No abstract

Senecioneae is the largest tribe of Asteraceae, comprised of ca. 150 genera and 3,000 species. Approximately one‐third of its species are placed in Senecio, making it one of the largest genera of flowering plants. Despite considerable efforts to classify and understand the striking morphological diversity in Senecioneae, little is known about its intergeneric relationships. This lack of phylogenetic understanding is predominantly caused by conflicting clues from morphological characters, the large size of the tribe, and the absence of a good delimitation of Senecio. Phylogenetic analyses of nrITS and plastid DNA sequence data were used to produce a hypothesis of evolutionary relationships in Senecioneae and a new, monophyletic, delimitation of Senecio. The results of separate and combined phylogenetic analyses of the two datasets were compared to previous taxonomic treatments, morphological and karyological data, and biogeographic patterns. These studies indicate that the subtribal delimitation of Senecioneae needs to be revised to reflect exclusively monophyletic subtribes. This would involve abolishing subtribes Adenostylinae, Blennospermatinae, and Tephroseridinae and recognizing subtribes Abrotanellinae, Othonninae, and Senecioninae. Moreover, Tussilagininae may need to be split into three or four subtribes: Brachyglottidinae, Chersodominae, Tussilagininae, and perhaps Doronicinae. On the intergeneric level, these phylogenies provide new insights into evolutionary relationships, resulting in a first approximation of a comprehensive phylogeny for the tribe. Most species currently assigned to Senecio form a well supported clade. Thus, a new delimitation of Senecio is proposed, which involves transferring the species of Aetheolaena, Culcitium, Hasteola, Iocenes, Lasiocephalus, and Robinsonia to Senecio and removing several Senecio groups that are only distantly related to the core of Senecio. Area optimization analyses indicate a strong African influence throughout the evolutionary history of Senecioneae, predominantly in subtribes Senecioninae and Othonninae.

Soldanella contains 16 species of herbaceous perennials that are endemic to the central and south European high mountains. The genus is ecogeographically subdivided into forest/montane and alpine species. Evolutionary relationships and large-scale biogeographic patterns were inferred from parsimony analyses of the internal transcribed spacer (ITS) regions of nuclear ribosomal DNA, and genetic distance analyses based on amplified fragment length polymorphism (AFLP) markers. The ITS region proved useful for examining subgeneric relationships and testing hypotheses on genus-wide divergence times, whereas the AFLP markers were suitable for studying relationships among closely related taxa and biogeographic patterns of divergence. Neither ITS nor AFLP data supported sectional delimitations, particularly those related to the grouping of S. alpina (sect. Soldanella) with S. pusilla (sect. Tubiflores), which may be the result of hybridization. Additional results and conclusions drawn are (1) Soldanella is derived from an ancestor of Asian origin with a montane ecology; (2) estimates of divergence times suggest a late Quaternary origin of the genus; (3) alpine species of sect. Tubiflores diverged from within a paraphyletic sect. Soldanella of mainly montane species; (4) alpine and montane species of Soldanella experienced different cycles of range expansion and contraction during late Quaternary climatic changes, resulting in differential patterns of geographic distribution; and (5) AFLP divergence among montane species from eastern Europe was lower than between alpine species; we hypothesize that the latter differentiated in allopatric regions of expansion during glacials, while the former experienced secondary contact at lower elevations in more southern refugia.

One of the longstanding questions in phylogenetic systematics is how to address incongruence among phylogenies obtained from multiple markers and how to determine the causes. This study presents a detailed analysis of incongruent patterns between plastid and ITS/ETS phylogenies of Tribe Senecioneae (Asteraceae). This approach revealed widespread and strongly supported incongruence, which complicates conclusions about evolutionary relationships at all taxonomic levels. The patterns of incongruence that were resolved suggest that incomplete lineage sorting (ILS) and/or ancient hybridization are the most likely explanations. These phenomena are, however, extremely difficult to distinguish because they may result in similar phylogenetic patterns. We present a novel approach to evaluate whether ILS can be excluded as an explanation for incongruent patterns. This coalescence-based method uses molecular dating estimates of the duration of the putative ILS events to determine if invoking ILS as an explanation for incongruence would require unrealistically high effective population sizes. For four of the incongruent patterns identified within the Senecioneae, this approach indicates that ILS cannot be invoked to explain the observed incongruence. Alternatively, these patterns are more realistically explained by ancient hybridization events.

Nuclear DNA sequence variation of the internal transcribed spacer (ITS) and amplified fragment length polymorphisms (AFLPs) were used to illuminate the evolutionary history of Pritzelago alpina, a herbaceous perennial of (sub)alpine to nival habitats of the European high mountains. Maximum likelihood analysis of ITS sequences of P. alpina, Hornungia petraea and Hymenolobus procumbens (the 'Pritzelago alliance') resolved P. alpina and H. petraea as sister taxa. ITS divergence estimates support an origin for P. alpina in the Late Tertiary, while intraspecific diversification started in the Late Quaternary (0.4-0.9 million years ago). AFLP analysis of 76 individuals of P. alpina, representing 24 localities across its entire west-east distribution, identified four mountain lineages in Cantabria, the Pyrenees, (south-) western Alps, and northeastern Alps/Tatras/Carpathians. In an analysis of molecular variance (amova), 14.3% of the total variation derived from this separation. However, relationships among these lineages remained unresolved in neighbour-joining and principal co-ordinates analyses, suggesting a population history of near simultaneous vicariance. Comparison with our previous ITS/AFLP study of Anthyllis montana (Fabaceae) indicates that the two co-distributed but altitudinally differentiated plant species exhibit temporally concordant but spatially discordant patterns of genetic variation. Moreover, levels of AFLP divergence were significantly lower in P. alpina than in the submediterranean, lower-elevation A. montana. Together, these data are consistent with a 'displacement refugia model', which predicts that European mountain plant species associated with lower- and upper-elevation habitats had a different cycle of range contraction into (long-term) glacial and (short-term) interglacial refugia, respectively.

The genus Linum consists of over 180 species, the most famous being L. usitatissimum, the source of linen and linseed oil. The eight genera of Linaceae subf. Linoideae, of which Linum is the largest, exhibit a complex biogeographic distribution, inhabiting all continents except Antarctica. Numerous species in Linoideae are heterostylous, but the ancestral breeding system of the group has not been determined. We present phylogenetic analyses of 44 species representing all eight genera of subf. Linoideae and 37 species of Linum, with data from the chloroplast (ndhF, trnL-F, trnK3′ intron) and the nuclear ITS, with Hugonia (Linaceae subf. Hugonioideae) as outgroup. Sequences of rbcL from 48 species of Linaceae, including five species from Hugonioideae and seven species from other families of Malpighiales, were analyzed independently. Our results suggest that Linaceae and subf. Linoideae are monophyletic, but Linum is not. Anisadenia, Reinwardtia, and Tirpitzia are found to be the basal members of Linoideae. The rest of the subfamily forms two major lineages: a blue-flowered clade (Linum sections Linum and Dasylinum) and a yellow-flowered clade (Linum sects. Linopsis, Syllinum, and Cathartolinum, and the genera Cliococca, Hesperolinon, Radiola, and Sclerolinon). Diversification of Linoideae may have begun 46–51 mya, probably in Southeast Asia. Linum appears to have arisen in Eurasia, from which it spread to Africa, North America, South America, and Australasia. Our analyses indicate that neither heterostyly nor homostyly can yet be confirmed as the ancestral state in Linoideae or Linaceae, but provide strong evidence that breeding system is evolutionarily labile in this group.

Research Summary• Here, we investigated the origin and genetic diversity of four alpine plant species co-occurring in the Spanish Sierra Nevada and other high mountains in southwestern Europe by analysis of amplified fragment length polymorphisms (AFLPs).• In Kernera saxatilis , Silene rupestris and Gentiana alpina we found intraspecific phylogroups corresponding to mountain regions as predicted by the vicariance hypothesis. Moreover, genetic distances between Sierra Nevada and Pyrenees populations were always higher than those between populations from the Pyrenees and the south-western Alps/Massif Central. This suggests successive disruption of gene exchange between mountain ranges as postglacial climatic warming proceeded from south to north.• In Papaver alpinum , our data indicate that a central Pyrenean population arose via long-distance dispersal from the Sierra Nevada, and that vicariant separation events between the Sierra Nevada and the Pyrenees and between the Pyrenees and the south-western Alps occurred simultaneously.• Overall, Sierra Nevada populations of all species investigated here preserve unexpectedly high (or not exceptionally reduced) genetic diversity. This testifies to the important influence of long-term isolation, i.e. vicariance, on genetic diversity through fostering the accumulation of new mutations and/or the fixation of ancestral ones.

Anthyllis montana is a submediterranean, herbaceous plant of the southern and central European mountains. The internal transcribed spacer (ITS) regions of nuclear ribosomal DNA were sequenced from multiple accessions of the species and several closely related taxa. In addition, amplified fragment length polymorphism (AFLP) was analysed from 71 individuals of A. montana collected in 20 localities, mainly in the Pyrenees, Alps, Italian Peninsula and Balkans. Our ITS phylogeny showed a sequential branching pattern in A. montana, implying a western Mediterranean origin followed by an eastward migration. ITS clock calibrations suggest that speciation of A. montana took place at the Pliocene-Pleistocene boundary, while intraspecific divergence dates to Late Quaternary times (i.e. 0.7 million years ago). The AFLP analyses revealed a major genetic (west/east) subdivision within A. montana, probably caused by the massive glaciation of the Alps during this latter time period. The present-day absence of A. montana from vast parts of the Alps, which appear ecologically suitable for the species, together with the finding of evenly distributed AFLP variability within each of the two western and eastern lineages identified, is taken as evidence for a largely static Late Quaternary history without large-scale migration. High levels of AFLP variation observed among populations, together with weak or absent patterns of isolation by distance, seem to be in accord with long-term population insularization and distributional stasis. However, recent small-scale migration and a narrow hybrid zone between western and eastern lineages need to be postulated to explain the intermediate genetic composition of individuals from the Maritime Alps, a well-known suture-zone for other plant and animal species.