Internal Transcribed Spacer 2 (nu ITS2 rRNA) Sequence-Structure Phylogenetics: Towards an Automated Reconstruction of the Green Algal Tree of Life

L). Some have advocated the use of the nuclear-encoded, internal transcribed spacer two (ITS2) as an alternative to the traditional chloroplast markers. However, the ITS2 is broadly perceived to be insufficiently conserved or to be confounded by introgression or biparental inheritance patterns, precluding its broad use in phylogenetic reconstruction or as a DNA barcode. A growing body of evidence has shown that simultaneous analysis of nucleotide data with secondary structure information can overcome at least some of the limitations of ITS2. The goal of this investigation was to assess the feasibility of an automated, sequence-structure approach for analysis of IT2 data from a large sampling of phylum Chlorophyta.Sequences and secondary structures from 591 chlorophycean, 741 trebouxiophycean and 938 ulvophycean algae, all obtained from the ITS2 Database, were aligned using a sequence structure-specific scoring matrix. Phylogenetic relationships were reconstructed by Profile Neighbor-Joining coupled with a sequence structure-specific, general time reversible substitution model. Results from analyses of the ITS2 data were robust at multiple nodes and showed considerable congruence with results from published phylogenetic analyses.Our observations on the power of automated, sequence-structure analyses of ITS2 to reconstruct phylum-level phylogenies of the green algae validate this approach to assessing diversity for large sets of chlorophytan taxa. Moreover, our results indicate that objections to the use of ITS2 for DNA barcoding should be weighed against the utility of an automated, data analysis approach with demonstrated power to reconstruct evolutionary patterns for highly divergent lineages

Coalescent Simulations Reveal Hybridization and Incomplete Lineage Sorting in Mediterranean Linaria

We examined the phylogenetic history of Linaria with special emphasis on the Mediterranean sect. Supinae (44 species). We revealed extensive highly supported incongruence among two nuclear (ITS, AGT1) and two plastid regions (rpl32-trnLUAG, trnS-trnG). Coalescent simulations, a hybrid detection test and species tree inference in *BEAST revealed that incomplete lineage sorting and hybridization may both be responsible for the incongruent pattern observed. Additionally, we present a multilabelled *BEAST species tree as an alternative approach that allows the possibility of observing multiple placements in the species tree for the same taxa. That permitted the incorporation of processes such as hybridization within the tree while not violating the assumptions of the *BEAST model. This methodology is presented as a functional tool to disclose the evolutionary history of species complexes that have experienced both hybridization and incomplete lineage sorting. The drastic climatic events that have occurred in the Mediterranean since the late Miocene, including the Quaternary-type climatic oscillations, may have made both processes highly recurrent in the Mediterranean flora

San Bernardino Cave (Italy) and the appearance of Levallois technology in Europe: results of a radiometric and technological reassessment.

The introduction of Levallois technology in Europe marked the transition from the Lower to the early Middle Paleolithic. This new method of flake production was accompanied by significant behavioral changes in hominin populations. The emergence of this technological advance is considered homogeneous in the European archaeological record at the Marine isotopic stage (MIS) 9/MIS 8 boundary. In this paper we report a series of combined electron spin resonance/U-series dates on mammal bones and teeth recovered from the lower units of San Bernardino Cave, Italy, and the technological analyses of the lithic assemblages. San Bernardino Cave has yielded the earliest evidence of Levallois production on the Italian Peninsula recovered to date. In addition to our results and the review of the archaeological record, we describe the chronological and geographical differences between European territories and diversities in terms of technological developments. The belated emergence of Levallois technology in Italy compared to western Europe corresponds to the late Italian Neanderthal speciation event. The new radiometric dates and the technological analyses of San Bernardino Cave raise the issue of the different roles of glacial refugia in the peopling and the spread of innovative flaking strategies in Europe during the late Middle Pleistocene