Classification of the tribe Cardueae in natural subtribes has always been a challenge due to the lack of support of some critical branches in previous phylogenies based on traditional Sanger markers. With the aim to propose a new subtribal delimitation, we applied a Hyb-Seq approach to a set of 76 Cardueae species representing all the subtribes and informal groups defined in the tribe, targeting 1061 nuclear conserved orthology loci (COS) designed for Compositae and obtaining chloroplast coding regions as byproduct of off-target reads. For the extraction of target nuclear data, we used two strategies, PHYLUCE and HybPiper, and 776 and 1055 COS loci were recovered with each of them, respectively. Additionally, 87 chloroplast genes were assembled and annotated. With the three datasets, phylogenetic relationships within the tribe were reconstructed under approaches of concatenation (using supermatrices as input for maximum likelihood analysis with RAxML) and coalescence (species tree estimated with ASTRAL based on the individual gene trees of each COS locus). The phylogenetic analyses of the nuclear datasets fully resolved virtually all nodes with very high support. Although nuclear and plastid tree topologies are highly congruent, they still present some incongruences, which are shortly discussed. On the basis of the phylogenies obtained, we propose a new taxonomic scheme of 12 monophyletic and morphologically consistent subtribes: Carlininae, Cardopatiinae, Echinopsinae, Dipterocominae (new), Xerantheminae (new), Berardiinae (new), Staehelininae (new), Onopordinae (new), Carduinae (redelimited), Arctiinae (new), Saussureinae (new), and Centaureinae. Another main key result of the study was the high resolution recovered at the backbone of the Cardueae tree, which led to obtain better inter-subtribal relationships. Using as tree base the nuclear HybPiper phylogeny, we updated the temporal framework for the origin and diversification of the tribe and subtribes. Overall, the power of Hyb-Seq is demonstrated to solve relationships traditionally suggested by morphology but never recovered with support using Sanger sequencing of a few DNA markers.

Target enrichment is a cost-effective sequencing technique that holds promise for elucidating evolutionary relationships in fast-evolving lineages. However, potential biases and impact of bioinformatic sequence treatments in phylogenetic inference have not been thoroughly explored yet. Here, we investigate this issue with an ultimate goal to shed light into a highly diversified group of Compositae (Asteraceae) constituted by four main genera: Arctium, Cousinia, Saussurea, and Jurinea. Specifically, we compared sequence data extraction methods implemented in two easy-to-use workflows, PHYLUCE and HybPiper, and assessed the impact of two filtering practices intended to reduce phylogenetic noise. In addition, we compared two phylogenetic inference methods: (1) the concatenation approach, in which all loci were concatenated in a supermatrix; and (2) the coalescence approach, in which gene trees were produced independently and then used to construct a species tree under coalescence assumptions. Here we confirm the usefulness of the set of 1061 COS targets (a nuclear conserved orthology loci set developed for the Compositae) across a variety of taxonomic levels. Intergeneric relationships were completely resolved: there are two sister groups, Arctium-Cousinia and Saussurea-Jurinea, which are in agreement with a morphological hypothesis. Intrageneric relationships among species of Arctium, Cousinia, and Saussurea are also well defined. Conversely, conflicting species relationships remain for Jurinea. Methodological choices significantly affected phylogenies in terms of topology, branch length, and support. Across all analyses, the phylogeny obtained using HybPiper and the strictest scheme of removing fast-evolving sites was estimated as the optimal. Regarding methodological choices, we conclude that: (1) trees obtained under the coalescence approach are topologically more congruent between them than those inferred using the concatenation approach; (2) refining treatments only improved support values under the concatenation approach; and (3) branch support values are maximized when fast-evolving sites are removed in the concatenation approach, and when a higher number of loci is analyzed in the coalescence approach.

No abstract

Silene sennenii is an extremely narrow endemic species from the north-eastern Iberian Peninsula, with only five populations. Its habitat, severely affected by urban, industrial, and agricultural land use, is highly vulnerable, and makes of S. sennenii, a seriously endangered taxon. Its pollination ecology is studied and compared among populations. Flowers of S. sennenii are distinguished by several morphological and physiological characters, including night emission of scent, which are related to nocturnal pollination. Although visited by insects at night and during day, selective insect exclusion experiments show that this plant is pollinated mainly at night. However, differences among populations are observed in visitation rates and reproductive success, which indicates that the system composed by the plant and its pollinators show evidences of disruption in some populations. The causes and consequences of this disruption are analyzed, with a focus on differences in population size, habitat quality, and genetic diversity. The results are discussed from the perspective of the vulnerability of established mutualisms, and the consequences for the survival of the species.

The main objective of the online Mangrove Reference Database and Herbarium is to give a current and historic overview of the global, regional and local distribution of true mangrove species. This database has been initiated in 2001 by the Vlaams Instituut voor de Zee (VLIZ) and the Flanders Marine Data and Information Center (VMDC) in collaboration with the Université Libre de Bruxelles (ULB) and the Vrije Universiteit Brussel (VUB). All the data are based on records containing species location information (literature, maps, herbaria, expert access, etc…) and all mangroves species (approximately 75) display distribution information from many study sites around the world. All the mangrove zones around the world are recorded in this database and a particular species list is available for those sites that have been studied or sampled. This can be viewed and zoomed on easily using a GIS-interface. In addition, the database provides information and pictures of plant physiognomy and ecological adaptations to the intertidal mangrove habitat. Attention is also paid to the nomenclature, systematic (incl. the most recent phylogeny of APGII) as well as vernacular (information can be visualized on synonyms, vernacular names and direct child taxa). Finally, all the information in the database is completed by a Mangrove Reference Herbarium in collaboration with the National Botanical Garden of Belgium and the Belgian Biodiversity Platform, while collaboration with other international herbaria is furthered. Herbarium boards can be consulted using webtools to zoom in on diagnostic characteristics. In summary, the Mangrove Reference Database and Herbarium (abbreviated to 'Mangroves ' in Aphia) has different purposes:to provide a relational database for all true mangrove plant species using an expandable taxonomic tree; to display a fact sheet for each mangrove plant species including basic information with photographs, a scanned herbarium specimen and distribution data;to provide a searchable online distribution map for each species based on point-locations submitted by researchers world-wide (through papers, herbaria or through online access). The aim is to display historic as well as current distribution maps by filtering the data in the database with the respect to the time the fieldwork/collection was done;to preserve a herbarium reference specimen for each true mangrove species; and, on a longer term, to provide an automated determination key to identify mangroves world-wide.This online Mangrove Reference database is an additional step in the knowledge of mangrove species distribution through several examples in many study sites. It is a dynamic database that gives a widespread view of literature, herbaria and other references on mangrove distribution and invites researchers to collaborate on understanding the functioning of this threatened ecosystem.The database is continually updated and can be accessed through: