Species tree phylogeny and biogeography of the Neotropical genus Pradosia (Sapotaceae, Chrysophylloideae)

Recent phylogenetic studies in Sapotaceae have demonstrated that many genera need to be redefined to better correspond to natural groups. The Neotropical genus Pradosia is believed to be monophyletic and includes 26 recognized species. Here we reconstruct the generic phylogeny by a species-tree approach using *BEAST, 21 recognized species (36 accessions), sequence data from three nuclear markers (ITS, ETS, and RPB2), a relaxed lognormal clock model, and a fossil calibration. We explore the evolution of five selected morphological characters, reconstruct the evolution of habitat (white-sand vs. clayish soils) preference, as well as space and time by using a recently developed continuous diffusion model in biogeography. We find Pradosia to be monophyletic in its current circumscription and to have originated in the Amazon basin at ~47.5Ma. Selected morphological characters are useful to readily distinguish three clades. Preferences to white-sand and/or clay are somewhat important for the majority of species, but speciation has not been powered by habitat shifts. Pradosia brevipes is a relative young species (~1.3Ma) that has evolved a unique geoxylic life strategy within Pradosia and is restricted to savannahs. Molecular dating and phylogenetic pattern indicate that Pradosia reached the Brazilian Atlantic coast at least three times: at 34.4Ma (P. longipedicellata), at 11.7Ma (P. kuhlmannii), and at 3.9Ma (weakly supported node within the red-flowered clade). © 2015 Elsevier Inc

Estimating the Phanerozoic history of the Ascomycota lineages : Combining fossil and molecular data

Peer reviewe

Paleo-Drainage Basin Connectivity Predicts Evolutionary Relationships across Three Southeast Asian Biodiversity Hotspots

Understanding factors driving diversity across biodiversity hotspots is critical for formulating conservation priorities in the face of ongoing and escalating environmental deterioration. While biodiversity hotspots encompass a small fraction of Earth's land surface, more than half the world's plants and two-thirds of terrestrial vertebrate species are endemic to these hotspots. Tropical Southeast (SE) Asia displays extraordinary species richness, encompassing four biodiversity hotspots, though disentangling multiple potential drivers of species richness is confounded by the region's dynamic geological and climatic history. Here, we use multilocus molecular genetic data from dense multispecies sampling of freshwater fishes across three biodiversity hotspots, to test the effect of Quaternary climate change and resulting drainage rearrangements on aquatic faunal diversification. While Cenozoic geological processes have clearly shaped evolutionary history in SE Asian halfbeak fishes, we show that paleo-drainage re-arrangements resulting from Quaternary climate change played a significant role in the spatiotemporal evolution of lowland aquatic taxa, and provide priorities for conservation efforts. [Freshwater; geology; halfbeak; island radiation; Miocene; Pleistocene; river; Southeast Asia.

Towards a natural classification of Sapotaceae subfamily Chrysophylloideae in the Neotropics

Generic limits of Chrysophyllum and Pouteria (Chrysophylloideae, Sapotaceae) have been found to be untenable. We here search for natural lineages in Neotropical Chrysophylloideae by sampling 101 terminals for molecular sequences of nuclear ribosomal DNA (external and internal transcribed spacer), the nuclear gene RPB2 and 17 morphological characters. Data were analysed with Bayesian inference and parsimony jackknifing. Morphological traits were finally optimized onto the tree to identify the most coherent characters. The resulting phylogenetic tree suggests that the limits of the well-known genera Chrysophyllum and Pouteria must be amended. Diploon, Ecclinusa and Elaeoluma can be maintained and Chrysophyllum sections Ragala section Prieurella and the satellite genera Achrouteria, Cornuella, Martiusella and Nemaluma merit generic resurrection. Lucuma may be restored if the type species belongs to the clade. The accepted genera Chromolucuma, Pradosia and Sarcaulus gain strong clade support, but are embedded in a core clade of Pouteria and may be relegated to the subgeneric level if morphological studies cannot provide evidence concurring with narrow generic concepts. Circumscriptions of Micropholis and Chrysophyllum sections Chrysophyllum and Villocuspis remain unclear and must be explored by using an extended taxon sampling. We predict that yet-to-be-analysed species of Pouteria sections Franchetella, Gayella, Oxythece and Pouteria and members of the currently accepted genera Chromolucuma, Pradosia and Sarcaulus will fall inside the core clade of Pouteria when analysed. © 2017 The Linnean Society of London

Phylogeny and biogeography of the plant family Calceolariaceae

Calceolaria L., Jovellana Ruiz & Pav., and Porodittia G. Don (=Stemotria Wettst. & Harms) toghether constitute the family Calceolariaceae consisting of approximately 300 species distributed manily in South America. The present thesis shows that using morphology as basis for sectional delimitations in the genus Calceolaria is not sufficient to define monophyletic groups. Comparing information from nuclear versus chloroplast sequence data reveal extensive topological discordance, neither of which can easily be related to morphological features. The putative sister relationship between Calceolaria and Jovellana is confirmed, while the phylogenetic position of Porodittia is revealed to be nested deep inside Calceolaria. For Jovellana, a small genus present disjunctly across the Pacific Ocean in South America and New Zealand, a taxonomic revision suggest synonymisation of two previousy recognised species in New Zealand with a larger circumscribed J. sinclairii while the distributional disjunction is revealed as a result of long distance dispersal of recent date. This thesis also explores the presumed close relationship between the origin of the Andes and the evlutionary distriution history of Calceolaria. Biogeographic models for reconstruction of ancestral areas are used to estimate the orgin of the family. By extending the model to simultaneous estiamation of ancestral area in three dimensions based in specimen data a correlation between the uplift history of the Andes and the radiation events of Calceolaria can be established. By optimising morphological traits relating to growth habit and pollination of the genus in a phylogenetic framework, and relating these to the ancestral area reconstruction and the uplift history of the Andes, a suggested radiation pattern for Calceolaria can be established. This pattern follow a south to north trend with an origin in lowland Chile or low Andean slopes, with subsequent radiations to the north correlated with the Altiplano region and the Huancabamba deflection. The pattern also show a correlation between the uplift history of the Andes and the radiation of Calceolaria. This further suggests that the divergence patterns of a group of species cannot be understood without extensive information on not only the phylogeny, but also the prefferred ecological niches and other mechanisms important for radiation success

Data Organisation

This talk presented general data organisation principles. It was delivered during the course Introduction to Data Management Practices for National Genomics Infrastructure organised by NBIS Data Management team in September 2023.  The target audience is research infrastructure staff at a data producing sequencing facility. The objective was that the audience at the end of the talk should be able to: Understand the relation between data organisation and principles of Open Science and FAIR Organise and document their project files and metadata in a structured way Understand data deliveries in a context where the connection between data and metadata is maintained throughout the data life cycle. </ul

Tutorial

Tutorial on how to set up and modify a species tree diffusion analysi

Towards a natural classification of Sapotaceae subfamily Chrysophylloideae in Oceania and Southeast Asia based on nuclear sequence data

Generic limits within subfamily Chrysophylloideae (Sapotaceae) from Oceania and Southeast Asia are reconciled based on a molecular phylogeny. We analysed sequences of nuclear ribosomal DNA (ETS, ITS) and the nuclear gene RPB2 with BEAST and parsimony jackknifing, using a sample of 168 terminals. Eight morphological characters were traced on a condensed majority-rule consensus tree to identify diagnostic character combinations for the genera. Accepted genera with character support are Magodendron, Pichonia, Planchonella, Pycnandra, Sersalisia, and Van-royena, while Beccariella and Niemeyera require amendment. Beccariella, a widely distributed group, is an illegitimate later homonym and we propose that the genus Pleioluma is resurrected in its place. The Australian genus Niemeyera is paraphyletic, but it is rendered monophyletic by reinstating Amorphospermum for N. antiloga. Beauvisagea, Blabeia, Fontbrunea, and Krausella are all segregates of Planchonella and rejected, while Wokoia is a later synonym of Pichonia. Planchonella baillonii, an endemic species of New Caledonia, is the sole member of an old lineage and firmly placed as the sister to a clade comprising the other congeners. Planchonella sandwicensis, a Hawaiian species, previously proposed to be a distinct genus, is a member of Planchonella. In the Pacific, P. tahitensis (including P. grayana) is a polymorphic species, widely distributed and adapted to a wide range of habitats. We provide a generic key (excluding Xantolis), diagnostic character combinations for all genera, and the necessary taxonomic combinations for Pichonia, Planchonella, Pleioluma, and Sersalisia to render each genus monophyletic

The largest endemic genus in New Caledonia grows: three new species of Pycnandra (Sapotaceae) restricted to ultramafic substrate with updated subgeneric keys

International audiencePycnandra Benth., a member of subfamily Chrysophylloideae (Sapotaceae), is the largest endemic genus in New Caledonia and is subdivided into six subgenera. It circumscribes 59 species, plus an additional three described here, and nine additional species that remain undescribed for various reasons. We here use nrDNA data of ETS, ITS, and RPB2, analyse it within a Bayesian framework using BEAST, and place the new species in their respective subgenera. Pycnandra perplexa Swenson &amp; Gâteblé is placed in subgenus Achradotypus and given a preliminary IUCN Red List assessment of Near Threatened (NT). It is confined to the ultramafic massif of southern Grande Terre and separated from the similar species P. griseosepala Vink, which is confined to non-ultramafic mountains north of the large southern ultramafic plateau. Pycnandra kopetoensis Munzinger &amp; Swenson and P. margueriteae Munzinger &amp; Swenson are two new micro-endemic species known only from their type localities, where habitats have been destroyed by deforestation, deliberate fires and mining activities. Pycnandra kopetoensis is named after Mount Kopéto, placed in subgenus Leptostylis, and given a preliminary assessment as Critically Endangered (CR). Pycnandra margueriteae is from a small remnant forest near Bourail and categorised as Critically Endangered (CR). Revised identification keys for subgenus Achradotypus, Leptostylis and Pycnandra are provided