Data from: Phylogenetic footprints of an Antarctic radiation: the Trematominae (Notothenioidei, Teleostei)

The teleost suborder Notothenioidei is restricted to the Southern Ocean and has been described as a species flock spanning the whole of it. Within the suborder, the subfamily Trematominae is important for coastal Antarctic ecosystems. The eleven Trematomus species occupy a large range of ecological niches. The genus is monophyletic if the genus Pagothenia (two additional species) and Cryothenia amphitreta, also nested within it, are included. Although the Trematominae have received much interest, the relationships among these fourteen species are still unclear. Several recent studies have tried to resolve these interrelationships; however no complete and clear picture has emerged, probably because of the use of a low number of insufficiently variable markers. The only common results places T. scotti as the sister-group of the rest of the subfamily and T. loennbergi close to T. lepidorhinus. We use here more variable markers. Four nuclear markers, two of which are new, and a mitochondrial marker for the biggest trematomine sampling ever gathered (14 species, 78 specimens). We found that several nuclear haplotypes are shared by several species (mostly in very closely related species). The haplotype patterns coupled with the cytogenetics of the subfamily suggest that a phenomenon of incomplete lineage sorting is likely to be at play. Using a calibration linked to fossil evidence, we evaluate the relative ages of each clade within the Trematominae to assess the proximity of the speciation events to one another. The main trematomine diversification was recent and sudden

Trematomus_radiation_BEAST

XML file used for the *BEAST analysi

Is the species flock concept operational? The Antarctic shelf case.

10 pagesInternational audienceThere has been a significant body of literature on species flock definition but not so much about practical means to appraise them. We here apply the five criteria of Eastman and McCune for detecting species flocks in four taxonomic components of the benthic fauna of the Antarctic shelf: teleost fishes, crinoids (feather stars), echinoids (sea urchins) and crustacean arthropods. Practical limitations led us to prioritize the three historical criteria (endemicity, monophyly, species richness) over the two ecological ones (ecological diversity and habitat dominance). We propose a new protocol which includes an iterative fine-tuning of the monophyly and endemicity criteria in order to discover unsuspected flocks. As a result nine " full " species flocks (fulfilling the five criteria) are briefly described. Eight other flocks fit the three historical criteria but need to be further investigated from the ecological point of view (here called " core flocks "). The approach also shows that some candidate taxonomic components are no species flocks at all. The present study contradicts the paradigm that marine species flocks are rare. The hypothesis according to which the Antarctic shelf acts as a species flocks generator is supported, and the approach indicates paths for further ecological studies and may serve as a starting point to investigate the processes leading to flock-like patterning of biodiversity

Case 3 of Table 1.

<p>This situation is a mix of case 1 and case 2. A taxonomic decision would simply lead to case 2, where supplementary data about the tempo of diversification would then be required (see text).</p

Protocol to use the five criteria of Eastman and McCune [17] to detect and evaluate species flocks.

<p>The first three criteria (3 K) are the species diversity (« speciosity ») of the taxonomic component, its level of endemicity, and its monophyly. The two other criteria (2 K) are habitat dominance (in biomass) and ecological diversity. The modulation loop means that the geographical range and the taxonomic rank may have to be redefined in order to discover unsuspected flocks.</p

Case 2 of Table 1.

<p>The set of species under focus is monophyletic but contains an internal subpart that is secondarily « exported » outside the area of reference (red circle). See text for discussion.</p

Three situations for the taxon of reference (columns) are to be considered: it is monophyletic, paraphyletic or polyphyletic.

<p>There are also three situations to consider for the components of this taxon in the given area of reference (lines): monophyletic, paraphyletic or polyphyletic. To explain the table, we consider again the example of the non-notothenioid fish family Liparidae. It is monophyletic as a family (first column), however its components of the Antarctic shelf are polyphyletic because they are each related to Arctic liparids (bottom line). So the Antarctic liparid situation is the bottom left cell. Case 2 (when a taxon originating in the area of reference secondarily “exports” a part of its descent outside this area, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0068787#pone-0068787-g004" target="_blank">Fig. 4</a>) is discussed in the text.</p

Case 1 of Table 1.

<p>A set of species is paraphyletic (blue) with a taxonomic entity embedded within (purple) it that is restricted to the area of reference (red circle): A simple taxonomic decision could fulfill the two criteria of monophyly and endemicity. Indeed the taxonomic decision would render the whole set of species monophyletic (purple becomes blue).</p