Botanical Journal of the Linnean Society , 2007, 155 , 223–226.     

The skull and the palaeoecological significance of Labidosaurus hamatus, a captorhinid reptile from the Lower Permian of Texas

The cranial skeleton of the large captorhinid reptile Labidosaurus hamatus , known only from the Lower Permian of Texas, is described on the basis of new, undescribed specimens. Labidosaurus is distinguished from other captorhinids by the more extreme sloping of the ventral (alveolar) margin of the premaxilla, a low dorsum sellae of the parabasisphenoid, a reduced prootic, a narrow stapes, and a relatively small foramen intermandibularis medius. Despite the presence of a single row of teeth in each jaw, the skull of Labidosaurus resembles most closely those of moradisaurines, the large multiple-tooth-rowed captorhinids of the latest Early and Middle Permian. A phylogenetic analysis confirms that the single-tooth-rowed L. hamatus is related most closely to moradisaurines within Captorhinidae, a relationship that supports the hypothesis of a diphyletic origin for multiple rows of marginal teeth in captorhinids (in the genus Captorhinus and in the clade Moradisaurinae). In view of the close relationship between L. hamatus and moradisaurines, which are regarded to have been herbivorous, L. hamatus is a critical taxon for studies of the evolution of herbivory in early tetrapods. L. hamatus shares several trademark features of herbivorous adaptation with moradisaurines, which suggest that this captorhinid species was omnivorous. As such, it represents a transitional taxon between faunivorous basal reptiles and the herbivorous moradisaurines.  © 2007 The Linnean Society of London, Zoological Journal of the Linnean Society , 2007, 149 , 237–262.     

A phylogenetic analysis of the genus Eunice (Eunicidae, polychaete, Annelida)

Species of Eunice are distributed worldwide, inhabiting soft and hard marine bottoms. Some of these species play significant roles in coral reef communities and others are commercially important. Eunice is the largest and most poorly defined genus in Eunicidae. It has traditionally been subdivided in taxonomically informal groups based on the colour and dentition of subacicular hooks, and branchial distribution. The monophyly of Eunice and of its informal subgroups is tested here using cladistic analyses of 24 ingroup species based on morphological data. In the phylogenetic hypothesis resulting from the present analyses Eunice and its subgroups are paraphyletic; the genus may be divided in at least two monophyletic groups, Eunice s.s. and Leodice , but several species do not fall inside these two groups. Most of the traditional characters used in the taxonomy of Eunice are homoplasies; however, characters used for the first time in this study, such as certain jaw characters and characters derived from a close examination of chaetal variation along the body, are promising sources of phylogenetic signal.  © 2007 The Linnean Society of London, Zoological Journal of the Linnean Society , 2007, 150 , 413–434.     

Relationships, classification and evolution of Scleranthus (Caryophyllaceae) as inferred from analysis of morphological characters

Study of floral anatomy, micromorphology, palynology and onotogeny has revealed new characters for phylogenetic analysis in the genus Scleranthus . Cladistic analysis of these characters, along with those previously available, suggests that the genus consists of Eurasian/Mediterranean and Australasian sister clades. Gynoecial morphology and development are closely similar in all species, suggesting the genus is monophyletic despite its disjunct northern and southern hemisphere distribution. Variation in pollen:ovule ratios and their implications for the evolution of Scleranthus species are also discussed and it is concluded that a range of breeding strategies intermediate between autogamy and xenogamy exists in the genus. Single-stamened species of Scleranthus are likely to be obligate autogams, despite their comparatively high pollen:ovule ratios in relation to autogamic species of other genera.  © 2002 The Linnean Society of London, Botanical Journal of the Linnean Society , 2002, 140 , 15–29.     

A new species of Exostyles (Leguminosae, Papilionoideae, Swartzieae s.l.), from Paraná State, Brazil

A new species Exostyles godoyensis Soares-Silva & Mansano (Leguminosae, Papilionoideae, Swartzieae), endemic to Paraná state in southern Brazil, is described and illustrated. The new species is distinct from all the other species of Exostyles in having a leaf with up to five leaflets, while the other species have at least seven leaflets per leaf. The new species is distinct from Exostyles amazonica Yakovlev in its longer stamen filaments and ovary stipe and from E. glabra Vogel and E. venusta Schott by its shorter anthers. In addition to these morphological characters E. godoyensis has a disjunct geographical distribution.  © 2004 The Linnean Society of London, Botanical Journal of the Linnean Society , 2004, 146 , 103–106.     

Towards a monophyletic genus Albinaria (Gastropoda, Pulmonata): the first molecular study into the phylogenetic position of eastern Albinaria species

Recent molecular phylogenetic studies of the terrestrial snail genus Albinaria have caused a radical reassessment of its taxonomy. These studies, however, were limited to western species. This paper examines mitochondrial 12S sequences and nuclear ITS1 & 2 sequences of both eastern and western species, and demonstrates that Albinaria, in its most recent definition, is not monophyletic. Both molecular datasets place ' Albinaria ' hedenborgi from Lebanon in a well-supported clade with species of the genus Cristataria , distributed south-east of the vicariant range of Albinaria . The remaining species from Cyprus, Turkey and Greece constitute a well-supported monophyletic group. These two clades form geographical clusters, whereas Albinaria in the current definition (including ' A. '  hedenborgi ) has a disjunct distribution. ' A.' hedenborgi should therefore be classified with Cristataria , together with the morphologically similar and geographically close ' A. '  nadimi .  © 2005 The Linnean Society of London, Zoological Journal of the Linnean Society , 2005, 143 , 531−542.     

Systematics of the genera of Bodotriidae (Crustacea: Cumacea)

The cumacean family Bodotriidae includes 382 species in 31 genera grouped in three subfamilies: Bodotriinae, Mancocumatinae and Vaunthompsoniinae. Generic diagnoses are based on few characters that often have overlapping states among genera, complicating the understanding of the relationships within the group. The goals of this study are to illuminate the phylogenetic relationships among the genera of the Bodotriidae using morphological characters and to review the systematics of the family. For this purpose, all species within each genus were studied from the literature to code all the variability of genera for 109 variable morphological characters. Phylogenetic analyses show that there is independent reduction of the pleopods in two clades from a plesiomorphic state of five pairs, while the number of exopods of peraeopods has been reduced gradually in more derived groups of bodotriids. The subfamily Bodotriinae is the most derived and the Vaunthompsoniinae the most basal, and is paraphyletic with the Mancocumatinae embedded within it. No discriminatory characters were found between the subfamilies Mancocumatinae and Vaunthompsoniinae and they are not clearly separated in the phylogeny. Mancocumatinae is synonymized with Vaunthompsoniinae and all the genera of the former Mancocumatinae should be included within Vaunthompsoniinae. Analyses of character evolution justify a few other taxonomic changes. All genera were redescribed based on all the coded characters and a complete list of all valid species for each genus is included. Finally, dichotomous keys for identification to genus level are provided.  © 2007 The Linnean Society of London, Zoological Journal of the Linnean Society , 2007, 151 , 1–58.     

Phylogeography of the freshwater crayfish Cherax destructor Clark (Parastacidae) in inland Australia: historical fragmentation and recent range expansion

The yabby, Cherax destructor Clark, is the most widespread species in the most widespread genus of Australian freshwater crayfish. It has a distribution that spans several distinct drainage basins and biogeographical regions within semiarid and arid inland Australia. Here we report a study designed to investigate patterns of genetic variation within the species and hypotheses put forward to account for its extensive distribution using DNA sequences from the mitochondrial 16S rRNA gene region. Results of phylogenetic analyses contradicted previous allozyme data and revealed relatively deep phylogenetic structure in the form of three geographically correlated clades. The degree of genetic divergences between clades (8–15 bp) contrasted with the relatively limited haplotype diversity within clades (1–3 bp). Network-based analyses confirmed these results and revealed genetic structure on both larger and more restricted geographical scales. Nevertheless some haplotypes and 1-step clades had large distributions, some of which crossed boundaries between river basins and aquatic biogeographical regions. Thus both older and more recent historical processes, including fragmentation on a larger geographical scale and more recent range expansion on a local scale, appear to be responsible for the observed pattern of genetic variation within C. destructor . These results support elements of alternative hypotheses previously put forward to account for the evolutionary history of C. destructor and the origin of its large distribution.  © 2004 The Linnean Society of London, Biological Journal of the Linnean Society , 2004, 83 , 539–550.     

Systematics of the spider genus Metabus O. P.-Cambridge, 1899 (Araneoidea: Tetragnathidae) with additions to the tetragnathid fauna of Chile and comments on the phylogeny of Tetragnathidae

The spider genus Metabus (Tetragnathidae) previously included nine species: the type M. gravidus O. P.-Cambridge, 1899 – junior synonym of Leucauge ocellata (Keyserling) – from Central America and eight species from Chile. In this paper, the classification of the Metabus species-complex is revised, and two new genera, with three new species and five new combinations, are described. Allende gen. nov. is created for four Chilean species not congeneric with the type of Metabus : the type A. puyehuensis sp. nov. , A. patagiatus (Simon) comb. nov. , A. nigrohumeralis (F. O. P.-Cambridge) comb. nov. and A. longipes (Nicolet) comb. nov. Further additions to the Chilean fauna are under the new genus Mollemeta gen. nov. – created for M. edwardsi (Simon) comb. nov. – and three new species of Chrysometa : C. acinosa sp. nov. , C. levii sp. nov. and C. maitae sp. nov. Metabus now includes four species: M. ocellatus (Keyserling) comb. nov. , M. debilis (O. P.-Cambridge) comb. nov. , M. ebanoverde sp. nov. and M. conacyt sp. nov. All of these species were included in a phylogenetic analysis of 38 tetragnathid and 12 orbicularian outgroup terminals scored for 105 morphological and behavioural characters. The results suggest that Metabus as previously circumscribed is polyphyletic. The phylogenetic relationships within tetragnathids are briefly discussed. © 2007 The Linnean Society of London, Zoological Journal of the Linnean Society , 2007, 151 , 285–335.     

Sarcinomyces sideticae, a new black yeast from historical marble monuments in Side (Antalya, Turkey)

A new species of Sarcinomyces , a melanized fungus with meristematic development, is described. On the basis of small subunit and internal transcribed sequence regions of ribosomal DNA sequencing, the new species was accommodated in the anamorph genus Sarcinomyces (Herpotrichiellaceae, Chaetothyriales) close to S. petricola .  © 2007 The Linnean Society of London, Botanical Journal of the Linnean Society , 2007, 154 , 373–380.     

Taxonomy and sexual dimorphism of a new species of Loxoconcha (Podocopida: Ostracoda) from the Pleistocene of the Japan Sea

A new ostracod, Loxoconcha kamiyai sp. nov. in the Family Loxoconchidae, is described from the Pleistocene Omma Formation of Japan. Its geological and geographical distributions suggest that this species was once endemic to the Japan Sea, where it would have evolved until the Pliocene. Since the early Pleistocene, this species would have become extinct within this marginal sea during glacial maxima, probably due to its narrower salinity tolerances and geographical distributions than those of extant species inhabiting the euryhaline environments in other seas. The distributional patterns of pore systems in this species strongly suggest its closest phylogenetic affinities to a living species, Loxocorniculum mutsuense . These two species show a unique adult sexual dimorphism in the anterior element of the hingement. Taking the female hingement morphology as a standard, the male hingement can be explained in terms of heterochrony, i.e. paedomorphosis. Sexual hingement dimorphism with paedomorphosis occurs in only one phylogenetic group of the genus Loxoconcha , which is distinguished by the ontogenetic distributional patterns of pore systems. This morphology may represent relict primitive characters of ancient ostracods and could be an important character for evaluating the history of sexual dimorphism in ostracods since the Palaeozoic.  © 2008 The Linnean Society of London, Zoological Journal of the Linnean Society , 2008, 153 , 239–251.     

Morphological character evolution and molecular trees in sepiids (Mollusca: Cephalopoda): is the cuttlebone a robust phylogenetic marker?

The sepiids are characterized by their cuttlebone or sepion, an internal shell resulting from secondary mineralization of a chitinous 'gladius'. The various species are identified using a combination of shell criteria and 'soft-part' characters. Using mitochondrial genes, we established phylogenetic relationships of sepiids including the three accepted genera ( Sepia , Sepiella , Metasepia ) and a species complex of uncertain status ( Doratosepion ). We showed the Sepia genus to be paraphyletic and found no direct correlation between geographical distribution and systematics. We mapped, on the molecular tree, shell characteristics commonly used as reliable diagnostic criteria for taxonomy. Due to the plasticity of the shell, these characters did not appear phylogenetically informative. In an attempt to define systematic categories related to phylogenetic relationships, new clear synapomorphies need to be established for each genus, necessitating a revision of the genus Sepia .  © 2006 The Linnean Society of London, Biological Journal of the Linnean Society , 2006, 89 , 139–150.