Phylogenomic and Ecological Systematics of Melocactus (Cactaceae)

Pucciniomycotina is a subphylum with a high diversity in terms of habitat and life history strategies that include plant parasites, animal associates (including opportunistic human pathogens), saprobes and antagonists of other fungi. The class Cystobasidiomycetes within this subphylum is a representative of such diversity and remains understudied. Their role in nature and the associations they establish with their hosts for most of the species is still unknown. In this study we used taxonomic and phylogenetic methods to present an inventory of strains in this class collected for more than 20 years from all over the world and preserved in the Aime Lab Culture Collection. Molecular and morphological data for six new species in the genera Bannoa, Buckleyzyma, Halobasidium and Sakaguchia were also presented. Additionally, mating experiments were performed by pairing strains of Bannoa; this is the second time in the genus that clamp connections and basidia are observed. We also found that newly described species of Bannoa can be co-inhabitants of sori of rust fungi. In general, antagonistic interactions can occur through: 1) direct physical contact between two fungi, i.e., mycoparasitism; or, 2) the production of antimicrobial compounds. In the Cystobasidiomycetes, direct physical antagonistic interaction which is associated with sexual states has been reported in species of Cystobasidium, Naohidea, Cyphobasidium and Occultifur. On the other hand, the production of antimicrobial compounds which mainly occurs between the yeast stage of the fungi and other organisms has only been reported in Cystobasidium pallidumand Hasegawazyma lactosa. We also hypothesize that the common ancestor to Cystobasidiomycetes is a mycoparasite due to the fact that this life strategy is present in most of the lineages in the class. To test this hypothesis, we grouped into five categories the host association or substrate from which strains of extant species in the Cystobasidiomycetes were isolated, i.e.,animals, plants, fungi, aquatic or decaying organic matter. We constructed a resolved phylogeny for the class based on seven locito study the evolutionary origins of mycoparasitism through ancestral character reconstruction with representation of all described species. Our analysis suggests that the most likely hypothesis is that the most recent common ancestor of the Cystobasidiomycetes was associated to fungi.

Aim The study aimed to establish areas of endemism and distribution patterns for Neotropical species of the genus Piper in the Neotropical and Andean regions by means of parsimony analysis of endemicity (PAE) and track‐compatibility analysis.Location The study area includes the Neotropical region and the Northern Andean region (Páramo‐Punan subregion).Methods We used distribution information from herbarium specimens and recent monographic revisions for 1152 species of Piper from the Neotropics. First, a PAE was attempted in order to delimit the areas of endemism. Second, we performed a track‐compatibility analysis to establish distribution patterns for Neotropical species of Piper. Terminology for grouping Piper is based on recent phylogenetic analyses.Results The PAE yielded 104 small endemic areas for the genus Piper, 80 of which are in the Caribbean, Amazonian and Paranensis subregions of the Neotropical region, and 24 in the Páramo‐Punan subregion of the Andean region. Track‐compatibility analysis revealed 26 generalized tracks, one in the Páramo‐Punan subregion (Andean region), 19 in the Neotropical region, and six connecting the Andean and Neotropical regions. Both the generalized tracks and endemic areas indicate that distribution of Piper species is restricted to forest areas in the Andes, Amazonia, Chocó, Central America, the Guayana Shield and the Brazilian Atlantic coast.Main conclusions Piper should not be considered an Andean‐centred group as it represents two large species components with distributions centred in the Amazonian and Andean regions. Furthermore, areas of greater species richness and/or endemism are restricted to lowland habitats belonging to the Neotropical region. The distribution patterns of Neotropical species of Piper could be explained by recent events in the Neotropical region, as is the case for the track connecting Chocó and Central America, where most of the species rich groups of the genus are found. Two kinds of event could explain the biogeography of a large part of the Piper taxa with Andean–Amazonian distribution: pre‐Andean and post‐Andean events.

Phylogenetic relationships within an endemic group of Malagasy 'assassin spiders’ (Araneae, Archaeidae): ancestral character reconstruction, convergent evolution and biogeography

The Horn of Africa supports a unique and rich diversity of squamate reptiles. Among them, the gecko genus Hemidactylus stands out as the most species-rich genus of the region. In this study, we assembled a genetic and morphological data set of 22 Hemidactylus species that form a clade termed the African radiation, which is part of the arid clade of the genus. We reconstructed their phylogenetic relationships using both concatenation-based approaches and species tree inference. Hemidactylus laevis, H. ophiolepoides, and H. somalicus have been sequenced and placed in a phylogenetic context for the first time in this study. Our results confirm the phylogenetic placement of these species within the African radiation of the genus. Early diversification within the clade, however, remains obscure. According to the analysis of concatenated data, H. laevis is sister to the rest of the clade, whereas the species tree analyses inferred the African radiation to be formed by two subclades, northern and southern, and H. laevis belonging to the former. We integrate evidence from multiple sources including genetic differentiation at both mitochondrial and nuclear levels, morphological disparification, and coalescent-based species delimitation to support the existence of two new species of Hemidactylus. We provide a formal description of these two new species, one from northern Ethiopia, Eritrea, and westernmost Somaliland, and one from southern Ethiopia, northern Kenya, and easternmost South Sudan. Furthermore, we found that of the morphological traits examined, the numbers of supralabials and infralabials bear phylogenetic signal and we were able to tentatively infer the phylogenetic placement of species for which genetic data are still missing.

Phylogenetic relationships between fungus-associated Neotropical species of the genera Hirtodrosophila, Mycodrosophila and Zygothrica (Diptera, Drosophilidae), with insights into the evolution of breeding sites usage

The objectives of the research were : (1) to determine the distribution pattern, association, and interaction of plant species, (2) to determine the relationship between life form and the distribution pattern of species, and (3) to comparethe association chance of distribution patterns. Quadrate method was used in this project. Determination of speciesdistribution pattern was calculated using Poisson Distribution formula, and the determination of association was calculated using Contingency Table. The result indicated that: (1) The species richness were dominated by grasses, reaching 42.42%. Of the 33 observed species, 21 of them were in a clumped distribution, 7 species in a regular, and 5 species were at random pattern. (2) There are relationship between life form and the distribution of the plant species. The multi-plants tend to have a clumped distribution pattern, and single plant tend to have a regular or random distribution pattern. (3) The species of clumped distribution tend to have negative association to the species which of regular and random distribution pattern. However among the species which had the regular distribution pattern tend to have positive association. (4) The calculated results of the interaction more supported the individualistic concept of the plant association than community as an integrated unit.© 2002 Jurusan Biologi FMIPA UNS SurakartaKey words: distribution pattern, association, interaction, grassland, Baluran National Park

Weed species composition and distribution pattern in the maize crop under the influence of edaphic factors and farming practices: A case study from Mardan, Pakistan

Phylogeny and intraspecific variability of holoparasitic Orobanche (Orobanchaceae) inferred from plastid rbcL sequences

Host jumps by microbial symbionts are often associated with bursts of species diversification driven by the exploitation of new adaptive zones. The objective of this study was to infer the evolution of habitat preference (decaying plants, soil, living fungi, and living plants), and nutrition mode (saprotrophy and mycoparasitism) in the fungal genus Trichoderma to elucidate possible interkingdom host jumps and shifts in ecology. Host and ecological role shifts were inferred by phylogenetic analyses and ancestral character reconstructions. The results support several interkingdom host jumps and also show that the preference for a particular habitat was gained or lost multiple times. Diversification analysis revealed that mycoparasitism is associated with accelerated speciation rates, which then suggests that this trait may be linked to the high number of species in Trichoderma. In this study it was also possible to infer the cryptic roles that endophytes or soil inhabitants play in their hosts by evaluating their closest relatives and determining their most recent ancestors. Findings from this study may have implications for understanding certain evolutionary processes such as species radiations in some hyperdiverse groups of fungi, and for more applied fields such as the discovery and development of novel biological control strategies.

Background: Echeveria and Pachyphytum are two closely related Neotropical genera in the Crassulaceae. Several species in Echeveria possess characters cited as diagnostic for Pachyphytum such as a clearly defined stem, a nectary scale on the inner face of petals and as inflorescence a scorpioid cyme or cincinnus. Pachyphytum has been identified as monophyletic while Echeveria as polyphyletic in previous molecular phylogenetic analysess. Hypothesis: The objective of this paper is to identify the phylogenetic position of a rare species with restricted distribution in Echeveria, E. heterosepala that possesses the diagnostic characters of Pachyphytum to better understand the generic limits between these two genera. We expect this species to be closely related to Pachyphytum. Methods: Bayesian inference and Maximum Likelihood analyses were carried out using 47 taxa, including as ingroup, species of Echeveria, Graptopetalum, Lenophyllum, Pachyphytum, Sedum, Thompsonella and Villadia and as outgroup, species in Dudleya. Analyses were conducted based on plastid (rpl16, trnL-F) and nuclear (ETS, ITS) markers. Ancestral character reconstruction was carried out under a parsimony criterion based on the molecular trees retrieved by the phylogenetic analyses. Four morphological characters were considered: defined stem, type of inflorescence, nectary scale in petals and position of sepals. Results: Accessions of E. heterosepala were retrieved in a well-supported clade group comprising exclusively Echeveria species. Therefore this species belongs to Echeveria although possessing characters similar to Pachyphytum and moreover it was not identified closely related to this genus. None of the traits considered have taxonomic importance. The node at the Pachyphytum clade identified unambiguous character states such as stem present, straight sepals, nectary scale on petals, however these character states were identified in the rest of the clades as well. Remarkably, the monophyly of Pachyphytum was corroborated, while Echeveria remains poorly understood.

Fallacia is distinguished morpho-anatomically from Navicula sensu lato based on the possession of an H-shaped chloroplast, lateral sterna and a finely porous conopeum, but whether this genus is monophyletic is still in question. Three new Fallacia species are described based on morphology and SSU rRNA and rbcL gene sequences: Fallacia tateyamensis sp. nov., Fallacia bosoensis sp. nov. and Fallacia laevis sp. nov. We performed the first comprehensive molecular and morphological phylogenetic analyses of 31 Fallacia species based on 11 new sequences from six species and 23 morphological characters. We also documented the detailed morphogenesis of Fallacia for the first time. Fallacia is not monophyletic. Both morphological and DNA sequence data supported the separation of Rossia from Fallacia, while the phylogenetic position of Pseudofallacia is uncertain. We recognized four morphogroups in Fallacia by morphological and molecular phylogenetic analyses. Ancestral character reconstruction indicated that diatoms in Sellaphoraceae evolved from the possession of two lateral narrow parallel depressions covered by narrow nonporous conopea, to lyre-shaped canals covered by wide porous conopea. Lanceolate canals and the presence of areolae in canals evolved multiple times independently.

Phylogeny of Helieae (Gentianaceae): Resolving taxonomic chaos in a Neotropical clade

Cumulative mutation and new selection strategies for Trichoderma harzianum 3PCE6 hypercelulolytic mutants

The Palpimanidae are one of five extant Palpimanoidea families that occur mainly in South America and Africa, although there are lineages in Madagascar, islands of the Indian Ocean, and parts of Asia. Here we examine the role of plate tectonics in shaping the distribution of Palpimanidae. We perform molecular sequencing via target enrichment, which makes use of fragmented DNA, because most specimens are stored in natural history museum collections and were not properly preserved for molecular sequencing. We perform phylogenetic analysis, divergence dating, and ancestral range reconstructions to assess whether continental vicariance shaped the evolution of Palpimanidae. We also examine evolution of eye loss via ancestral character reconstruction. We report the first Palpimanidae phylogeny based on genomic data that samples the majority of Chediminae genera. Results suggest that Palpimanidae originated in the Triassic, with diversification spanning the Jurassic to the Cretaceous. Vicarance played a role in early diversification, with later range expansion out of Africa. Based on morphology and phylogenetic analysis, Sceliraptor is synonymized with Sarascelis, Sceliscelis is synonymized with Scelidocteus, and the new genus and species Sitamacho tao gen. nov., sp. nov. is described, with three species transferred from Hybosida.

The evolution of dwarf shrubs in alpine environments: a case study of Alchemilla in Africa.