In this study we present phylogenetic and molecular phylogenetic diversity analyses of moss taxa from a total of 655 genera of mosses. Three loci were sampled: chloroplast ribosomal small protein 4, the intronic region of the mitochondrial NADH dehydogenase subunit 5, and partial sequences of the nuclear 26S ribosomal RNA. Maximum likelihood and Bayesian phylogenetic analyses were performed on individual loci and on multilocus data sets. A measure of phylogenetic diversity was calculated and constrasted among major lineages of mosses. We reveal many instances of incongruence among genomic partitions, but, overall, our analyses describe relationships largely congruent with previous studies of the major groups of mosses. Moreover, our greater sampling highlights the possible non-monophyly of many taxonomic families, particularly in the haplolepideous and pleurocarpous mosses. Comparisons of taxic and phylogenetic diversity among genera indicate that the Dicranidae (haplolepideous taxa) include about 15% of moss genera, but nearly 30% of the phylogenetic diversity. By contrast, the Hypnanae (hypnalian pleurocarps) contain about 45% of moss genera, but a lower percentage of phylogenetic diversity. Agreement between numbers of genera and phylogenetic diversity within other moss clades are remarkably consistent.

Genetic variation was surveyed at nine microsatellite loci and the mitochondrial control region (868 bp) to test for the presence of genetic stock structure in young-of-the-year Atlantic bluefin tuna (Thunnus thynnus thynnus) from the Mediterranean Sea. Bluefin tuna were sampled over a period of 5 years from the Balearic and Tyrrhenian seas in the western basin of the Mediterranean Sea, and from the southern Ionian Sea in the eastern basin of the Mediterranean Sea. Analyses of multilocus microsatellite genotypes and mitochondrial control region sequences revealed no significant heterogeneity among collections taken from the same location in different years; however, significant spatial genetic heterogeneity was observed across all samples for both microsatellite markers and mitochondrial control region sequences (FST=0.0023, P=0.038 and PhiST=0.0233, P=0.000, respectively). Significant genetic differentiation between the Tyrrhenian and Ionian collections was found for both microsatellite and mitochondrial markers (FST=0.0087, P=0.015 and PhiST=0.0367, P=0.030, respectively). These results suggest the possibility of a genetically discrete population in the eastern basin of the Mediterranean Sea.

Despite compelling evidence that adaptation to local climate is common in plant populations, little is known about the evolutionary genetics of traits that contribute to climatic adaptation. A screen of natural accessions of Arabidopsis thaliana revealed Tsu-1 and Kas-1 to be opposite extremes for water-use efficiency and climate at collection sites for these accessions differs greatly. To provide a tool to understand the genetic basis of this putative adaptation, Kas-1 and Tsu-1 were reciprocally crossed to create a new mapping population. Analysis of F 3 families showed segregating variation in both δ 13 C and transpiration rate, and as expected these traits had a negative genetic correlation (r g = −0.3). 346 RILs, 148 with Kas-1 cytoplasm and 198 with Tsu-1 cytoplasm, were advanced to the F 9 and genotyped using 48 microsatellites and 55 SNPs for a total of 103 markers. This mapping population was used for QTL analysis of δ 13 C using F 9 RIL means. Analysis of this reciprocal cross showed a large effect of cytoplasmic background, as well as two QTL for δ 13 C. The Kas-1 × Tsu-1 mapping population provides a powerful new resource for mapping QTL underlying natural variation and for dissecting the genetic basis of water-use efficiency differences.K E Y W O R D S : Adaptation, Arabidopsis thaliana, carbon isotope ratio, correlated traits, drought avoidance, drought escape, drought tolerance, transpiration, water-use efficiency.

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The class Sphagnopsida (Bryophyta) includes two genera: Ambuchanania and Sphagnum. Ambuchanania contains just one rare species known from two Tasmanian localities, but Sphagnum comprises a speciose clade of mosses that dominates many wetland ecosystems, especially in the boreal zone of the Northern Hemisphere. Recent phylogenetic analyses have resolved well-supported clades within Sphagnum, but polarizing Sphagnum evolution has been problematic because the genus is so isolated that it is difficult to determine homologies between morphological and/or molecular traits within Sphagnum with those of any potential outgroup. DNA sequences from 16 genomic regions representing the mitochondrial, chloroplast, and nuclear genomes (ca. 16 kilobases) were obtained from 24 species of Sphagnum plus one species each from Takakia and Andreaea in order to resolve a rooted phylogeny. Two tropical species, S. sericeum and S. lapazense, were resolved as sister to the rest of the genus and are extremely divergent from all other sphagna. The main Sphagnum lineage consists of two clades; one includes the sections Sphagnum, Rigida, and Cuspidata, and the other includes Subsecunda, Acutifolia, and Squarrosa. The placement of section Subsecunda is weakly supported, but other nodes are strongly supported by maximum parsimony, maximum likelihood, and Bayesian analyses. In addition to homogeneous Bayesian analyses, heterogeneous models were employed to account for different patterns of nucleotide substitution among genomic regions.