A new lineage of lichenized basidiomycetes inferred from a two-gene phylogeny: The Lepidostromataceae with three species from the tropics

The lichen habit has apparently evolved independently in at least five major clades of mushroom-forming basidiomycetes (Agaricomycetes). Tracing the origin of lichenization in these groups depends on a clearer understanding of the phylogenetic relationships of basidiolichens to other fungi. We describe here a new family of basidiolichens made up of tropical, soil-inhabiting fungi that form lichenized, scale-like squamules and erect, coral-like fruiting structures. These structures are common to two basidiolichen genera, Multiclavula and Lepidostroma. Molecular studies have confirmed the phylogenetic position of Multiclavula species in the Cantharellales, but Lepidostroma species have never been sequenced. We obtained nuclear small and large subunit ribosomal sequences from specimens of L. calocerum collected in Costa Rica and Mexico and also from specimens of two Multiclavula spp. recently described from Rwanda. The phylogenetic placement of these fungi within the Agaricomycetes was investigated using likelihood and Bayesian analyses. Our results indicate that L. calocerum and the Rwandan species form a natural group unrelated to Multiclavula and sister to the Atheliales, members of which are neither lichen-forming nor clavarioid. The independent evolution of morphologically similar forms in so many groups of basidiomycetes is a remarkable example of convergence, indicating similar pathways to lichenization in these fungi.     

Reconstructing the evolution of agarics from nuclear gene sequences and basidiospore ultrastructure

Traditional classifications of agaric fungi involve gross morphology of their fruit bodies and meiospore print-colour. However, the phylogeny of these fungi and the evolution of their morphological and ecological traits are poorly understood. Phylogenetic analyses have already demonstrated that characters used in traditional classifications of basidiomycetes may be heavily affected by homoplasy, and that non-gilled taxa evolved within the agarics several times. By integrating molecular phylogenetic analyses including domains D1–D3 and D7–D8 of nucLSU rDNA and domains A–C of the RPB1 gene with morphological and chemical data from representative species of 88 genera, we were able to resolve higher groups of agarics. We found that the species with thick-walled and pigmented basidiospores constitute a derived group, and hypothesize that this specific combination of characters represents an evolutionary advantage by increasing the tolerance of the basidiospores to dehydration and solar radiation and so opened up new ecological niches, e.g. the colonization of dung substrates by enabling basidiospores to survive gut passages through herbivores. Our results confirm the validity of basidiospore morphology as a phylogenetic marker in the agarics.     

Global biogeography of the ectomycorrhizal /sebacina lineage (Fungi,Sebacinales) as revealed from comparative phylogenetic analyses

Compared with plants and animals, large‐scale biogeographic patterns of microbes including fungi are poorly understood. By the use of a comparative phylogenetic approach and ancestral state reconstructions, we addressed the global biogeography, rate of evolution and evolutionary origin of the widely distributed ectomycorrhizal (EcM) /sebacina lineage that forms a large proportion of the Sebacinales order. We downloaded all publicly available internal transcribed spacer (ITS) sequences and metadata and supplemented sequence information from three genes to construct dated phylogenies and test biogeographic hypotheses. The /sebacina lineage evolved 45–57 Myr ago that groups it with relatively young EcM taxa in other studies. The most parsimonious origin for /sebacina is inferred to be North American temperate coniferous forests. Among biogeographic traits, region and biome exhibited stronger phylogenetic signal than host family. Consistent with the resource availability (environmental energy) hypothesis, the ITS region is evolving at a faster rate in tropical than nontropical regions. Most biogeographic regions exhibited substantial phylogenetic clustering suggesting a strong impact of dispersal limitation over a large geographic scale. In northern Holarctic regions, however, phylogenetic distances and phylogenetic grouping of isolates indicate multiple recent dispersal events.     

Spatial heterogeneity of the species composition of a clavarioid fungi’s compex in the Eurasian Arctic

Using the example of a model group of macromycete (clavarioid fungi), a large-scale investigation into the mycological complex of the Eurasian Arctic is conducted. The species composition of clavarioid fungi’s complex is revealed in all longitudinal sectors and latitudinal subzones, and a comparative analysis is carried out. It has been determined that, among groups of aphyllophoroid fungi, the clavarioid life form is the most adapted to the extremally psychrophilic conditions of the Arctic. It is shown that the near-oceanic sectors are the richest, whereas the continental sectors are much poorer. The distribution of the species composition of fungi conforms to the similar distribution of flowering plants, especially hemicryptophytes. The average annual quantity of atmospheric precipitation is the leading climatic factor. The differences make it possible to subdivide the Eurasian Arctic into four mycogeographical regions: Atlantic (European), Siberian, Chukotian (Beringian), and High Arctic.     

Covarion shifts cause a long-branch attraction artifact that unites microsporidia and archaebacteria in EF-1alpha phylogenies

Microsporidia branch at the base of eukaryotic phylogenies inferred from translation elongation factor 1alpha (EF-1alpha) sequences. Because these parasitic eukaryotes are fungi (or close relatives of fungi), it is widely accepted that fast-evolving microsporidian sequences are artifactually "attracted" to the long branch leading to the archaebacterial (outgroup) sequences ("long-branch attraction," or "LBA"). However, no previous studies have explicitly determined the reason(s) why the artifactual allegiance of microsporidia and archaebacteria ("M + A") is recovered by all phylogenetic methods, including maximum likelihood, a method that is supposed to be resistant to classical LBA. Here we show that the M + A affinity can be attributed to those alignment sites associated with large differences in evolutionary site rates between the eukaryotic and archaebacterial subtrees. Therefore, failure to model the significant evolutionary rate distribution differences (covarion shifts) between the ingroup and outgroup sequences is apparently responsible for the artifactual basal position of microsporidia in phylogenetic analyses of EF-1alpha sequences. Currently, no evolutionary model that accounts for discrete changes in the site rate distribution on particular branches is available for either protein or nucleotide level phylogenetic analysis, so the same artifacts may affect many other "deep" phylogenies. Furthermore, given the relative similarity of the site rate patterns of microsporidian and archaebacterial EF-1alpha proteins ("parallel site rate variation"), we suggest that the microsporidian orthologs may have lost some eukaryotic EF-1alpha-specific nontranslational functions, exemplifying the extreme degree of reduction in this parasitic lineage.     

An evidence-based consensus for the classification of arbuscular mycorrhizal fungi (Glomeromycota)

The publication of a large number of taxon names at all levels within the arbuscular mycorrhizal fungi (Glomeromycota) has resulted in conflicting systematic schemes and generated considerable confusion among biologists working with these important plant symbionts. A group of biologists with more than a century of collective experience in the systematics of Glomeromycota examined all available molecular–phylogenetic evidence within the framework of phylogenetic hypotheses, incorporating morphological characters when they were congruent. This study is the outcome, wherein the classification of Glomeromycota is revised by rejecting some new names on the grounds that they are founded in error and by synonymizing others that, while validly published, are not evidence-based. The proposed “consensus” will provide a framework for additional original research aimed at clarifying the evolutionary history of this important group of symbiotic fungi.     

Evolutionary history of Na,K-ATPases and their osmoregulatory role

The Na/K pump, or Na,K-ATPase, is a key enzyme to the homeostasis of osmotic pressure, cell volume, and the maintenance of electrochemical gradients. Its α subunit, which holds most of its functions, belongs to a large family of ATPases known as P-type, and to the subfamily IIC, which also includes H,K-ATPases. In this study, we attempt to describe the evolutionary history of IIC ATPases by doing phylogenetic analysis with most of the currently available protein sequences (over 200), and pay special attention to the relationship between their diversity and their osmoregulatory role. We include proteins derived from many completed or ongoing genome projects, many of whose IIC ATPases have not been phylogenetically analyzed previously. We show that the most likely origin of IIC proteins is prokaryotic, and that many of them are present in non-metazoans, such as algae, protozoans or fungi. We also suggest that the pre-metazoan ancestor, represented by the choanoflagellate Monosiga brevicollis, whose genome has been sequenced, presented at least two IIC-type proteins. One of these proteins would have given rise to most current animal IIC ATPases, whereas the other apparently evolved into a lineage that, so far, has only been found in nematodes. We also propose that early deuterostomes presented a single IIC gene, from which all the extant diversity of vertebrate IIC proteins originated by gene and genome duplications. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Novel insights into evolution of protistan polyketide synthases through phylogenomic analysis

Polyketide synthase (PKS) enzymes are large multi-domain complexes that structurally and functionally resemble the fatty acid synthases involved in lipid metabolism. Polyketide biosynthesis of secondary metabolites and hence functional PKS genes are widespread among bacteria, fungi and streptophytes, but the Type I was formerly known only from bacteria and fungi. Recently Type I PKS genes were also uncovered in the genomes of some alveolate protists. Here we show that the newly sequenced genomes of representatives of other protist groups, specifically the chlorophytes Ostreococcus tauri, O. lucimarinus, and Chlamydomonas reinhardtii, and the haptophyte Emiliania huxleyi also contain putative modular Type I PKS genes. Based on the patchy phylogenetic distribution of this gene type among eukaryotic microorganisms, the question arises whether they originate from recent lateral gene transfer from bacteria. Our phylogenetic analyses do not indicate such an evolutionary history. Whether Type I PKS genes originated several times independently during eukaryotic evolution or were rather lost in many extant lineages cannot yet be answered. In any case, we show that environmental genome sequencing projects are likely to be a valuable resource when mining for genes resembling protistan PKS I genes.     

NETGEN: generating phylogenetic networks with diploid hybrids

SUMMARY: NetGen is an event-driven simulator that creates phylogenetic networks by extending the birth-death model to include diploid hybridizations. DNA sequences are evolved in conjunction with the topology, enabling hybridization decisions to be based on contemporary evolutionary distances. NetGen supports variable rate lineages, root sequence specification, outgroup generation and many other options. This note describes the NetGen application and proposes an extension of the Newick format to accommodate phylogenetic networks. AVAILABILITY: NetGen is written in C and is available in source form at http://www.phylo.unm.edu/~morin/.     

Phylogeny-based developmental analyses illuminate evolution of inflorescence architectures in dogwoods (Cornus s. l., Cornaceae)

? Inflorescence architecture is important to angiosperm reproduction, but our knowledge of the developmental basis underlying the evolution of inflorescence architectures is limited. Using a phylogeny-based comparative analysis of developmental pathways, we tested the long-standing hypothesis that umbel evolved from elongated inflorescences by suppression of inflorescence branches, while head evolved from umbels by suppression of pedicels. ? The developmental pathways of six species of Cornus producing different inflorescence types were characterized by scanning electron microscopy (SEM) and histological analysis. Critical developmental events were traced over the molecular phylogeny to identify evolutionary changes leading to the formation of umbels and heads using methods accounting for evolutionary time and phylogenetic uncertainty. ? We defined 24 developmental events describing the developmental progression of the different inflorescence types. The evolutionary transition from paniculate cymes to umbels and heads required alterations of seven developmental events occurring at different evolutionary times. ? Our results indicate that heads and umbels evolved independently in Cornus from elongated forms via an umbellate dichasium ancestor and this process involved several independent changes. Our findings shed novel insights into head and umbel evolution concealed by outer morphology. Our work illustrates the importance of combining developmental and phylogenetic data to better define morphological evolutionary processes.     

Phylogenetic analysis reveals a scattered distribution of autumn colours

Background and Aims

Leaf colour in autumn is rarely considered informative for taxonomy, but there is now growing interest in the evolution of autumn colours and different hypotheses are debated. Research efforts are hindered by the lack of basic information: the phylogenetic distribution of autumn colours. It is not known when and how autumn colours evolved.

Methods

Data are reported on the autumn colours of 2368 tree species belonging to 400 genera of the temperate regions of the world, and an analysis is made of their phylogenetic relationships in order to reconstruct the evolutionary origin of red and yellow in autumn leaves.

Key Results

Red autumn colours are present in at least 290 species (70 genera), and evolved independently at least 25 times. Yellow is present independently from red in at least 378 species (97 genera) and evolved at least 28 times.

Conclusions

The phylogenetic reconstruction suggests that autumn colours have been acquired and lost many times during evolution. This scattered distribution could be explained by hypotheses involving some kind of coevolutionary interaction or by hypotheses that rely on the need for photoprotection.Key words: Autumn colour, leaf colour, comparative analysis, coevolution, photoprotection, phylogenetic analysis     

Origin and evolution of fungus farming in wood-boring Coleoptera – a palaeontological perspective

Insect–fungus mutualism is one of the better-studied symbiotic interactions in nature. Ambrosia fungi are an ecological assemblage of unrelated fungi that are cultivated by ambrosia beetles in their galleries as obligate food for larvae. Despite recently increased research interest, it remains unclear which ecological factors facilitated the origin of fungus farming, and how it transformed into a symbiotic relationship with obligate dependency. It is clear from phylogenetic analyses that this symbiosis evolved independently many times in several beetle and fungus lineages. However, there is a mismatch between palaeontological and phylogenetic data. Herein we review, for the first time, the ambrosia system from a palaeontological perspective. Although largely ignored, families such as Lymexylidae and Bostrichidae should be included in the list of ambrosia beetles because some of their species cultivate ambrosia fungi. The estimated origin for some groups of ambrosia fungi during the Cretaceous concurs with a known high diversity of Lymexylidae and Bostrichidae at that time. Although potentially older, the greatest radiation of various ambrosia beetle lineages occurred in the weevil subfamilies Scolytinae and Platypodinae during the Eocene. In this review we explore the evolutionary relationship between ambrosia beetles, fungi and their host trees, which is likely to have persisted for longer than previously supposed.     

A review and synthesis on the systematics and evolution of jellyfish blooms: advantageous aggregations and adaptive assemblages

Pelagic gelatinous invertebrates in many diverse phyla aggregate, bloom, or swarm. Although typically portrayed as annoying to humans, such accumulations probably are evolutionary adaptations to the environments of pelagic gelatinous zooplankton. We explore this proposition by systematic analysis completed in three steps. First, using the current morphological taxonomic framework for Scyphozoa, we summarize relevant information on species that aggregate, bloom, and swarm and on those species that do not. Second, we establish a molecular phylogenetic framework for assessing evolutionary relationships among classes and many orders of Medusozoa and among most families of Scyphozoa (particularly Discomedusae). Third, we interpret the phylogenetic distribution of taxa and of characteristics of jellyfish that aggregate, bloom, or swarm, in terms of species diversity—a proxy for evolutionary success. We found that: (1) Medusae that occur en masse are not randomly distributed within the Phylum Cnidaria but instead they are found primarily within the Scyphozoa which have a metagenic life history. (2) Midwater and deep-sea medusae rarely bloom or swarm. (3) Epibenthic medusae do not swarm. (4) Large carnivores that feed on large prey do not bloom strongly. (5) Large medusae that feed exclusively on small prey both bloom and swarm. (6) Pelagia, the only holoplanktonic, epipelagic scyphomedusan, both blooms and swarms, demonstrating that a metagenic life cycle is not required for blooming or swarming at sea. (7) Environmental change (overfishing, species introductions, and eutrophication) may induce or inhibit blooms. (8) Taxa that bloom or swarm are often more diverse than taxa that do not. (9) Speciation in scyphozoans can occur rapidly. (10) Morphological stasis in holozooplankton masks genetic variability. (11) Selection for convergent evolution in the sea is strong because mass occurrence has evolved multiple times in independent evolutionary lineages under similar circumstances. Thus, attributes possessed by many taxa that occur en masse appear to be evolutionarily advantageous, i.e., adaptations. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users. Guest editors: K. A. Pitt & J. E. Purcell Jellyfish Blooms: Causes, Consequences, and Recent Advances     

Do lichens domesticate photobionts like farmers domesticate crops? Evidence from a previously unrecognized lineage of filamentous cyanobacteria

Phylogenetic diversity of lichen photobionts is low compared to that of fungal counterparts. Most lichen fungi are thought to be associated with just four photobiont genera, among them the cyanobacteria Nostoc and Scytonema, two of the most important nitrogen fixers in humid ecosystems. Although many Nostoc photobionts have been identified using isolated cultures and sequences, the identity of Scytonema photobionts has never been confirmed by culturing or sequencing. We investigated the phylogenetic placement of presumed Scytonema photobionts and unicellular morphotypes previously assigned to Chroococcus, from tropical Dictyonema, Acantholichen, Coccocarpia, and Stereocaulon lichens. While we confirm that filamentous and unicellular photobiont morphotypes belong to a single clade, this clade does not cluster with Scytonema but represents a novel, previously unrecognized, highly diverse, exclusively lichenized lineage, for which the name Rhizonema is available. The phylogenetic structure observed in this novel lineage suggests absence of coevolution with associated mycobionts at the species or clade level. Instead, highly efficient photobiont strains appear to have evolved through photobiont sharing between unrelated, but ecologically similar, coexisting lineages of lichenized fungi ("lichen guilds"), via the selection of particular photobiont strains through and subsequent horizontal transfer among unrelated mycobionts, a phenomenon not unlike crop domestication.     

Glavarioid fungi of the Solomon Islands

Twenty-five species in 13 genera are recorded. New taxa are Clavaria vermicularis Ft. var. latispora var. nov., Clavulinopsis brevipes Corner var. termitarii var. nov., C. fusispora Corner, C. solomonensis Corner, Physalacria solomonensis Corner, Pterula gordyus (Speg.) Corner var. macrospora var. nov., P. robusta Corner, Ramaria solomonensis Corner, R. zippelii (Lév.) Corner var. cristatospora var. nov. (also from Borneo), and Ramariopsis kunzei (Ft.) Donk var. megaspora var. nov. (also from Borneo and Tibet). The clavarioid flora is essentially Malaysian and pantropic.     

Explaining Dioscorides' "double difference": why are some mushrooms poisonous, and do they signal their unprofitability?

The adaptive significance of toxins in mushrooms has received very little consideration, although it is clear that poisons have appeared (and/or disappeared) many times in mushrooms' evolutionary history. One possibility is that poisons have evolved in some mushroom species to deter their consumption by would-be fungivores before spore dispersal. If this is so, then one might expect poisonous mushrooms to signal their unprofitability in some way. In this study, we have conducted the first formal analysis of the ecological and morphological traits associated with edible and poisonous mushrooms in North America and Europe. Poisonous mushrooms do not tend to be more colorful or aggregated than edible mushrooms, but they are more likely to exhibit distinctive odors even when phylogenetic relationships are accounted for. This raises the intriguing possibility that some poisonous species of mushrooms have evolved warning odors (and perhaps tastes) to enhance avoidance learning by fungivores.     

Multiple evolutionary origins lead to diversity in the metabolic profiles of ambrosia fungi

Ambrosia fungi are an ecological assemblage cultivated by ambrosia beetles as required nutrient sources. This mutualism evolved in multiple beetle and fungus lineages. Whether convergence in ecology led to convergent metabolism in ambrosia fungi is unknown. We compared the assimilation of 190 carbon sources in five independent pairs of ambrosia fungi and closely related, non-ambrosial species. Ecological convergence versus phylogenetic divergence in carbon source use was tested using variation partitioning. We found no convergence in carbon utilization capacities. Instead, metabolic variation was mostly explained by phylogenetic relationships. In addition, carbon usage in ambrosia fungi was equally diverse as that in non-ambrosial species. Thus, carbon metabolism of each ambrosia fungus is determined by its inherited metabolism, not the transition towards symbiosis. In contrast to other fungus-farming systems of termites and attine ants, the fungal symbionts of ambrosia beetles are functionally diverse, reflecting their independent evolutionary origins.     

The evolution of larval morphology and swimming performance in ascidians

The complexity of organismal function challenges our ability to understand the evolution of animal locomotion. To meet this challenge, we used a combination of biomechanics, phylogenetic comparative analyses, and theoretical morphology to examine evolutionary changes in body shape and how those changes affected swimming performance in ascidian larvae. Results of phylogenetic comparative analyses suggest that coloniality evolved at least three times among ascidians and that colonial species have a convergent larval morphology characterized by a large trunk volume and shorter tail length in proportion to the trunk. To explore the functional significance of this evolutionary change, we first verified the accuracy of a mathematical model of swimming biomechanics in a solitary (C. intestinalis) and a colonial (D. occidentalis) species and then ran numerous simulations of the model that varied in tail length and trunk volume. The results of these simulations were used to construct landscapes of speed and cost of transport predictions within a trunk volume/tail length morphospace. Our results suggest that the reduction of proportionate tail length in colonial species resulted in improved energetic economy of swimming. The increase in the size of larvae with the origin of coloniality facilitated faster swimming with negligible energetic cost, but may have required a reduction in adult fecundity. Therefore, the evolution of ascidians appears to be influenced by a trade-off between the fecundity of the adult stage and the swimming performance of larvae.