Coprinellus radicellus, a new species with northern distribution

A new coprophilous species, Coprinellus radicellus, is presented and described on the basis of morphological characters and a species phylogeny inferred from ITS1–5.8S–ITS2 and beta-tubulin gene sequences. The species is characterized by lageniform pileo- and caulocystidia, 8- to 11-μm long ellipsoid basidiospores with a central germ-pore, globose cheilocystidia, an often rooting stipe, the lack of pleurocystidia and velar elements. These characters distinguish C. radicellus from all other described species in subsection Setulosi. It comes closest to C. brevisetulosus (Arnolds) Redhead, Vilgalys & Moncalvo and C. pellucidus (P. Karst.) Redhead, Vilgalys & Moncalvo both morphologically and phylogenetically, but is distinct from both. Another five representatives of morphologically recognizable groups of subsection Setulosi were included in the phylogenetic analyses and found were distinct from C. radicellus, both morphologically and phylogenetically. To date, this new species is known only from Scandinavia, which is surprising in view of the uniform geographical distributions of most setulose Coprinellus species. A key to coprophilous taxa of Coprinellus with pileo- and caulocystidia is presented. Three new combinations are proposed.     

The mushroom family Psathyrellaceae: evidence for large-scale polyphyly of the genus Psathyrella

Psathyrella is the archetypal little brown mushroom genus with few easily discernable characters causing it to be considered a "clean-up" genus for other small brown-spored saprotrophic species found worldwide. While molecular studies have demonstrated that mushroom genera based on homoplastic morphological characters are artificial, the degree of phylogenetic heterogeneity contained within Psathyrella and Psathyrellaceae has never been appropriately addressed. For this study, 132 ribosomal sequences from approximately one-tenth of the known Psathyrella species worldwide, including representatives of most subgeneric subdivisions, and three closely related coprinoid genera (Parasola, Coprinopsis, Coprinellus) were evaluated using multiple phylogenetic methods, including likelihood, with Agaricaceae as the outgroup. Our results indicated that Psathyrella was polyphyletic. Conservatively, the genus can be separated into 11 clades of which five can be raised to generic status. Most species of Psathyrella, including its type species P. gracilis, formed a large clade with Coprinellus, which appeared to be derived from within Psathyrella. Generic limits of Parasola, Lacrymaria, and Coprinopsis should be reevaluated. Several taxa previously synonymized based on morphological features were phylogenetically distinct. Morphological features traditionally used to subdivide Psathyrella appeared to be mostly convergent (homoplasious) when traced upon the resulting phylogenies, although several had high RI values. These results were interpreted in light of the two major taxonomic treatments of Psathyrella and revealed substantial inconsistencies between the molecular- and morphology-derived inferences of relationships.     

Phylogenetic relationships among species and genera of Lycoperdaceae based on ITS and LSU sequence data from north European taxa

Phylogenetic relationships, limits of species, and genera within Lycoperdaceae, were inferred by use of ITS and LSU nu-rDNA sequence data. Lycoperdaceae was confirmed as monophyletic, and Mycenastrum corium as a sister taxon to the ingroup. Four major clades were identified and received weak to moderate support and correspond with the genera Lycoperdon, Bovista, Calvatia, and Disciseda. The Lycoperdon clade includes species from Lycoperdon, Vascellum, Morganella, Handkea, Bovistella, and Calvatia. The structure within the Lycoperdon clade is unresolved and several clades are more or less unsupported, which suggests treating the supported Lycoperdon clade as the genus Lycoperdon. L. nigrescens and L. caudatum occur on single branches and their phylogenetic positions could not be resolved. The phylogenetic analyses identified 31 species of Lycoperdon, 11 species of Bovista, six species of Calvatia, and two species of Disciseda. In Lycoperdon three new species were recognized. A new species closely related to B. limosa is identified and discussed. A classification of Lycoperdaceae is proposed based on the results of the phylogenetic analyses. Morphological characters of species within and among identified clades are discussed.     

Evolutionary history of the genus Capra (Mammalia, Artiodactyla): discordance between mitochondrial DNA and Y-chromosome phylogenies

The systematics of the genus Capra remain controversial in spite of studies conducted using morphology, mtDNA, and allozymes. Here, we assess the evolutionary history of Capra (i) using phylogenetic analysis of two nuclear genes located on the Y-chromosome and (ii) previously published and new cytochrome b sequences. For the Y-chromosome phylogeny, we sequenced segments from the amelogenin (AMELY) and zinc finger (ZFY) genes from all of the eight wild taxa and from domestic goats (Capra hircus). Phylogenetic analysis of the Y-chromosome data revealed two well-defined clades. The domestic goat (C. hircus), the bezoar (Capra aegagrus), and the markhor (C. falconeri) belong to one clade (ML bootstrap value [BP]: 98%), suggesting that domestic goats originated from one or both of these wild species. The second clade (ML BP: 92%) is comprised of all the other wild species. Horn morphology is generally concordant with the Y-chromosome phylogeny. The mtDNA data also revealed two well-defined clades. However, the species in each clade are different from those inferred from the Y-chromosome data. To explain the discordance between Y-chromosome and mtDNA phylogenies, several hypotheses are considered. We suggest that a plausible scenario involves mtDNA introgression between ancestral taxa before the relatively recent colonization of Western Europe, the Caucasus Mountains, and East Africa by Capra populations.     

Supermatrix data highlight the phylogenetic relationships of photosynthetic stramenopiles

Molecular data had consistently recovered monophyletic classes for the heterokont algae, however, the relationships among the classes had remained only partially resolved. Furthermore, earlier studies did not include representatives from all taxonomic classes. We used a five-gene (nuclear encoded SSU rRNA; plastid encoded rbcL, psaA, psbA, psbC) analysis with a subset of 89 taxa representing all 16 heterokont classes to infer a phylogenetic tree. There were three major clades. The Aurearenophyceae, Chrysomerophyceae, Phaeophyceae, Phaeothamniophyceae, Raphidophyceae, Schizocladiophyceae and Xanthophyceae formed the SI clade. The Chrysophyceae, Eustigmatophyceae, Pinguiophyceae, Synchromophyceae and Synurophyceae formed the SII clade. The Bacillariophyceae, Bolidophyceae, Dictyochophyceae and Pelagophyceae formed the SIII clade. These three clades were also found in a ten-gene analysis. The approximately unbiased test rejected alternative hypotheses that forced each class into either of the other two clades. Morphological and biochemical data were not available for all 89 taxa, however, existing data were consistent with the molecular phylogenetic tree, especially for the SIII clade.     

First reliable record of a fossil species of Anthomyiidae (Diptera), with comments on the definition of recent and fossil clades in phylogenetic classification

All previous records of fossil Anthomyiidae are shown to be unsubstantiated. A female anthomyiid of a new genus and species is hereby described from a piece of Dominican amber (Upper Eocene-Oligocene). Character analysis suggests that the fossil, Coenosopsites poinari gen. & sp. nov. , belongs to a Neotropical clade with two recent genera, Phaonantho Albuquerque and Coenosopsia Malloch. Evidence for a sister-group relationship between Coenosopsites poinari and the genus Coenosopsia is provided. Clades are the only acceptable units of phylogenetic classification. Combining fossil and recent clades in phylogenetic classification requires them to be temporally delimited. Proper application of phylogenetic definitions is essential for this purpose. It is proposed that the units of phylogenetic classification should be taxa for recent clades and plesia for fossil clades. A taxon is defined as node-based with reference to its recent species, while a plesion is defined as apomorphy-based. The term lineage is proposed for a recent clade defined as stem-based with reference to its recent sister group. Individual recent species represent clades that can be incorporated into phylogenetic classification as minimal taxon units. Individual fossil species may not represent clades and thus do not count as proper units of phylogenetic classification. However, the names of fossil species are readily construed also to signify plesia with the fossil species as their only known component. As such, they are proper units of phylogenetic classification.     

The geographical pattern of speciation and floral diversification in the neotropics: the tribe sinningieae (gesneriaceae) as a case study

The geographical pattern of speciation and the relationship between floral variation and species ranges were investigated in the tribe Sinningieae (Gesneriaceae), which is found mainly in the Atlantic forests of Brazil. Geographical distribution data recorded on a grid system of 0.5 x 0.5 degree intervals and a near-complete species-level phylogenetic tree of Sinningieae inferred from a simultaneous analysis of seven DNA regions were used to address the role of geographical isolation in speciation. Geographical range overlaps between sister lineages were measured across all nodes in the phylogenetic tree and analyzed in relation to relative ages estimated from branch lengths. Although there are several cases of species sympatry in Sinningieae, patterns of sympatry between sister taxa support the predominance of allopatric speciation. The pattern of sympatry between sister taxa is consistent with range shifts following allopatric speciation, except in one clade, in which the overlapping distribution of recent sister species indicates speciation within a restricted geographical area and involving changes in pollinators and habitats. The relationship between floral divergence and regional sympatry was also examined by analyzing floral contrasts, phenological overlap, and the degree of sympatry between sister clades. Morphological contrast between flowers is not increased in sympatry and phenological divergence is more apparent between allopatric clades than between sympatric clades. Therefore, our results failed to indicate a tendency for sympatric taxa to minimize morphological and phenological overlap (geographic exclusion and/or character displacement hypotheses). Instead, they point toward adaptation in phenology to local conditions and buildup of sympatries at random with respect to flower morphology. Additional studies at a lower geographical scale are needed to identify truely coexisting species and the components of their reproductive isolation.     

Colletotrichum gloeosporioides s.l. associated with Theobroma cacao and other plants in Panama: multilocus phylogenies distinguish host-associated pathogens from asymptomatic endophytes

Colletotrichum interacts with numerous plant species overtly as symptomatic pathogens and cryptically as asymptomatic endophytes. It is not known whether these contrasting ecological modes are optional strategies expressed by individual Colletotrichum species or whether a species' ecology is explicitly pathogenic or endophytic. We explored this question by inferring relationships among 77 C. gloeosporioides s.l. strains isolated from asymptomatic leaves and from anthracnose lesions on leaves and fruits of Theobroma cacao (cacao) and other plants from Panamá. ITS and 5'-tef1 were used to assess diversity and to delineate operational taxonomic units for multilocus phylogenetic analysis. The ITS and 5'-tef1 screens concordantly resolved four strongly supported lineages, clades A-D: Clade A includes the ex type of C. gloeosporioides, clade B includes the ex type ITS sequence of C. boninense, and clades C and D are unidentified. The ITS yielded limited resolution and support within all clades, in particular the C. gloeosporioides clade (A), the focal lineage dealt with in this study. In contrast the 5'-tef1 screen differentiated nine distinctive haplotype subgroups within the C. gloeosporioides clade that were concordant with phylogenetic terminals resolved in a five-locus nuclear phylogeny. Among these were two phylogenetic species associated with symptomatic infections specific to either cacao or mango and five phylogenetic species isolated principally as asymptomatic infections from cacao and other plant hosts. We formally describe two new species, C. tropicale and C. ignotum, that are frequent asymptomatic associates of cacao and other Neotropical plant species, and epitypify C. theobromicola, which is associated with foliar and fruit anthracnose lesions of cacao. Asymptomatic Colletotrichum strains isolated from cacao plants grown in China included six distinct C. gloeosporioides clade taxa, only one of which is known to occur in the Neotropics.     

58 Determining the total dietary fiber content in hawaiian marine algae

The taxonomic validity of the genus Hydropuntia Montagne (1843) (including Polycavernosa) within the Gracilariaceae (Gracilariales, Rhodophyta) is controversial. Morphological characters that define species of Hydropuntia are said to be variable and to overlap with those of Gracilaria. Here we present a global phylogenetic study of the family based on a Bayesian analysis of a large rbc L DNA sequence dataset indicating that the genus Hydropuntia forms a well supported monophyletic clade within the family, and recognize Hydropuntia as a genus distinct from Gracilaria. We also conducted smaller phylogenetic analyses in which thirty four Hydropuntia rbc L sequences resulted in two major clades within the genus, comprising a Caribbean clade and an Indo-Pacific clade. Diagnostic reproductive stages that separate these two clades will be illustrated.     

Phylogeny and historical biogeography of African ground squirrels: the role of climate change in the evolution of Xerus

We used phylogenetic and phylogeographical methods to infer relationships among African ground squirrels of the genus Xerus. Using Bayesian, maximum-parsimony, nested clade and coalescent analyses of cytochrome b sequences, we inferred interspecific relationships, evaluated the specific distinctness of Cape (Xerus inauris) and mountain (Xerus princeps) ground squirrels, and tested hypotheses for historical patterns of gene flow within X. inauris. The inferred phylogeny supports the hypothesized existence of an 'arid corridor' from the Horn of Africa to the Cape region. Although doubts have been raised regarding the specific distinctness of X. inauris and X. princeps, our analyses show that each represents a distinct well-supported, monophyletic lineage. Xerus inauris includes three major clades, two of which are geographically restricted. The distributions of X. inauris populations are concordant with divergences within and disjunctions between other taxa, which have been interpreted as results of Plio-Pleistocene climate cycles. Nested clade analysis, coalescent analyses, and analyses of genetic structure support allopatric fragmentation as the cause of the deep divergences within this species.     

Ecological limits and diversification rate: alternative paradigms to explain the variation in species richness among clades and regions

Diversification rate is one of the most important metrics in macroecological and macroevolutionary studies. Here I demonstrate that diversification analyses can be misleading when researchers assume that diversity increases unbounded through time, as is typical in molecular phylogenetic studies. If clade diversity is regulated by ecological factors, then species richness may be independent of clade age and it may not be possible to infer the rate at which diversity arose. This has substantial consequences for the interpretation of many studies that have contrasted rates of diversification among clades and regions. Often, it is possible to estimate the total diversification experienced by a clade but not diversification rate itself. I show that the evidence for ecological limits on diversity in higher taxa is widespread. Finally, I explore the implications of ecological limits for a variety of ecological and evolutionary questions that involve inferences about speciation and extinction rates from phylogenetic data.     

Phylogeny and taxonomy of the North American clade of the Ceratocystis fimbriata complex

Ceratocystis fimbriata is a widely distributed, plant pathogenic fungus that causes wilts and cankers on many woody hosts. Earlier phylogenetic analyses of DNA sequences revealed three geographic clades within the C. fimbriata complex that are centered respectively in North America, Latin America and Asia. This study looked for cryptic species within the North American clade. The internal transcribed spacer regions (ITS) of the rDNA were sequenced, and phylogenetic analysis indicated that most isolates from the North American clade group into four host-associated lineages, referred to as the aspen, hickory, oak and cherry lineages, which were isolated primarily from wounds or diseased trees of Populus, Carya, Quercus and Prunus, respectively. A single isolate collected from P. serotina in Wisconsin had a unique ITS sequence. Allozyme electromorphs also were highly polymorphic within the North American clade, and the inferred phylogenies from these data were congruent with the ITS-rDNA analyses. In pairing experiments isolates from the aspen, hickory, oak and cherry lineages were interfertile only with other isolates from their respective lineages. Inoculation experiments with isolates of the four host-associated groupings showed strong host specialization by isolates from the aspen and hickory lineages on Populus tremuloides and Carya illinoensis, respectively, but isolates from the oak and cherry lineages did not consistently reveal host specialization. Morphological features distinguish isolates in the North American clade from those of the Latin American clade (including C. fimbriata sensu stricto). Based on the phylogenetic evidence, interfertility, host specialization and morphology, the oak and cherry lineages are recognized as the earlier described C. variospora, the poplar lineage as C. populicola sp. nov., and the hickory lineage as C. caryae sp. nov. A new species associated with the bark beetle Scolytus quadrispinosus on Carya is closely related to C. caryae and is described as C. smalleyi.     

Systematics, biogeography, and evolution of the Neotropical peacock basses Cichla (Perciformes: Cichlidae)

To investigate forces influencing diversification in Neotropical fishes, the phylogenetic relationships among species and populations of the cichlid genus Cichla were examined. Mitochondrial DNA was sequenced for 454 individuals of the 5 nominal Cichla species and several putative undescribed species. Phylogenetic analyses support the distinction of two major clades of Cichla. Clade A includes C. temensis and two undescribed species from the lower Amazonas and Xingu Rivers. Clade B includes C. orinocensis, C. monoculus, C. ocellaris. C, intermedia, and an undescribed species from the upper Madeira River. Species boundaries were relatively well-circumscribed for clade B, while incomplete lineage sorting was inferred for clade A. Three probable instances of introgression were observed, including a regional population of C. orinocensis from the Negro River that shows a history of introgression. Biogeographic patterns from Cichla are partially congruent with those seen in several other Neotropical fish clades, and the diversification of Cichla species is inferred to result from both vicariance and sympatric divergence.     

Discerning evolutionary processes in patterns of tamarin (genus Saguinus) craniofacial variation

Quantitative genetic theory specifies evolutionary expectations for morphological diversification by genetic drift in a monophyletic clade. If genetic drift is responsible for the evolutionary morphological diversification of a clade, patterns of within- and between-taxon morphological variance/covariance should be proportional. We tested for proportionality of within- and between-species craniofacial morphological variation in 12 species of tamarins (genus Saguinus). We found that within- and between-taxon morphological variations across the entire genus were not proportional, and hence not likely to be due to genetic drift alone. The primary deviation from proportionality is that size and size-related shape in the cranium is more variable relative to other aspects of cranial morphology than expected under genetic drift, suggesting differential size selection between the two major clades, the small-bodied and large-bodied tamarins. Within each of these major clades, most of the interspecific variation is consistent with the pattern expected under genetic drift, although specific contrasts may indicate the involvement of differential selection. Morphological distances among taxa do not correspond very closely to the phylogeny derived from mtDNA. In particular, S. oedipus and S. geoffroyi are very distinct morphologically from the rest of the tamarins, although they are phylogenetically the sister clade to a clade containing S. midas and S. bicolor. Morphological similarity is not a good guide to phylogenetic affinity in the tamarins, especially with regard to deeper nodes in the phylogenetic tree.     

Molecular evolutionary relationships in the avian genus Anthus (Pipits: Motacillidae)

Nucleotide sequences for 1035 bp of the mitochondrial cytochrome b gene were used to determine the molecular evolutionary relationships of species in the cosmopolitan avian genus Anthus. Phylogenetic analysis of these mtDNA sequences supported four major clades within the genus: (1) the small-bodied African pipits, (2) a largely Palearctic clade, (3) a largely South American clade, and (4) an African-Eurasian-Australian clade. Anthus hellmayri, A. correndera, and A. rubescens are shown to be paraphyletic. The possibility of paraphyly within A. similis is instead inferred to be the discovery of a new species and supported by reference to the museum voucher specimen. Sequence divergence suggests a Pliocene/Miocene origin for the genus. Although Anthus cytochrome b is found not to be behaving in a clocklike fashion across all taxa, speciation during the Pleistocene epoch can be reasonably inferred for the 66% of sister pairs that are diverging in a clocklike manner. Base compositions at each codon position are similar to those found across a growing number of avian lineages. The resulting phylogenetic hypothesis is compared to previous hypotheses of Anthus relationships, all of which deal with relationships of a particular species or a particular species complex; roughly half of these previous hypotheses are supported.     

Molecular phylogeny of Banza (Orthoptera: Tettigoniidae), the endemic katydids of the Hawaiian Archipelago

The extant endemic katydids (Orthoptera: Tettigoniidae) of the Hawaiian Archipelago include one to three species per high island and a single species on Nihoa, all currently placed in the genus Banza. These acoustic insects provide an excellent opportunity for investigating the evolution of reproductive isolation and speciation, but such studies require an understanding of phylogenetic relationships within the group. We use maximum parsimony, likelihood-based Bayesian inference, and maximum likelihood to infer phylogenetic relationships among these taxa, based on approximately 2kb of mitochondrial cytochrome oxidase I and cytochrome b. Our results strongly support two distinct high island clades: one clade ("Clade I") composed of species from Kauai, Oahu, Molokai, and Lanai and another clade ("Clade II") composed of species from Maui and Hawaii (Banza unica, from Oahu, may be basal to both these clades, but its placement is not well resolved). Within these clades, some inferred relationships are strongly supported, such as the sister status of B. kauaiensis (Kauai) and B. parvula (Oahu) within Clade I, but other relationships remain more ambiguous, such as the relative position of B. brunnea (Maui) within Clade II. Although a detailed reconstruction of the historical biogeography of the Hawaiian katydids is difficult, we use our genetic data combined with the known geological history of the Hawaiian Islands to set limits on plausible historical scenarios for diversification of this group. Beyond these historical biogeographic inferences, our results indicate possible cryptic speciation on both Oahu and Hawaii, as well as what may be unusually high average rates of nucleotide substitution. The present work sets the stage for future genetic and experimental investigations of this group.     

Phylogenetic relationships of Cryphonectria and Endothia species, based on DNA sequence data and morphology

The fungal genera Endothia and Cryphonectria include some of the most important pathogens of forest trees. Despite available new technology, no comprehensive comparative study based on DNA sequence data and morphology has been done on the available isolates representing these two genera. The main objectives of this study were to assess the phylogenetic relationships among species of Cryphonectria and Endothia, for which cultures are available, and to establish a taxonomic framework based on DNA sequence and morphological data, which will aid future studies and identification of species in these and related genera. Comparisons were based on sequence variation found in the ITS region of the ribosomal RNA operon and two regions of the β-tu-bulin gene. In addition, the morphology of these species was examined. The phylogenetic data indicated that Endothia and Cryphonectria reside in two distinct phylogenetic clades. Cryphonectria parasitica, C. macrospora, C. nitschkei, C. eucalypti and C. radicalis represented the Cryphonectria clade. Endothia gyrosa and E. singularis were included in the Endothia clade. An isolate representing E. viridistroma grouped outside the Endothia clade and separately from other groups. Other clades outside the one encompassing Cryphonectria were those represented by the C. cubensis isolates and fungi isolated from Elaeocarpus dentatus originating from New Zealand. These clades could be distinguished from Endothia and Cryphonectria, based on anamorph morphology, stromatal structure and ascospore septation. Cryphonectria and Endothia, therefore, appear to be paraphyletic and taxonomic relationships for these fungi need to be revised.     

Phylogeny-based delimitation of species boundaries and contact zones in the trilling chorus frogs (Pseudacris)

Although the trilling chorus frogs (subclade within Pseudacris: Hylidae) have been important in studies of speciation, continental patterns of genetic diversity within and among species have not been elucidated. As a result, this North American clade has been the subject of substantial taxonomic debate. In this study, we examined the phylogenetic relationships among the trilling Pseudacris and tested previously hypothesized scenarios for speciation using 2.4 kb of mitochondrial 12S and 16S rRNA genes from 253 populations. Bayesian phylogenetic analyses, in combination with published morphological and behavioral data, support recognition of at least nine species, including an undescribed species from the south-central United States. Evidence is presented for substantial geographic subdivision within P. brachyphona (northern and southern clades) and P. feriarum (coastal and inland clades). Discordance between morphology/behavior and molecular data in several individuals suggests occasional hybridization between sympatric species. These results require major revision of range limits for several taxa, in particular, P. maculata, P. triseriata, and P. feriarum. Hypothesis tests using parametric bootstrapping strongly reject previously proposed scenarios for speciation in the group. The tests also support recognition of the geographically restricted taxon P. kalmi as a distinct species. Results of this study provide both a firm phylogenetic basis for future studies of speciation in the trilling Pseudacris and a taxonomic framework for conservation efforts.     

Homoplasy in genome-wide analysis of rare amino acid replacements: the molecular-evolutionary basis for Vavilov's law of homologous series

Background  

Rare genomic changes (RGCs) that are thought to comprise derived shared characters of individual clades are becoming an increasingly important class of markers in genome-wide phylogenetic studies. Recently, we proposed a new type of RGCs designated RGC_CAMs (after Conserved Amino acids-Multiple substitutions) that were inferred using genome-wide identification of amino acid replacements that were: i) located in unambiguously aligned regions of orthologous genes, ii) shared by two or more taxa in positions that contain a different, conserved amino acid in a much broader range of taxa, and iii) require two or three nucleotide substitutions. When applied to animal phylogeny, the RGC_CAM approach supported the coelomate clade that unites deuterostomes with arthropods as opposed to the ecdysozoan (molting animals) clade. However, a non-negligible level of homoplasy was detected.