Phylogeny and evolution of Didymosphaeriaceae (Pleosporales): new Iranian samples and hosts, first divergence estimates, and multiple evidences of species mis-identifications

Didymosphaeriaceae is a cosmopolitan family of Ascomycetes including pathogens, saprobes, and endophytes living in a variety of substrates. While a monophyletic origin of the family is now widely accepted, the monophyly of some species, their worldwide distribution, and the timing of their origin is still disputed or unexplored. We first investigated Didymosphaeriaceae species diversity in six provinces of Iran with special focus on East Azarbaijan province: based on morphological features and analyses of concatenated internal transcribed spacer regions of the rDNA operon (ITS), large subunit rDNA (LSU) and beta-tubulin, only eight samples out of 1150 contained Didymosphaeroid fungi belonging to either Paraconiothyrium fuckelii or Kalmusia variispora; our sampling indicates 4 plants as new natural hosts of these fungi. We then performed an updated phylogenetic analysis of the Didymosphaeriaceae. Results indicate that the genera Paraconiothyrium and Kulmasia are polyphyletic as the likely result of previous species mis-assignments. We finally provided the first divergence estimates of the Didymosphaeriaceae using ITS. Bayesian relaxed clock analyses support an ancient (early Paleogene) origin of the family and a recent (late Neogene) diversification of extant genus compatible with a high loss of diversity in the past and/or of a still fragmented sampling of Didymosphaeriaceae diversity.

Long-distance dispersal shaped the diversity of tribe Dorstenieae (Moraceae)

AimThe Neotropics have the highest terrestrial biodiversity on earth. Investigating the relationships between the floras of the Neotropics and other tropical areas is critical to understanding the origin and evolution of this mega-diverse region. Tribe Dorstenieae (Moraceae) has a pantropical distribution and almost equal number of species on both sides of the Atlantic. In this study, we investigate the relationship between the African and Neotropical floras using Dorstenieae (15 genera, 156 species, Moraceae) as a model clade.Locationthe Neotropics and Africa.MethodsWe used a targeted enrichment strategy with herbarium samples and a nuclear bait set to assemble a data set of 102 genes sampled from 83 (53%) species and fifteen genera (100%) of Dorstenieae, and five outgroup species. Phylogenetic relationships were reconstructed with maximum likelihood and coalescent approaches. This phylogeny was dated with a Bayesian relaxed clock model and four fossil calibrations. The biogeographic history of the group was then reconstructed with several dispersal-extinction-cladogenesis models (incl. DEC and DEC+J).ResultsThe crown-group ages of Dorstenieae and Dorstenia were estimated in the Cretaceous (65.8-79.8 Ma) and the Paleocene (50.8-67.3 Ma), respectively. Tribe Dorstenieae as a whole appears to have originated in the joint area of continental Africa, Madagascar and Asia-Oceania area. The Neotropical species of Dorstenia diversified in the Eocene (29.8-44.7 Ma) and formed a clade nested within the African lineages in the genus. Brosimum s.l., with a crown-group age at the period of the Oligocene and Miocene (14.9-31.1 Ma), represents another Neotropical clade in Dorstenieae.Main conclusionsTribe Dorstenieae originated in the joint area of continental Africa, Madagascar and Asia-Oceania area in the Cretaceous and then dispersed into Neotropics twice. Neotropical diversification after long-distance dispersal across the Atlantic is the most plausible explanation for the extant distribution pattern of Dorstenieae.

Bayesian detection of convergent rate changes of conserved noncoding elements on phylogenetic trees

Conservation of DNA sequence over evolutionary time is a strong indicator of function, and gain or loss of sequence conservation can be used to infer changes in function across a phylogeny. Changes in evolutionary rates on particular lineages in a phylogeny can indicate shared functional shifts, and thus can be used to detect genomic correlates of phenotypic convergence. However, existing methods do not allow easy detection of patterns of rate variation, which causes challenges for detecting convergent rate shifts or other complex evolutionary scenarios. Here we introduce PhyloAcc, a new Bayesian method to model substitution rate changes in conserved elements across a phylogeny. The method assumes several categories of substitution rate for each branch on the phylogenetic tree, estimates substitution rates per category, and detects changes of substitution rate as the posterior probability of a category switch. Simulations show that PhyloAcc can detect genomic regions with rate shifts in multiple target species better than previous methods and has a higher accuracy of reconstructing complex patterns of substitution rate changes than prevalent Bayesian relaxed clock models. We demonstrate the utility of PhyloAcc in two classic examples of convergent phenotypes: loss of flight in birds and the transition to marine life in mammals. In each case, our approach reveals numerous examples of conserved non-exonic elements with accelerations specific to the phenotypically convergent lineages. Our method is widely applicable to any set of conserved elements where multiple rate changes are expected on a phylogeny.

Age estimation for the genus Cymbidium (Orchidaceae: Epidendroideae) with implementation of fossil data calibration using molecular markers (ITS2 & matK) and phylogeographic inference from ancestral area reconstruction

Intercontinental dislocations between tropical regions harboring two-thirds of the flowering plants have always drawn attention from taxonomists and biogeographers. One such family belonging to angiosperms is Orchidaceae with an herbaceous habit and high species diversity in the tropics. Here, we investigate the evolutionary and biogeographical history of the genus Cymbidium, which represents a monophyletic subfamily (Epidendroideae) of the orchids and comprises 50 odd species that are distinctly distributed in tropical to temperate regions. Much is not known about correlations among the level of CAM activity (one of the photosynthetic pathways often regarded as an adaptation to water stress in land plants), habitat, life forms, and phylogenetic relationships of orchids from an evolutionary perspective. A relatively well-resolved and highly supported phylogeny for Cymbidium orchids is reconstructed based on sequence analysis of ITS2 and matK regions from the chloroplast DNA available in public repositories viz. GenBank at NCBI. This study examines a genus level analysis by integrating different molecular matrices to existing fossil data on orchids in a molecular Bayesian relaxed clock employed in BEAST and assessed divergence times for the genus Cymbidium with a focus on evolutionary history of photosynthetic characters. Our study has enabled age estimations (45Ma) as well as ancestral area reconstruction for the genus Cymbidium using BEAST by addition of previously analyzed two internal calibration points.

From Gondwana to Europe: inferring the origins of Mediterranean Macrothele spiders (Araneae : Hexathelidae) and the limits of the family Hexathelidae

The family Hexathelidae ranks among the smaller mygalomorph spider families. Most species are endemic to the Australasian region and the family was traditionally considered an example of a Gondwanan lineage. However, recent studies have cast some doubt on the monophyly of the family. Macrothele is the only genus with an out-of-Gondwana distribution. The bulk of the Macrothele diversity is found in South-east Asia, few species are known from central Africa and two species inhabit Europe: Macrothele calpeiana (Walckenaer, 1805) from the Iberian Peninsula and Macrothele cretica Kulczynski, 1903 endemic to Crete. Here we investigate the origins of the European Macrothele species by means of a multi-locus phylogenetic approach and by inferring the time frame of the diversification of the genus using Bayesian relaxed clock methods. We also provide further insights into the phylogenetic status of the family Hexathelidae. Our results indicate that the diversification of Macrothele traces back to the period of the Gondwana break-up and its present-day distribution most likely reflects the subsequent tectonic plate movements. The two European species were not recovered as sister taxa, suggesting that Macrothele colonised the Mediterranean region twice independently. The polyphyly of the family Hexathelidae is further confirmed and the subfamily Atracinae is identified as the conflicting lineage.

Age estimation for Asian Cymbidium (Orchidaceae: Epidendroideae) with implementation of fossil data calibration using molecular markers (ITS2 & matK) implying phylogeographic inference

Intercontinental dislocations between tropical regions harboring two-thirds of the flowering plants have always drawn attention from taxonomists and bio-geographers. The focus had always been on woody land plants rather than on herbs. Orchidaceae is one such family belonging to angiosperms, with an herbaceous habit and high species diversity in the tropics. Here, we investigate the evolutionary and bio-geographical history of the genus Cymbidium, which represents a monophyletic subfamily (Epidendroideae) of the orchids and comprises 50 odd species that are disjunctly distributed in tropical to temperate regions. A relatively well-resolved and highly supported phylogeny of Cymbidiums was reconstructed based on sequence analyses of internal transcribed spacer (ITS2) regions and maturaseK (matK) from the chloroplast region available on the public domain in GenBank at NCBI. Crassulacean acid metabolism (CAM) is one of the photosynthetic pathways regarded as adaptation to water stress in land plants. Hardly any information exists on correlations among the level of CAM activity, habitat, life form, and phylogenetic relationship of a plant group from an evolutionary perspective. This study examines a genus level analyses by integrating ITS and matK data to all fossil data available on orchids in a molecular Bayesian relaxed clock employed in BEAST and assessed divergence times for the genus Cymbidium with a focus on evolutionary plasticity of photosynthetic characters. Our study has enabled age estimations for the genus Cymbidum (12Ma) for the first time using BEAST by addition of previously analyzed two internal calibration points.

Age estimation for Asian Cymbidium (Orchidaceae: Epidendroideae) with implementation of fossil data calibration using molecular markers (ITS2 & matK) implying phylogeographic inference

Intercontinental dislocations between tropical regions harboring two-thirds of the flowering plants have always drawn attention from taxonomists and bio-geographers. The focus had always been on woody land plants rather than on herbs. Orchidaceae is one such family belonging to angiosperms, with an herbaceous habit and high species diversity in the tropics. Here, we investigate the evolutionary and bio-geographical history of the genus Cymbidium, which represents a monophyletic subfamily (Epidendroideae) of the orchids and comprises 50 odd species that are disjunctly distributed in tropical to temperate regions. A relatively well-resolved and highly supported phylogeny of Cymbidiums was reconstructed based on sequence analyses of internal transcribed spacer (ITS2) regions and maturaseK (matK) from the chloroplast region available on the public domain in GenBank at NCBI. Crassulacean acid metabolism (CAM) is one of the photosynthetic pathways regarded as adaptation to water stress in land plants. Hardly any information exists on correlations among the level of CAM activity, habitat, life form, and phylogenetic relationship of a plant group from an evolutionary perspective. This study examines a genus level analyses by integrating ITS and matK data to all fossil data available on orchids in a molecular Bayesian relaxed clock employed in BEAST and assessed divergence times for the genus Cymbidium with a focus on evolutionary plasticity of photosynthetic characters. Our study has enabled age estimations for the genus Cymbidum (12Ma) for the first time using BEAST by addition of previously analyzed two internal calibration points.

Phylogenetic revision of Backhousieae (Myrtaceae): Neogene divergence, a revised circumscription of Backhousia and two new species

Backhousieae is a small tribe of Myrtaceae composed of two genera (Backhousia and Choricarpia) endemic to Australia. Phylogenetic analyses (parsimony, maximum likelihood and Bayesian) were performed on a combined chloroplast (matK, trnH–psbA, trnC–psbM, trnL–F, rps16) and nuclear (internal transcribed spacers) dataset for all nine species of Backhousia, two species of Choricarpia and two undescribed species. Backhousieae is monophyletic; however, Choricarpia is embedded within Backhousia. In all analyses there were four strongly supported clades containing two to four taxa, with no support for relationships among clades, and the relationships of B. bancroftii and B. citriodora remain unresolved. Bayesian relaxed-clock molecular dating indicated that the Backhousieae has been potentially present in rainforest across Australia for more than 50 million years. The current distribution of Backhousia is inferred to be largely due to the contraction of Australian rainforest in the Neogene. New combinations in Backhousia are made for the two species of Choricarpia, and B. gundarara and B. tetraptera are described as new species. B. gundarara is known only from the Kimberley region of Western Australia, widely disjunct from the remaining Backhousia in eastern Queensland and New South Wales, and appears to be a lineage isolated by increasing aridity during the Miocene.