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Premise: Despite intensive research, the pathways and driving forces behind the evolution of derived woodiness on oceanic islands remain obscure. The genus Daucus comprises mostly herbs (therophytes, hemicryptophytes) with few rosette treelets (chamaephytes) endemic to various Macaronesian archipelagos, suggesting their independent evolution. To elucidate the evolutionary pathways to derived woodiness, we examined phylogenetic relationships and the habit and secondary xylem evolution in Daucus and related taxa. Methods: Sixty taxa were surveyed for molecular markers, life history, and habit traits. Twenty‐one species were considered for wood anatomical characters. A dated phylogeny was estimated using Bayesian methods. The evolution of selected traits was reconstructed using parsimony and maximum likelihood. Results: Daucus dispersed independently to the Canary Islands (and subsequently to Madeira), Cape Verde, and the Azores in the late Miocene and Pleistocene. Life span, reproductive strategy, and life form were highly homoplastic; the ancestor of Daucus was probably a monocarpic, biennial hemicryptophyte. Rosette treelets evolved independently in the Canarian‐Madeiran lineage and in Cape Verde, the latter within the last 0.13 Myr. Treelets and hemicryptophytes did not differ in wood anatomy. Pervasive axial parenchyma in wood occurred more often in polycarpic rather than monocarpic species. Conclusions: Life span and life form in Daucus are evolutionarily labile and may change independently of wood anatomy, which is related to plant reproductive strategy rather than to life form. Insular woodiness may evolve rapidly (as demonstrated in D. bischoffii), and in Daucus, it does not seem to be an adaptation to lower the risk of xylem embolism. [ABSTRACT FROM AUTHOR]

Dietary shifts can alter the relative availability of different nutrients and are therefore associated with metabolic adaptation in animals. The Coccinellidae (ladybirds) exhibits three major types of feeding habits and provides a useful model to study the effects of dietary changes on the evolution of mitogenomes, which encode proteins directly involved in energy metabolism. Here, mitogenomes of three coccinellid species were newly sequenced. These data were combined with other ten previously sequenced coccinellid mitogenomes to explore the relationship between mitogenome evolution and diets. Our results indicate that mitogenomic data can be effectively used to resolve phylogenetic relationships of Coccinellidae. Strong codon usage bias in coccinellid mitogenomes was predominantly determined by nucleotide composition. The 13 mitochondrial protein‐coding genes (PCGs) globally evolved under negative constraints, with some PCGs showing a stronger purifying selection. Six PCGs (nad3, nad4L, and nad5 from Complex I; cox1 and cox3 from Complex IV; and atp6 from Complex V) displayed signs of positive selection. Of these, adaptive changes in cox3 were potentially associated with metabolic differences resulting from dietary shifts in Coccinellidae. Our results provide insights into the adaptive evolution of coccinellid mitogenomes in response to both dietary shifts and other life history traits. [ABSTRACT FROM AUTHOR]

Abstract: Interest in methods that estimate speciation and extinction rates from molecular phylogenies has increased over the last decade. The application of such methods requires reliable estimates of tree topology and node ages, which are frequently obtained using standard phylogenetic inference combining concatenated loci and molecular dating. However, this practice disregards population‐level processes that generate gene tree/species tree discordance. We evaluated the impact of employing concatenation and coalescent‐based phylogeny inference in recovering the correct macroevolutionary regime using simulated data based on the well‐established diversification rate shift of delphinids in Cetacea. We found that under scenarios of strong incomplete lineage sorting, macroevolutionary analysis of phylogenies inferred by concatenating loci failed to recover the delphinid diversification shift, while the coalescent‐based tree consistently retrieved the correct rate regime. We suggest that ignoring microevolutionary processes reduces the power of methods that estimate macroevolutionary regimes from molecular data. [ABSTRACT FROM AUTHOR]

To reconstruct the phylogeographic history of the Holarctic carnivorous genus Leptodora (Crustacea: Cladocera: Haplopoda). We studied the DNA of between one and five specimens each from 28 populations distributed across the Holarctic, but with emphasis on Eurasia. We sequenced a mitochondrial (cytochrome c oxidase subunit I) and a nuclear (elongation factor-1α) gene, and combined this molecular information with geological and palaeoclimatological data. Haplotype networks and phylogenetic trees were constructed using a Bayesian and maximum likelihood approach. A molecular clock was applied. Leptodora consists of three clades ( Leptodora kindtii in Europe, Leptodora richardi in China and Japan, and Leptodora sp. in North America), with insular subclades in Japan and in the eastern Mediterranean. The North American clade was not studied in detail. Leptodora richardi is the more thermophilic of the three. It extends from the Tropic of Cancer in the south to the Heilong Basin in the north. The western European L. kindtii is more cold-water adapted than the eastern Mediterranean subclade. 'West European' and 'Chinese' clades are broadly separated by a hybrid zone in Siberia and European Russia as far west as the Volga. These hybrids have the mitochondrial DNA of L. kindtii, the nuclear DNA of L. richardi and the low-temperature preference of L. kindtii, and may have formed as recently as the Holocene hypsithermal. A pure L. kindtii population in the Upper Irtysh catchment, east of the Dzungarian Gates, has been sequestered in endorheic Lake Wulungu, Xinjiang, since the mid-Pleistocene. Application of a molecular clock places the most recent common ancestor of the North American, East Asian and European populations in the mid-Miocene. The North American taxon is still living in isolation, while the Eurasian taxa, separated by the Alpine folding, made contact again in the Pleistocene, when the cold-stenothermic L. kindtii repeatedly moved eastwards across Siberia and back. The population in Xinjiang is a relict of an early wave coming from western Europe: it crossed the Dzungarian Gates during a humid mid-Pleistocene event, probably corresponding to the Apsheron transgression in the Caspian Basin. Later aridity isolated it there, and it started accumulating private haplotypes. The Holocene Euro-Siberian hybrid zone may eventually engulf all European populations. [ABSTRACT FROM AUTHOR]

Aim To reconstruct the temporal, geographical and eco-climatological differentiation of the genus Anthemis (Compositae, Anthemideae) in the circum-Mediterranean region, in order to evaluate the relative importance of geographical vs. climatological differentiation processes in influencing the actual distribution patterns in this plant group. Location The circum-Mediterranean region, including the Iberian Peninsula, northern Africa, the Italian and Balkan peninsulas, the Aegean region and Anatolia, the Caucasus, the Arabian Peninsula and western Asia. Methods The phylogeny of the genus Anthemis was obtained from a maximum likelihood analysis based on nuclear ribosomal DNA (nrDNA) internal transcribed spacer (ITS) sequence data, and the chronology of diversification was derived using a penalized likelihood approach. The reconstruction of the spatial diversification of the genus was based on a dispersal/vicariance (DIVA) analysis. Eco-climatological niche differentiation was inferred by optimizing 19 bioclimatic variables onto the phylogeny. A multi-dimensional hypervolume, proposed as a representation of the eco-climatological niche and defined by the combination of ranges for all bioclimatic variables, was calculated for each taxon and each internal node. To identify ‘eco-climatological vicariance’ events in the phylogeny, the pairwise overlap among hypervolumes of sister groups was calculated. Finally, the temporal and clade-wise relative importance of geographical vs. eco-climatological vicariance events was estimated. Results The temporal reconstruction shows a constant increase of lineages through the last 12 Myr. The geographical reconstruction suggests that Anthemis diverged from the rest of the Compositae–Anthemideae in the eastern Mediterranean region, and from there radiated into the whole circum-Mediterranean region through successive dispersal and vicariance events. The reconstruction of the eco-climatological niches suggests a progressive adaptation from a montane-humid climate towards arid environments and the typical mediterranean climate. Main conclusions The results presented here involved phylogenetic, geographical and eco-climatological reconstructions; joint analyses of all of these aspects have assessed the relative importance of geological vs. climatic forces that have affected the distributional history of the genus Anthemis. Large-scale differentiation patterns triggered by geological forces appear to have influenced the evolutionary history of the genus in a rather constant manner over the last 12 Myr, whereas climatic forces seem to have played an important role in two phases of the radiation process: at around 9 Ma, when the area experienced the onset of a trend towards aridification, and during the last 3.5 Myr, with the establishment of the typical mediterranean climate and the influence of Pleistocene climate oscillations. [ABSTRACT FROM AUTHOR]

Aim The clade Campanulaceae in the Cretan area is rich in endemics, with c. 50% of its species having restricted distributions. These species are analysed in the context of a larger phylogeny of the Campanulaceae. Divergence times are calculated and hypotheses of vicariance and dispersal are tested with the aim of understanding whether Cretan lineages represent remnants of an older continental flora. Location The Cretan area: Crete and the Karpathos Islands (Greece). Methods We obtained chloroplast DNA sequence data from rbcL, atpB and matK genes for 102 ingroup taxa, of which 18 are from the Cretan area, 11 are endemics, and two have disjunct, bi-regional distributions. We analysed the data usingbeast, a Bayesian approach that simultaneously infers the phylogeny and divergence times. We calibrated the tree by placing a seed fossil in the phylogeny, and used published age estimates as a prior for the root. Results The phylogenetic reconstruction shows that all Campanula species fall within a well-supported campanuloid clade; however, Campanula is highly polyphyletic. The Cretan endemics do not form a monophyletic group, and species are scattered throughout the campanuloid clade. Therefore, the Cretan taxa did not evolve following a single vicariance or dispersal event. Most Cretan lineages represent remnants of an older continental flora, with the exception of one clade that radiated in situ after island isolation, and one lineage that appears to have arrived by dispersal. Main conclusions Most Cretan species were present in the islands at the time of their isolation, and very little long-distance dispersal to Crete and diversification within Crete has occurred since then. Endemism is probably driven by loss of species on the mainland after island isolation. Species on the islands may have been more widespread in the past, but they are now restricted to often inaccessible areas, probably as a result of human pressure. [ABSTRACT FROM AUTHOR]

• LHY/CCA1 genes play a key role in the plant circadian clock system and are highly conserved among plant species. However, the evolutionary process of the LHY/ CCA1 gene family remains unclear in angiosperms. To obtain details of the phylogeny of these genes, this study characterized LHY/CCA1 genes in a model woody plant, Populus tree. • The evolutionary process of angiosperm LHY/CCA1 genes was elucidated using three approaches: comparison of exon–intron structures, reconstruction of phylogenetic trees and examination of syntenic relationships. In addition, the molecular evolutionary rates and the expression patterns of Populus LHYs were analyzed. • Gene duplication events of Populus LHYs and Arabidopsis LHY/CCA1 had occurred independently by different chromosomal duplication events arising in each evolutionary lineage. Populus LHYs were under purifying selection by estimating substitution rates of these genes. Further, Populus LHYs conserved diurnal expressions in leaves and stems but the transcripts of LHY2 were more abundant than those of LHY1 in Populus plants. • This study uncovered phylogenetic relationships of the LHY/ CCA1 gene family in angiosperms. In addition, the transcript abundance and the evolutionary differences between Populus LHY1 and LHY2 imply that Populus LHY2, rather than LHY1, may have a major role in the Populus clock system. [ABSTRACT FROM AUTHOR]

Aim Various data sets and methods of analysis were combined to produce the first comprehensive molecular phylogeny of the genus Tuber and to analyse its biogeography . Location Europe, North Africa, China, Asia, North America. Methods Phylogenetic relationships among Tuber species were reconstructed based on a data set of internal-transcribed spacer (ITS) sequences and various phylogenetic inference methods, specifically maximum parsimony, Bayesian analysis and neighbour joining. Tajima’s relative rate test showed that Tuber 18S rRNA, 5.8S rRNA, 5.8S-ITS2 rRNA and β-tubulin sequences evolved in a clock-like manner. These genes, combined or not, were employed for molecular clock estimates after construction of linearized trees usingmega 3.1. We reconstructed ancestral areas in the Northern Hemisphere by means of a dispersal–vicariance analysis (diva 1.1) based on current distribution patterns of the genus Tuber determined from the literature. Results The resulting molecular phylogeny divided the genus Tuber into five distinct clades, in agreement with our previously published studies. The Puberulum, Melanosporum and Rufum groups were diversified in terms of species and geographical distribution. In contrast, the Aestivum and Excavatum groups were less diversified and were located only in Europe or North Africa. Using a global molecular clock analysis, we estimated the divergence times for the origin of the genus and for the origin of several groups.diva inferred nine dispersal events and suggested that the ancestor of Tuber was originally present in Europe or was widespread in Eurasia. Equally optimal distributions were obtained for several nodes, suggesting different possible biogeographical patterns. Main conclusions Our analyses identified several discrepancies with the classical taxonomy of the genus, and we propose a new phylogenetic classification. According to molecular clocks, the radiation of the genus Tuber could have started between 271 and 140 Ma. Used in combination with the results obtained from time divergence estimates, this allows us to propose two equally probable scenarios of intra- and inter-continental diversification of the genus according to the geographic distribution of the most recent common ancestor in Europe or Eurasia. The biogeographical patterns imply intra-continental dispersal events between Europe and Asia and inter-continental dispersal events between North America and Europe or Asia, which are compatible with land connections during the Tertiary. [ABSTRACT FROM AUTHOR]

Macaranga and Mallotus (Euphorbiaceae s.s.) are two closely related, large paleo(sub)tropical genera. To investigate the phylogenetic relationships between and within them and to determine the position of related genera belonging to the subtribe Rottlerinae, we sequenced one plastid (trnL-F) and three nuclear (ITS, ncpGS, phyC) markers for species representative of these genera. The analyses demonstrated the monophyly of Macaranga and the paraphyly of Mallotus and revealed three highly supported main clades. The genera Cordemoya and Deuteromallotus and the Mallotus sections Hancea and Oliganthae form a basal Cordemoya s.l. clade. The two other clades, the Macaranga clade and the Mallotus s.s. clade (the latter with Coccoceras, Neotrewia, Octospermum, and Trewia), are sister groups. In the Macaranga clade, two basal lineages (comprising mostly sect. Pseudorottlera) and a crown group with three geographically homogenous main clades were identified. The phylogeny of the Mallotus s.s. clade is less clear because of internal conflict in all four data sets. Many of the sections and informal infrageneric groups of Macaranga and Mallotus do not appear to be monophyletic. In both the Macaranga and Mallotus s.s. clades, the African and/or Madagascan taxa are nested in Asian clades, suggesting migrations or dispersals from Asia to Africa and Madagascar. [ABSTRACT FROM AUTHOR]

Contents Summary 605 I. Introduction 606 II. Methodological issues 606 III. Insights into processes that give rise to species rich biomes 608 IV. Future directions: neutral ecological theory, community phylogenetic structure, and processes leading to species accumulation 612 V. Conclusions 613 Acknowledgements 614 References 614 Analytical methods are now available that can date all nodes in a molecular phylogenetic tree with one calibration, and which correct for variable rates of DNA substitution in different lineages. Although these techniques are approximate, they offer a new tool to investigate the historical construction of species-rich biomes. Dated phylogenies of globally distributed plant families often indicate that dispersal, even across oceans, rather than plate tectonics, has generated their wide distributions. By contrast, there are indications that animal lineages have undergone less long distance dispersal. Dating the origin of biome-specific plant groups offers a means of estimating the age of the biomes they characterize. However, rather than a simple emphasis on biome age, we stress the importance of studies that seek to unravel the processes that have led to the accumulation of large numbers of species in some biomes. The synthesis of biological inventory, systematics and evolutionary biology offered by the frameworks of neutral ecological theory and phylogenetic community structure offers a promising route for future work. [ABSTRACT FROM AUTHOR]

As currently defined, the 24 species of Schoenocaulon occur in three disjunct areas: north central Florida (one species, S. dubium), southern Peru (portion of the range of S. officinale), and the region from southeastern New Mexico-Texas south to Venezuela; the 20 species endemic to Mexico are geographically restricted. Species delimitations, often based on tepal morphology, have been problematic. Our analyses of ITS sequence data for all 27 species and infraspecific taxa support recognition of two new species and recircumscription and placement of elements of the polyphyletic S. ghieshreghtii and S. mortonii complexes. For taxa with adequate sampling, our data also indicate 11-12 cladospecies and 3-6 metaspecies according to the apomorphic species concept. The resolved phylogeny, correlated with geography and morphology, allows insight into biogeographical diversification and the evolution of some unusual morphological characters within the genus, such as nectary differentiation and tepal margin type. [ABSTRACT FROM AUTHOR]

• We developed a molecular phylogeny for Calochortus (Liliaceae) to reconstruct historical patterns of evolution. • Three cpDNA segments were sequenced and analyzed using parsimony. • We identified seven major, geographically cohesive clades centered mainly in the California Floristic Province. Section Calochortus is monophyletic; section Mariposa, paraphyletic; and section Cyclobothra, polyphyletic. Calochortus arose in the Coast Ranges, which were uplifited 3–5 million yr ago. Three of the four major floral syndromes evolved at least twice, associated with particular environments. Serpentine tolerance evolved at least seven times. • We argue that limited dispersal led to the narrow endemism of individual species, the geographic cohesion of clades, and parallel radiations in habitat preference, floral morphology, and serpentine tolerance. Chromosomal evolution allowed Calochortus to ‘double-up’ its regional radiations, preventing crosses between pairs of clades with overlapping ranges. Floral evolution in Calochortus is an example of consequent radiation, with selection for local diversification in habitat driving secondary specialization of flowers on the range of pollinators and abiotic conditions within each habitat, rather than selection to partition pollinators within habitats driving adaptive radiation. [ABSTRACT FROM AUTHOR]