A new cryptic species in the genus Tubariomyces (Inocybaceae, Agaricales)

A new Tubariomyces species from Italy, T. similis, is described and illustrated. It is phenotypically very close to T. hygrophoroides but, based on a combined ITS-LSU rDNA analysis, phylogenetically distinct.     

A morphological and molecular assessment of the genus Sinotubimorpha (Halymeniaceae, Rhodophyta)

A critical reassessment of the morphological features of two closely related red algal genera,Grateloupia C.Agardh and Sinotubimorpha W.X.Li & Z.F.Ding (Halymeniaceae),pointed out that members of the t...     

25Proposal of a new red algal genus in the ceramieae (ceramiaceae, ceramiales)

A new genus is proposed to accommodate four species belonging in the Ceramium flaccidum complex based on comparative vegetative morphology and rbc L sequence analysis: C. flaccidum (Harvey ex Kuetzing) Ardissone (1871), C. gracillimum, C. Agardh (1824), C. fimbriatum S. & G. (1924) and C. rectocorticum Dawson 1950. Comparative rbcL sequence analysis indicates that this complex forms a distinct monophyletic clade separate from other Ceramium species. Although C. flaccidum has been placed in Hormoseras Kuetzing 1841 (as H. flaccidum Harvey ex Kuetzing 1862), the type species of Hormoceras is Ceramium diaphanum . The new genus is characterized by alternate branching, incomplete cortication, production of three cortical filament initials of which the basipetal initial divides horizontally, and unicellular rhizoids terminating in pad-like structures produced from periaxial cells. Cortical filament development is discussed for related genera in the tribe Ceramieae ( Campylaephora, Carpoblepharis, Centroceras, Ceramium, Corallophila, Herpochondria, Microcladia, Reinboldiella ). Rbc L-based phylogenies indicate that the new genus is sister to Centroceras , a genus possessing three cortical filament initials. The phylogenetic relationships within the tribe may correlate with cortication patterns that characterize each genus     

New species and distinctive geographical divergences of the genus Sparassis (Basidiomycota): evidence from morphological and molecular data

Species of the genus Sparassis in East Asia were investigated using morphology and DNA sequences data. Phylogenetic analyses inferred from sequences of the internal transcribed spacer (ITS), the nuclear gene coding for the ribosomal large subunit (nLSU) and partial gene coding RNA polymerase subunit II (rpb2) strongly supported lineages corresponding to morphological features. Three taxa, S. subalpina, S. cystidiosa f. flabelliformis and S. latifolia were recognized from East Asia, and the former two taxa are new to science. The occurrence of S. latifolia in Japan and in the Russian Far East was confirmed. Geographical divergences of Sparassis in the Holarctic were observed. Most species have relatively narrow distribution ranges, and taxa with intercontinental distributions were not detected. Divergence of species in the Northern Hemisphere in different clades appears to have taken place at different times: the S. latifolia-crispa-radicata species complex appears to have undergone a recent radiation, while the S. subalpina-brevipes-spathularia species complex represents a relatively ancient speciation.     

Integrating molecular and morphological approaches for characterizing parasite cryptic species: implications for parasitology

Herein we review theoretical and methodological considerations important for finding and delimiting cryptic species of parasites (species that are difficult to recognize using traditional systematic methods). Applications of molecular data in empirical investigations of cryptic species are discussed from an historical perspective, and we evaluate advantages and disadvantages of approaches that have been used to date. Developments concerning the theory and practice of species delimitation are emphasized because theory is critical to interpretation of data. The advantages and disadvantages of different molecular methodologies, including the number and kind of loci, are discussed relative to tree-based approaches for detecting and delimiting cryptic species. We conclude by discussing some implications that cryptic species have for research programmes in parasitology, emphasizing that careful attention to the theory and operational practices involved in finding, delimiting, and describing new species (including cryptic species) is essential, not only for fully characterizing parasite biodiversity and broader aspects of comparative biology such as systematics, evolution, ecology and biogeography, but to applied research efforts that strive to improve development and understanding of epidemiology, diagnostics, control and potential eradication of parasitic diseases.     

The use of molecular and morphological characters to resolve the taxonomic identity of cryptic species: the case of Miniopterus manavi (Chiroptera, Miniopteridae)

Based on recent molecular phylogenetic studies, the Old World bat family Miniopteridae, composed of species in the genus Miniopterus , has been shown to contain complex paraphyletic species, many of which are cryptic based on convergent morphological characters. Herein we resolve the phylogenetic relationships and taxonomy of the species complex M . manavi on Madagascar and in the Comoro Archipelago, where these animals occur in different bioclimatic zones. First using mitochondrial cytochrome- b sequence data to define clades and then morphology to corroborate the molecular data, including comparisons to type specimens, we demonstrate that animals identified as this taxon are a minimum of three species: M . manavi sensu stricto occurs in at least the central portion of the Central Highlands; M . griveaudi has a broad distribution in lowland northern and central western Madagascar and the Comoros (Anjouan and Grande Comore), and M . aelleni sp. n. has been found in northern and western Madagascar and the Comoros (Anjouan). In each case, these three clades were genetically divergent and monophyletic and the taxa are diagnosable based on different external and craniodental characters. One aspect that helped to define the systematics of this group was isolation of DNA from one of the paratypes of M. manavi collected in 1896 and new topotypic material. Miniopterus manavi is most closely allied to a recently described species, M. petersoni . At several localities, M . griveaudi and M . aelleni have been found in strict sympatry, and together with M. manavi sensu stricto show considerable convergence in morphological characters, but are not immediate sister taxa. In defining and resolving the systematics of cryptic species, such as miniopterid bats, the process of defining clades with molecular tools, segregating the specimens accordingly, and identifying corroborative morphological characters has been notably efficient.     

Molecular phylogeny and larval morphological diversity of the lanternfish genus Hygophum (Teleostei: Myctophidae)

Larvae of the deep-sea lanternfish genus Hygophum (Myctophidae) exhibit a remarkable morphological diversity that is quite unexpected, considering their homogeneous adult morphology. In an attempt to elucidate the evolutionary patterns of such larval morphological diversity, nucleotide sequences of a portion of the mitochondrially encoded 16S ribosomal RNA gene were determined for seven Hygophum species and three outgroup taxa. Secondary structure-based alignment resulted in a character matrix consisting of 1172 bp of unambiguously aligned sequences, which were subjected to phylogenetic analyses using maximum-parsimony, maximum-likelihood, and neighbor-joining methods. The resultant tree topologies from the three methods were congruent, with most nodes, including that of the genus Hygophum, being strongly supported by various tree statistics. The most parsimonious reconstruction of the three previously recognized, distinct larval morphs onto the molecular phylogeny revealed that one of the morphs had originated as the common ancestor of the genus, the other two having diversified separately in two subsequent major clades. The patterns of such diversification are discussed in terms of the unusual larval eye morphology and geographic distribution.     

Phylogeny, diversity, and distribution inExostema (Rubiaceae): Implications of morphological and molecular analyses

The neotropical genusExostema comprises 25 species of trees and shrubs, ranging in distribution from Bolivia to Mexico and throughout the West Indies, with most species endemic to the Greater Antilles. Infrageneric relationships and species-level patterns of evolution were investigated in phylogenetic analyses using morphological, molecular, and combined data sets. All data sets resolved three main species groups which correspond to the three sections recognized byMcDowell (1996). However, the analyses of ITS sequence data placed the two South American species basal to the three main clades. Otherwise, the morphological and molecular data are highly compatible, and produce a more robust yet consistent phylogeny in the combined data analysis. Morphological evolution inExostema involves many specializations for xeric habitats, reflecting repeated ecological shifts from moist forest to exposed, seasonally dry environments during the diversification of the genus. Both moth and bee pollination syndromes are found inExostema, and shifts in pollination ecology appear pivotal to the differentiation of the three sections. Biogeographically,Exostema likely originated in South America and migrated via Central America to the Greater Antilles, where the morphological diversification and speciation are most extensive.     

Rapid radiation and cryptic speciation in squat lobsters of the genus Munida (Crustacea, Decapoda) and related genera in the South West Pacific: molecular and morphological evidence

Squat lobsters (genus Munida and related genera) are among the most diverse taxa of western Pacific crustaceans, though several features of their biology and phylogenetic relationships are unknown. This paper reports an extensive phylogenetic analysis based on mitochondrial DNA sequences (cytochrome c oxidase subunit I and 16S rRNA) and the morphology of 72 species of 12 genera of western Pacific squat lobsters. Our phylogenetic reconstruction using molecular data supports the recent taxonomic splitting of the genus Munida into several genera. Excluding one species (M. callista), the monophyly of the genus Munida was supported by Bayesian analysis of the molecular data. Three moderately diverse genera (Onconida, Paramunida, and Raymunida) also appeared monophyletic, both according to morphological and molecular data, always with high support. However, other genera (Crosnierita and Agononida) seem to be para- or polyphyletic. Three new cryptic species were identified in the course of this study. It would appear that the evolution of this group was marked by rapid speciation and stasis, or certain constraints, in its morphological evolution.     

A combination of molecular and morphological approaches resolves species in the taxonomically difficult genus Procladius Skuse (Diptera: Chironomidae) despite high intra-specific morphological variation

Molecular approaches for identifying aquatic macroinvertebrate species are increasingly being used but there is ongoing debate about the number of DNA markers needed to differentiate species accurately. Here, we use two mitochondrial genes (cytochrome oxidase I, cytochrome b) and a nuclear gene (carbamoylphosphate synthetase) to differentiate species variation within the taxonomically challenging chironomid genus Procladius from southern Australia, a genus which is important for pollution monitoring. The mitochondrial genes indicated cryptic species that were subsequently linked to morphological variation at the larval and pupal stage. Two species previously described based on morphological criteria were linked to molecular markers, and there was evidence for additional cryptic species. Each genetic marker provided different information, highlighting the importance of considering multiple genes when dissecting taxonomically difficult groups, particularly those used in pollution monitoring.     

Regional endemism and cryptic species revealed by molecular and morphological analysis of a widespread species of Neotropical catfish

The lower Central American landscape was fully emergent approximately three million years ago, an event which marked the beginning of the Great American biotic interchange. Freshwater fishes participated in the biotic interchange. Because primary freshwater fishes are restricted to freshwater, they provide an excellent system for investigating the interplay of historical and recent processes on the assembly, structure and diversity of the regions' aquatic ecosystems. We focused on examining the history of diversification for a species of catfish (Pimelodella chagresi) whose distribution spans multiple, isolated drainage basins across the Isthmian landscape and into north-western South America. Analysis of mitochondrial DNA haplotypes and morphological traits indicated that P. chagresi, as currently recognized, comprises a species complex. In addition, along the Pacific slope of Panama, repeated dispersion, diversification, extinction and possibly hybridization are thought to underlie a complex distribution of haplotypes. Overall, the results underscore the tremendous importance of historical processes on regional biodiversity.     

Extreme genetic diversity in the lizard Atlantolacerta andreanskyi (Werner, 1929): A montane cryptic species complex

ABSTRACT: BACKGROUND: Atlantolacerta andreanskyi is an enigmatic lacertid lizard that, according to the most recent molecular analyses, belongs to the tribe Eremiadini, family Lacertidae. It is a mountain specialist, restricted to areas above 2400 m of the High Atlas Mountains of Morocco with apparently no connection between the different populations. In order to investigate its phylogeography, 92 specimens of A. andreanskyi were analyzed from eight different populations across the distribution range of the species for up to 1108 base pairs of mitochondrial DNA (12S, ND4 and flanking tRNA-His) and 2585 base pairs of nuclear DNA including five loci (PDC, ACM4, C-MOS, RAG1, MC1R). RESULTS: The results obtained with both concatenated and coalescent approaches and clustering methods, clearly show that all the populations analyzed present a very high level of genetic differentiation for the mitochondrial markers used and are also generally differentiated at the nuclear level. CONCLUSIONS: These results indicate that A. andreanskyi is an additional example of a montane species complex.     

A molecular phylogeny of the lizard genus Phymaturus (Squamata,Liolaemini): Implications for species diversity and historical biogeography of southern South America

The lizard genus Phymaturus is widely distributed in Argentina and along the eastern edge of Chile between 25° and 45° south. We sampled 27 of the 38 currently recognized species plus 22 candidate species using two mitochondrial genes (cytb and 12S), four protein coding nuclear genes and seven anonymous nuclear loci, and present the first comprehensive molecular phylogenetic hypothesis for the clade. We recovered two large clades (the palluma or northern group and patagonicus or southern group) previously recognized on the basis of morphological and mitochondrial sequence evidence, and compared results obtained from concatenated-gene analyses with results of a coalescent-based species-tree approach (BEST). With both methods we identified four main clades within the palluma group (mallimaccii, roigorum, verdugo, and vociferator) and five main clades within the patagonicus group (calcogaster, indistinctus, payuniae, somuncurensis, and spurcus). We found several instances of non-monophyly with cytb and cases of incongruence between mitochondrial vs nuclear data for which we discuss alternative hypotheses. Although with lower support values, combined BEST results are more congruent with concatenated nuclear data than with combined concatenated analyses, suggesting that BEST is less influenced by demographic processes than combined concatenated analyses. We discuss the taxonomic, biogeographic and conservation implications of these results and how the future integration of phylogeographic and morphological approaches will allow the further testing of demographic and biogeographic hypotheses.     

Molecules and morphology suggest cryptic species diversity and an overall complex taxonomy of fish scale geckos, genus Geckolepis

The current classification of the Malagasy-Comoroan geckos of the genus Geckolepis recognizes three valid species and is based on morphological differences only. Species allocation of individuals is difficult, mainly because of the insufficiently known degree of variation and the frequent partial loss of the integument in preserved specimens. Here we study Geckolepis specimens from almost their entire known range. We combine molecular and morphological data to estimate species richness in the genus, and to assess the taxonomic validity of the morphological differences proposed. Analyses of mitochondrial (12S, ND4) and nuclear (RAG1, CMOS) gene sequences support three major clades in addition to the morphologically distinct G. polylepis (included for 12S only), and the presence of various divergent lineages within these clades, some occurring in sympatry. Among lineages, the external morphology seems to be comparatively conservative, and differences are faint in many cases. For each major lineage, we summarize the most diagnostic morphological characters that distinguish it from other lineages. The combined molecular and morphological data strongly indicate the presence of highly divergent lineages, three of which are tentatively referred to the names Geckolepis maculata, G. polylepis and G. typica, whereas three other major lineages are considered Confirmed Candidate Species. Among the remaining lineages, differentiation is shallower, and these may qualify for Deep Conspecific Lineages. In conclusion, our analysis provides evidence for an underestimation of species richness in the genus and a complex evolutionary history, not reflected by current Geckolepis species-level taxonomy.