A phylogenetic analysis of Antrodia s.l. based on nrDNA ITS sequences, with emphasis on rhizomorphic European species

The rhizomorphic European species of Antrodia, belonging to the traditionally called Antrodia radiculosa group, are investigated. On the basis of morphological and molecular analysis, the genus Fibroporia is supported. Specimens from Central Europe previously ascribed to Antrodia radiculosa constitute a species of their own, and are herein described as Fibroporia bohemica. Moreover, a new combination, Fibroporia citrina, is proposed.     

Molecular phylogeny of the genus Helix (Pulmonata: Helicidae)

The vast diversity of land snail forms is insufficiently understood even in seemingly familiar taxa. This holds for Helix Linnaeus, 1758, a genus with several common edible species which comprises the largest Western Palearctic snails. The taxonomy of this genus, which has a centre of diversity in the eastern Mediterranean, has recently undergone significant changes, in both the delimitation of the genus itself and its species‐level systematics. Here, we compare the lineage diversity of Helix, as revealed by two mitochondrial markers, with the conclusions of the recently published morphology‐based taxonomic revision. For the molecular analysis, we assembled a representative data set covering almost all species of the genus as recognized by the mentioned revision. We obtained sequences not only from fresh and preserved soft tissues but also from dried tissue remains (some of them decades old) from shell collections. Our results show that the genus Helix, in the narrow sense proposed by recent studies, is paraphyletic because the genus Tacheopsis was unambiguously revealed as one of the tip branches of Helix. The monophyly of several species, as presently recognized, was not supported; partly, this may be attributed to a lineage diversity overlooked so far. This holds also for the type species of the genus, H. pomatia, which comprises at least one additional lineage. Greece, the Aegean and western Turkey is the core area for the diversity of Helix and its relatives, and the region is probably a major long‐term refuge for large Helicidae. The highest species diversity is found along the Alpide belt from the western Balkans to southern Turkey. The diversity of Helix in Europe, north of Greece and the Apennines, is a result of a single European radiation. Our data also suggest that past human activities likely influenced the present‐day distributions of some species.     

Phylogeography and genetic relationships of North African <Emphasis Type="Italic">Bufo mauritanicus</Emphasis> Schlegel, 1841 estimated from mitochondrial DNA sequences

Genetic variation within the North African toad Bufo mauritanicus was estimated by sequencing partial 12S rRNA and 16S rRNA mitochondrial regions from widespread populations in Morocco, Algeria and Tunisia. Unlike many other wide ranging species from this area, B. mauritanicus demonstrated very low levels of intraspecific variation. The minimal intraspecific genetic variation may be due to a relatively recent, possibly post-glacial, expansion into its current range. Further phylogeographic studies of other North African species are needed to assess if this is a common biogeographical phenomenon. Phylogenetic analyses support immunological data that B. mauritanicus is part of a clade of predominantly sub-Saharan Bufo, recently assigned to a new genus Amietophrynus. Two different lineages within this clade, B. mauritanicus and the B. pardalis group, appear to have reverted from 20 chromosomes to the more typical 22 chromosomes found in most other Bufonids. However, the alternative hypothesis that the Bufo species with 20 chromosomes form a monophyletic lineage cannot be rejected.     

The phylogenetic relationship among Ectothiorhodospiraceae: a reevaluation of their taxonomy on the basis of 16S rDNA analyses

Sequences of the 16S rRNA gene were determined from all type strains of the recognized Ectothiorhodospira species and from a number of additional strains. For the first time, these data resolve the phylogenetic relationships of the Ectothiorhodospiraceae in detail, confirm the established species, and improve the classification of strains of uncertain affiliation. Two major groups that are recognized as separate genera were clearly established. The extremely halophilic species were removed from the genus Ectothiorhodospira and reassigned to the new genus Halorhodospira gen. nov., to recognize that the most halophilic eubacteria are species of this genus. These species are Halorhodospira halophila comb. nov., Halorhodospira halochloris comb. nov., and Halorhodospira abdelmalekii comb. nov. Among the slightly halophilic Ectothiorhodospira species, the classification of strains belonging to Ectothiorhodospira mobilis and Ectothiorhodospira shaposhnikovii was improved. Several strains that were tentatively identified as Ectothiorhodospira mobilis form a separate cluster on the basis of their 16S rDNA sequences and are recognized as two new species: Ectothiorhodospira haloalkaliphila sp. nov., which includes the most alkaliphilic strains originating from strongly alkaline soda lakes, and Ectothiorhodospira marina, describing isolates from the marine environment. Received: 12 October 1995 / Accepted: 1 December 1995     

Phylogeography and phylogenetic relationships of Malagasy tree and ground boas

Three species of boid snakes are recognized in Madagascar, namely the genus Sanzinia (one species and two subspecies) and the genus Acrantophis (two species). In the present study, we studied the patterns of genetic variation of these species across Madagascar using a fragment of the mitochondrial 16S rRNA gene in 77 specimens. To support the phylogenetic relationships of the lineages identified, three further gene fragments (cytochrome b, 12S rRNA and c‐mos) were analyzed in a reduced but representative set of samples. The results obtained corroborate that the genus Sanzinia includes two highly divergent mitochondrial lineages that evolved independently from each other on the east versus the west side of Madagascar. Each of these lineages presents a further subdivision that separates northern from southern groups. The nuclear marker showed no variation among the Malagasy boas, indicating either very low substitution rates in this gene or relatively recent speciation events coupled with high mitochondrial substitution rates. Because the broad geographic sampling detected no admixture among haplotypic lineages within Sanzinia, it is hypothesized that these may represent distinct species. Deviant haplotypes of snakes morphologically similar to Acrantophis dumerili indicate that this taxon may be a complex of two species as well. © 2008 The Linnean Society of London, Biological Journal of the Linnean Society, 2008, 95 , 640–652.     

Molecular diversity and distribution of eastern Atlantic and Mediterranean dogfishes Squalus highlight taxonomic issues in the genus

The alpha taxonomy of the globally distributed shark genus Squalus has been under intense investigation recently, and many new species have been described over the last decade. However, taxonomic uncertainty remains about several taxa. Without consistent nomenclature and the ability to reliably distinguish between the different Squalus species, basic data collection, downstream conservation and management efforts are seriously compromised. To aid in clarifying the taxonomic status of Squalus species in the eastern Atlantic and Mediterranean, we assessed species diversity at the molecular level and evaluated the consistency in species identification in the region. Samples from all nominal Squalus species recognized in the above regions were collected in an international effort and sequenced for regions of the mitochondrial COI and ND2 genes. These data were further analysed alongside publicly available sequences, including 19 of the 26 Squalus species globally recognized, to compare the regional genus‐level diversity with that found elsewhere. Our results confirm inconsistent species identification in the eastern Atlantic and Mediterranean Squalus, particularly concerning S. blainville and S. megalops, and reinforce the need to revise the status of S. megalops and S. mitsukurii as they may include several distinct species distributed around the world. The status of S. blainville is also discussed in the light of the current findings and its problematic taxonomic history.     

Phylogenomic analysis of pseudocryptic diversity reveals the new genus Deltalsia (Rhodomelaceae,Rhodophyta)

Molecular analyses, in combination with morphological studies, provide invaluable tools for delineating red algal taxa. However, molecular datasets are incomplete and taxonomic revisions are often required once additional species or populations are sequenced. The small red alga Conferva parasitica was described from the British Isles in 1762 and then reported from other parts of Europe. Conferva parasitica was traditionally included in the genus Pterosiphonia (type species P. cloiophylla in Schmitz and Falkenberg 1897), based on its morphological characters, and later transferred to Symphyocladia and finally to Symphyocladiella using molecular data from an Iberian specimen. However, although morphological differences have been observed between specimens of Symphyocladiella parasitica from northern and southern Europe they have yet to be investigated in a phylogenetic context. In this study, we collected specimens from both regions, studied their morphology and analyzed rbcL and cox1 DNA sequences. We determined the phylogenetic position of a British specimen using a phylogenomic approach based on mitochondrial and plastid genomes. Northern and southern European populations attributed to S. parasitica represent different species. Symphyocladiella arecina sp. nov. is proposed for specimens from southern Europe, but British specimens were resolved as a distant sister lineage to the morphologically distinctive Amplisiphonia, so we propose the new genus Deltalsia for this species. Our study highlights the relevance of using materials collected close to the type localities for taxonomic reassessments, and showcases the utility of genome-based phylogenies for resolving classification issues in the red algae.     

Evolution in the High Andes: The Phylogenetics of Muscisaxicola Ground-Tyrants

Phylogenetic relationships within the genus Muscisaxicola, a primarily Andean group of tyrant-flycatchers, were studied using complete sequences of the mitochondrial genes COII and ND3. Relationships among Muscisaxicola species were found to differ substantially from those of previous views, suggesting convergence in traditional avian taxonomic characters within the genus. The 11 species of large, gray, “typical” Muscisaxicola flycatchers (including M. grisea, newly restored to species status) formed a distinct clade, consisting of two major groups: a clade of 6 species breeding primarily in the central Andes and a clade of 5 species breeding primarily in the southern Andes. The other 2 species traditionally placed in this genus, M. fluviatilis, an Amazonian species, and M. maculirostris, were both rather divergent genetically from the typical species, although M. maculirostris may be the sister taxon to the typical clade. The patterns of sympatry exhibited by Muscisaxicola species in the high Andes appear to be the consequence of speciation and secondary contact within regions of the Andes, rather than a result of dispersal between regions. Diversification of the typical Muscisaxicola species appears to have occurred during the middle and late Pleistocene, suggesting generally that taxa of the high Andes and Patagonia may have been greatly influenced by mid-to-late Pleistocene events. There were likely several independent developments of migration within this genus, but migration is probably ancestral in the southern clade, with subsequent loss of migration in two taxa.     

New insights into the phylogenetics and biogeography of Arum (Araceae): unravelling its evolutionary history

The heat‐ and odour‐producing genus Arum (Araceae) has interested scientists for centuries. This long‐term interest has allowed a deep knowledge of some complex processes, such as the physiology and dynamics of its characteristic lure‐and‐trap pollination system, to be built up. However, mainly because of its large distributional range and high degree of morphological variation, species' limits and relationships are still under discussion. Today, the genus comprises 28 species subdivided into two subgenera, two sections and six subsections. In this study, the phylogeny of the genus is inferred on the basis of four plastid regions, and the evolution of several morphological characters is investigated. Our phylogenetic hypothesis is not in agreement with the current infrageneric classification of the genus and challenges the monophyly of several species. This demonstrates the need for a new infrageneric classification based on characters reflecting the evolution of this enigmatic genus. To investigate the biogeography of Arum deeply, further spatiotemporal analyses were performed, addressing the importance of the Mediterranean basin in the diversification of Arum. Our results suggest that its centre of origin was the European–Aegean region, and that major diversification happened during the last 10 Myr. © 2010 The Linnean Society of London, Botanical Journal of the Linnean Society, 2010, 163 , 14–32.     

Reproductive Asynchrony and the Divergence of Hawaiian Crickets

Asynchrony in reproductive behavior may contribute to reproductive isolation among sympatric species. While the 38 cryptic species of the genus Laupala are primarily distinguished on the basis of variation in pulse rate of male calling songs, additional phenotypes, such as asynchrony in reproductive behavior, may contribute to reproductive isolation in this genus. Here we document similarities and differences in the diel timing of two reproductive behaviors, male singing activity and insemination events. Asynchrony in the diel timing of male singing behavior was observed between two sympatric species, Laupala cerasina and Laupala paranigra, in the field. An interpopulational comparison within L. cerasina did not reveal variation in diel behavior patterns of singing between two locations. Asynchrony in the timing of copulation and sperm transfer between L. cerasina and L. paranigra was documented in the laboratory. The observed pattern of asynchrony in both the field and laboratory could have arisen in a number of ways. One possibility is that species diverged in sympatry because of interspecific interactions, producing a pattern of reproductive character displacement. Alternatively, the observed asynchrony in reproductive behavior may have played a role in the process of community assembly within this recently diverged cricket genus. The presence of interspecific variation and the absence of intraspecific variation revealed by our study do not support a pattern of reproductive character displacement for diel reproductive behavior, suggesting that the differences seen between species were not caused by recent species interactions.     

Integrating a Numerical Taxonomic Method and Molecular Phylogeny for Species Delimitation of Melampsora Species (Melampsoraceae,Pucciniales) on Willows in China

The species in genus Melampsora are the causal agents of leaf rust diseases on willows in natural habitats and plantations. However, the classification and recognition of species diversity are challenging because morphological characteristics are scant and morphological variation in Melampsora on willows has not been thoroughly evaluated. Thus, the taxonomy of Melampsora species on willows remains confused, especially in China where 31 species were reported based on either European or Japanese taxonomic systems. To clarify the species boundaries of Melampsora species on willows in China, we tested two approaches for species delimitation inferred from morphological and molecular variations. Morphological species boundaries were determined based on numerical taxonomic analyses of morphological characteristics in the uredinial and telial stages by cluster analysis and one-way analysis of variance. Phylogenetic species boundaries were delineated based on the generalized mixed Yule-coalescent (GMYC) model analysis of the sequences of the internal transcribed spacer (ITS1 and ITS2) regions including the 5.8S and D1/D2 regions of the large nuclear subunit of the ribosomal RNA gene. Numerical taxonomic analyses of 14 morphological characteristics recognized in the uredinial-telial stages revealed 22 morphological species, whereas the GMYC results recovered 29 phylogenetic species. In total, 17 morphological species were in concordance with the phylogenetic species and 5 morphological species were in concordance with 12 phylogenetic species. Both the morphological and molecular data supported 14 morphological characteristics, including 5 newly recognized characteristics and 9 traditionally emphasized characteristics, as effective for the differentiation of Melampsora species on willows in China. Based on the concordance and discordance of the two species delimitation approaches, we concluded that integrative taxonomy by using both morphological and molecular variations was an effective approach for delimitating Melampsora species on willows in China.     

New data on perittocrinids and hybocrinids (Crinoidea, Echinodermata) from the Middle Ordovician of the Baltic region

Age variation of radial plates of perittocrinids and aberrant cups of the hybocrinid genus Hoplocrinus from the Middle Ordovician of the St-Petersburg region are examined. Three patterns for the development of folds on the radial plates of perittocrinids are recognized. The differences between patterns are of species level. It is proposed here that the folded structures of perittocrinids (as well as the pore-structures of other pelmatozoans) were not only used for respiration, but also very likely for feeding. Tetracionocrinus transitor is a young individual of a species of the genus Perittocrinus or a paedomorphic species of this genus. The study of aberrant cups of Hoplocrinus suggests that its ancestor could have had biserial arms. Phylogenetic implications of this interpretation are discussed, and homologies within the phylum Echinodermata, reassessed. The three-armed genus Baerocrinus may be an aberrant form of a species of the genus Hoplocrinus.     

New generic proposal for the European Neogene large testudinids (Cryptodira) and the first phylogenetic hypothesis for the medium and large representatives of the European Cenozoic record

Fossil testudinids are known in Europe since the Eocene, with several taxa of medium size (from more than 0.3 m to less than 0.7 m) recognized in the Palaeogene record, most of them being poorly known. The size of several European Neogene taxa was larger (between 1 and 2 m). These large testudinids were relatively abundant and diverse, ranging from the early Miocene to the Pleistocene. However, there is a nomenclatural gap at the generic level for the Neogene forms, as their generally used assignment to the more primitive Eocene Cheirogaster cannot be sustained. This is because relatively little material has been assigned to the described species, and also because of the absence of a detailed study comparing all of the European taxa. Here, the European Cenozoic taxa are incorporated for the first time in a data matrix, so that a hypothesis on their phylogenetic relationships is justified. This study identified the large testudinids from the Neogene of Europe as belonging to a monophyletic clade, assigned to the new genus T itanochelon . The hitherto poorly understood ‘Testudo’ bolivari, proposed nearly a century ago but lacking diagnosis, is analysed in detail. It is recognized as the best‐represented large testudinid from the European record, and is identified as the type species of T itanochelon gen. nov. Its comparison with the other Neogene species allowed a detailed study of the new genus and an analysis of its phylogenetic relationships with the other European taxa. © 2014 The Linnean Society of London     

Using patterns of genetic structure based on microsatellite loci to test hypotheses of current hybridization,ancient hybridization and incomplete lineage sorting in Conradina (Lamiaceae)

Hybridization and/or incomplete sorting of ancestral polymorphism are commonly implicated to explain discordant phylogenetic analyses of closely related species complexes. One genus in which these phenomena have been suggested to have played major roles based on phylogenetic data is Conradina, a genus of mints (Lamiaceae) endemic to the southeastern USA containing several endangered species. The goals of this study were to use microsatellite data to better understand patterns of genetic structure in Conradina, to test hypotheses of recent or ancient hybridization and incomplete lineage sorting, and to clarify species boundaries. Individuals from 55 populations representing all Conradina species were genotyped using 10 microsatellite loci. Analyses of the patterns of genetic structure in Conradina revealed a clear differentiation of populations following recognized species boundaries, indicating that species have diverged from one another genetically and interspecific hybridization has not occurred recently. Neither ancient hybridization nor incomplete lineage sorting is supported as the sole cause of species nonmonophyly, suggesting that both may have contributed to patterns found in phylogenetic trees; however, analyses of other types of data may be more appropriate to distinguish between these two hypotheses. Because all described species appear to be valid entities, the current listing status of most endangered species of Conradina is appropriate; however, populations of Conradina canescens are genetically differentiated into three groups, each of which may merit species status, and several recently discovered populations of Conradina in Dunn's Creek State Park in Florida are highly differentiated genetically and also appear to represent a new species.