Biogeographic patterns in Mediterranean and Macaronesian species of Saxifraga (Saxifragaceae) inferred from phylogenetic analyses of ITS sequences

Classification Importance of Seed Morphology and Insights on Large-Scale Climate-Driven Strophiole Size Changes in the Iberian Endemic Chasmophytic Genus Petrocoptis (Caryophyllaceae)

Recruitment poses significant challenges for narrow endemic plant species inhabiting extreme environments like vertical cliffs. Investigating seed traits in these plants is crucial for understanding the adaptive properties of chasmophytes. Focusing on the Iberian endemic genus Petrocoptis A. Braun ex Endl., a strophiole-bearing Caryophyllaceae, this study explored the relationships between seed traits and climatic variables, aiming to shed light on the strophiole's biological role and assess its classificatory power. We analysed 2773 seeds (557 individuals) from 84 populations spanning the genus' entire distribution range. Employing cluster and machine learning algorithms, we delineated well-defined morphogroups based on seed traits and evaluated their recognizability. Linear mixed-effects models were utilized to investigate the relationship between climate predictors and strophiole area, seed area and the ratio between both. The combination of seed morphometric traits allows the division of the genus into three well-defined morphogroups. The subsequent validation of the algorithm allowed 87% of the seeds to be correctly classified. Part of the intra- and interpopulation variability found in strophiole raw and relative size could be explained by average annual rainfall and average annual maximum temperature. Strophiole size in Petrocoptis could have been potentially driven by adaptation to local climates through the investment of more resources in the production of bigger strophioles to increase the hydration ability of the seed in dry and warm climates. This reinforces the idea of the strophiole being involved in seed water uptake and germination regulation in Petrocoptis. Similar relationships have not been previously reported for strophioles or other analogous structures in Angiosperms.

Reinterpretation of an endangered taxon based on integrative taxonomy: The case of Cynara baetica (Compositae)

The Strait of Gibraltar, the gateway between the Atlantic Ocean and the Mediterranean Sea, has a convulsive geological history, with recurring closing and opening events since the late Miocene. As a consequence, this region has played a major role in the evolutionary history of many species. Cynara baetica (Compositae) is a diploid perennial herb distributed in both sides of this strait. It is currently subdivided into two subspecies: C. baetica subsp. baetica for the Spanish populations, and C. baetica subsp. maroccana for the Moroccan ones. Following three different approximations of species delimitation, including phylogenetic and population genetic analyses (based on three AFLP primer combinations and two intergenic spacers of cpDNA), ecological niche modeling (ENM) and morphological studies, this taxon is investigated and reinterpreted. The results obtained showed a clear genetic, morphological and ecological differentiation between the two taxa and the important role played by the Strait of Gibraltar as a geographical barrier. Based on this evidence, the current taxonomic treatment is modified (both taxa should recover their specific rank) and specific conservation guidelines are proposed for the newly delimited taxa.

Molecular phylogeny and evolutionary history of Moricandia DC (Brassicaceae)

Background

The phylogeny of tribe Brassiceae (Brassicaceae) has not yet been resolved because of its complex evolutionary history. This tribe comprises economically relevant species, including the genus Moricandia DC. This genus is currently distributed in North Africa, Middle East, Central Asia and Southern Europe, where it is associated with arid and semi-arid environments. Although some species of Moricandia have been used in several phylogenetic studies, the phylogeny of this genus is not well established.

Methods

Here we present a phylogenetic analysis of the genus Moricandia using a nuclear (the internal transcribed spacers of the ribosomal DNA) and two plastidial regions (parts of the NADH dehydrogenase subunit F gene and the trnT-trnF region). We also included in the analyses members of their sister genus Rytidocarpus and from the close genus Eruca.

Results

The phylogenetic analyses showed a clear and robust phylogeny of the genus Moricandia. The Bayesian inference tree was concordant with the maximum likelihood and timing trees, with the plastidial and nuclear trees showing only minor discrepancies. The genus Moricandia appears to be formed by two main lineages: the Iberian clade including three species, and the African clade including the four species inhabiting the Southern Mediterranean regions plus M. arvensis.

Discussion

We dated the main evolutionary events of this genus, showing that the origin of the Iberian clade probably occurred after a range expansion during the Messinian period, between 7.25 and 5.33 Ma. In that period, an extensive African-Iberian floral and faunal interchange occurred due to the existence of land bridges between Africa and Europa in what is, at present-days, the Strait of Gibraltar. We have demonstrated that a Spanish population previously ascribed to Rytidocarpus moricandioides is indeed a Moricandia species, and we propose to name it as M. rytidocarpoides sp. nov. In addition, in all the phylogenetic analyses, M. foleyi appeared outside the Moricandia lineage but within the genus Eruca. Therefore, M. foleyi should be excluded from the genus Moricandia and be ascribed, at least provisionally, to the genus Eruca.

Phylogeography of cliff-dwelling relicts with a highly narrow and disjunct distribution in the western Mediterranean

PREMISE OF THE STUDY

The high biodiversity in the Baetic-Rifan hotspot of Mediterranean region is shaped by complex geological and climatic histories and has been a subject of recent intensive studies. However, very little is known about phylogenetic and biogeographic history of three rare and critically endangered cliff-dwelling species of Sonchus in section Pustulati in this region.

METHODS

We investigated the genetic variation and phylogenetic relationships of populations based on nuclear (ITS/ETS) and plastid (3'trnL-ndhJ/psaI-accD) DNA sequences, and amplified fragment length polymorphisms (AFLPs). We performed a Bayesian relaxed molecular clock analysis with ITS data to estimate divergence times for major lineages.

KEY RESULTS

ITS/ETS and AFLP phylogenies showed high concordance and contrasted with cpDNA data. The divergence between S. masguindalii and S. fragilis was dated at 5.48 Ma, between S. fragilis and S. pustulatus at 3.89 Ma, and between the Baetic and Rifan S. pustulatus at 1.18 Ma. Within each distribution area, AFLP data showed a relatively high genetic structuring and moderate genetic diversity, the latter being impoverished in the Baetic populations.

CONCLUSIONS

Our results further confirm the hybrid origin of S. pustulatus, a critically endangered species. The origin and diversification of lineages appear to have occurred on the temporary land bridge that joined Iberian and North Africa during the Messinian Salinity Crisis (5.96-5.33 Ma) and the subsequent Zanclean flood that progressively refilled the Mediterranean Basin (5.33-3.60 Ma). The only Baetic populations of S. pustulatus most likely originated from the Rifan ones.

Internal transcribed spacer (ITS) evolution in populations of the hyperparasitic European mistletoe pathogen fungus, Sphaeropsis visci (Botryosphaeriaceae): The utility of ITS2 secondary structures

We investigated patterns of nucleotide polymorphism in the internal transcribed spacer (ITS) region for Sphaeropsis visci, a hyperparasitic fungus that causes the leaf spot disease of the hemiparasite European mistletoe (Viscum album). Samples of S. visci were obtained from Hungary covering all major infected forest areas. For obtaining PCR products we used a fast and efficient direct PCR approach based on a high fidelity DNA polymerase. A total of 140 ITS sequences were subjected to an array of complementary sequence analyses, which included analyses of secondary structure stability, nucleotide polymorphism patterns, GC content, and presence of conserved motifs. Analysed sequences exhibited features of functional rRNAs. Overall, polymorphism was observed within less conserved motifs, such as loops and bulges, or, alternatively, as non-canonical G-U pairs within conserved regions of double stranded helices. The secondary structure of ITS2 provides new opportunities for obtaining further valuable information, which could be used in phylogenetic analyses, or at population level as demonstrated in our study. This is due to additional information provided by secondary structures and their models. The combined score matrix was used with the methods implemented in the programme 4SALE. Besides the pseudoprotein coding method of 4SALE, the molecular morphometric character coding also has potential for gaining further information for phylogenetic analyses based on the geometric features of the sub-structural elements of the ITS2 RNA transcript.

Intraspecific diversity in Sinningia speciosa (Gesneriaceae: Sinningieae), and possible origins of the cultivated florist's gloxinia

BACKGROUND AND AIMS

The florist's gloxinia is a familiar houseplant in the Gesneriaceae, the botanical family that includes the African violet (Saintpaulia) and other ornamental species. The gloxinia's wild progenitor is Sinningia speciosa (Lodd.) Hiern, a Brazilian endemic. Although it has been cultivated for almost 200 years, little is known about the genetic diversity in S. speciosa, how the wild populations relate to one another or even where the cultivated forms originated. Using available wild collections, preliminary phenetic and phylogenetic investigations were conducted to elucidate the interspecific relationships within S. speciosa and to infer the origins of the cultivars.

METHODOLOGY

Amplified fragment length polymorphism (AFLP) analysis was applied to 24 accessions of S. speciosa (17 wild collections, seven cultivars) and one accession each of Sinningia guttata and Sinningia macrophylla. A maximum likelihood (ML) tree was also calculated from an alignment of the nuclear ribosomal internal transcribed spacer sequence from the same 26 accessions.

PRINCIPAL RESULTS

Dice/UPGMA and principal coordinates analysis of the AFLP data partitioned S. speciosa into several distinct clusters, one of which included S. macrophylla. All cultivated 'gloxinias' grouped together in a major cluster with plants from Rio de Janeiro. The AFLP results were compared with a phylogenetic analysis of the ribosomal spacer region, which was informative in S. speciosa. The ML tree generally supported the AFLP results, although several clades lacked strong statistical support.

CONCLUSIONS

Independent analyses of two different data sets show that S. speciosa is a diverse species comprised of several lineages. Genetic distance estimates calculated from the AFLP data were positively correlated with geographic distances between populations, indicating that reproductive isolation could be driving speciation in this taxon. Molecular markers are under development for population genetic studies in S. speciosa, which will make it possible to define evolutionarily significant units for purposes of conservation.

Historical isolation versus recent long-distance connections between Europe and Africa in bifid toadflaxes (Linaria sect. Versicolores)

BACKGROUND

Due to its complex, dynamic and well-known paleogeography, the Mediterranean region provides an ideal framework to study the colonization history of plant lineages. The genus Linaria has its diversity centre in the Mediterranean region, both in Europe and Africa. The last land connection between both continental plates occurred during the Messinian Salinity Crisis, in the late Miocene (5.96 to 5.33 Ma).

METHODOLOGY/PRINCIPAL FINDINGS

We analyzed the colonization history of Linaria sect. Versicolores (bifid toadflaxes), which includes c. 22 species distributed across the Mediterranean, including Europe and Africa. Two cpDNA regions (rpl32-trnL(UAG) and trnK-matK) were sequenced from 66 samples of Linaria. We conducted phylogenetic, dating, biogeographic and phylogeographic analyses to reconstruct colonization patterns in space and time. Four major clades were found: two of them exclusively contain Iberian samples, while the other two include northern African samples together with some European samples. The bifid toadflaxes have been split in African and European clades since the late Miocene, and most lineage and speciation differentiation occurred during the Pliocene and Quaternary. We have strongly inferred four events of post-Messinian colonization following long-distance dispersal from northern Africa to the Iberian Peninsula, Sicily and Greece.

CONCLUSIONS/SIGNIFICANCE

The current distribution of Linaria sect. Versicolores lineages is explained by both ancient isolation between African and European populations and recent events of long-distance dispersal over sea barriers. This result provides new evidence for the biogeographic complexity of the Mediterranean region.

Timing and tempo of early and successive adaptive radiations in Macaronesia

The flora of Macaronesia, which encompasses five Atlantic archipelagos (Azores, Canaries, Madeira, Cape Verde, and Salvage), is exceptionally rich and diverse.

Spectacular radiation of numerous endemic plant groups has made the Macaronesian islands an outstanding area for studies of evolution and speciation. Despite intensive investigation in the last 15 years, absolute age and rate of diversification are poorly known for the flora of Macaronesia. Here we report molecular divergence estimates and rates of diversification for five representative, putative rapid radiations of monophyletic endemic plant lineages across the core eudicot clade of flowering plants. Three discrete windows of colonization during the Miocene and early Pliocene are suggested for these lineages, all of which are inferred to have had a single colonization event followed by rapid radiation. Subsequent inter-archipelago dispersal events into Madeira and the Cape Verdes took place very recently during the late Pliocene and Pleistocene after initial diversification on the Canary Islands. The tempo of adaptive radiations differs among the groups, but is relatively rapid compared to continental and other island radiations. Our results demonstrate that opportunity for island colonization and successful radiation may have been constrained to discrete time periods of profound climatic and geological changes in northern African and the Mediterranean.

Range-wide phylogeography of Juniperus thurifera L., a presumptive keystone species of western Mediterranean vegetation during cold stages of the Pleistocene

We investigate the range-wide population structure and phylogeography of thuriferous juniper (Juniperus thurifera L.), a species with a highly disjunct distribution in the western Mediterranean. We genotyped a total of 327 individuals from 20 populations using amplified fragment length polymorphisms (AFLP). Different analyses such as principal co-ordinate analysis (PCoA), nonmetric multidimensional scaling of F(ST) distances among populations, unweighted pair group method with arithmetic mean (UPGMA), and Bayesian clustering revealed that the Strait of Gibraltar acted as an efficient barrier against gene flow between the Moroccan and European populations for a very long time, and consequently support that the Moroccan populations should be recognised as a distinct subspecies (J. thurifera L. subsp. africana (Maire) Romo and Boratyńsky). The Algerian population was genetically more closely related to the European than to the Moroccan ones, probably due to dispersal events from Europe to Algeria. With respect to the mainland European populations, our data are not conclusive to reject any of the two following hypotheses: (1) the Iberian Peninsula was subdivided into different gene pools, and was the source for the colonisation of the Pyrenees and the Alps; and (2) the pattern we see today is partly the result of immigration into the Iberian Peninsula, e.g. from the Alps. Finally, the Corsican population was closely related genetically to two northern Iberian populations most probably due to relatively recent long-distance dispersal.

Population structure of Hypochaeris salzmanniana DC. (Asteraceae), an endemic species to the Atlantic coast on both sides of the Strait of Gibraltar, in relation to Quaternary sea level changes

To detect potential Pleistocene refugia and colonization routes along the Atlantic coast, we analysed amplified fragment length polymorphisms (AFLPs) in 140 individuals from 14 populations of Hypochaeris salzmanniana (Asteraceae), an annual species endemic to the southwestern European and northwestern African coastal areas. Samples covered the total distributional range of the species, with eight populations in southwestern Spain and six populations in northwestern Morocco. Using nine primer combinations, we obtained 546 fragments in H. salzmanniana and its sister species H. arachnoidea of which 487 (89.2%) were polymorphic. The neighbour-joining tree shows that the populations south of the Loukos river in Morocco are clearly differentiated, having more polymorphic, private, and rare fragments, and higher genetic diversity, than all the other populations. The southernmost populations in Morocco, south of the river Sebou, form a large panmictic population. They are probably the oldest populations that have been relatively unaffected by stochastic processes resulting from Pleistocene glaciations. Northward migration of populations during this period may have resulted in loss of genetic diversity in specific regions, perhaps due to bottlenecks caused by rise in sea level during interglacial periods, and, in some cases, by changes in the breeding system.

On the origin of the sweet-smelling Parma violet cultivars (Violaceae): wide intraspecific hybridization, sterility, and sexual reproduction

Parma violets are reputed for their double, fragrant flowers and have been cultivated for centuries in Europe. However, due to a rather atypical morphology their taxonomic affinity has not been clarified. Authors have proposed an origin from three possible species, Viola alba, V. odorata, or V. suavis, or a hybrid origin. Using both ITS sequence variation and allozyme variation in 14 putative loci, we showed that the Parma violet cultivars have their origin within Viola alba and that they are best included in the Mediterranean subsp. dehnhardtii. There is no trace of interspecific hybridization. However, the cultivars appear to have a single origin in a wide hybrid within V. alba, involving parental plants from the eastern and western Mediterranean region; historical literature sources seem to indicate Turkey and Italy, respectively. The Parma violet cultivars possess high levels of allozyme heterozygosity and to some extent also within-individual ITS sequence variation. Losses of heterozygosity and within-individual ITS sequence variation in some of the cultivars indicate subsequent rare events of sexual reproduction, presumably through cleistogamous seed set. We unambiguously identify the closest wild relative of this group of cultivars, allowing growers to develop new selection procedures, and show a peculiar molecular process associated with human selection.

Molecular phylogenetic evidence for the geographic origin and classification of Canary Island Lotus (Fabaceae: Loteae)

Molecular phylogenetic analyses of Macaronesian Lotus and related genera were conducted to assess their biogeographic history and taxonomy. Macaronesian Lotus, which are typically classified within one of two subgenera, Lotus subgenus Pedrosia or L. subg. Rhyncholotus, are diagnosed by the presence of a forked or toothed style and differences in corolla morphology. Maximum parsimony and Bayesian analyses of internal transcribed spacer sequences identify a well-supported northwest African-Cape Verde Island clade that includes all members of Lotus subgenus Pedrosia+L. subg. Rhyncholotus. There is modest support for two independently nested clades containing the Canary Island species and two non-Canarian species, Lotus assakensis from Africa and Lotus azoricus endemic to the Azores. Biogeographic reconstruction based on a parsimony topology unequivocally identifies an African origin for the Canary Island group with subsequent back dispersal to the African continent and a single dispersal event to the Azores. A phylogeographic assessment of colonization and diversification patterns suggests that geographic isolation via interisland colonization of ecologically similar habitats is the primary mode of species diversification in Canary Island Lotus.

Relationships of the Macaronesian and Mediterranean floras: molecular evidence for multiple colonizations into Macaronesia and back-colonization of the continent in Convolvulus (Convolvulaceae)

A molecular phylogenetic analysis of the Macaronesian endemic species of Convolvulus was undertaken using data from the nuclear ribosomal internal transcribed spacer (ITS) regions. The results of the analysis support two introductions into Macaronesia from distantly related clades within Convolvulus and a subsequent back-colonization to the continent from within one of the clades. Hypothesized relationships between Macaronesian species and New World taxa and between the Canarian endemic C. caput-medusae and the Moroccan C. trabutianus are refuted. Both Macaronesian clades are shown to have Mediterranean sister groups although one is predominantly western Mediterranean and the other predominantly eastern Mediterranean in distribution. The patterns of colonization into Macaronesia demonstrated by Convolvulus and also by other multiple colonizing genera conform to either a pattern of phylogenetic distinctiveness or a checkerboard distribution of island lineages. Both are consistent with the hypothesis that niche preemption is responsible for the limited number of colonizations into the region. A review of sister group relationships demonstrates that, in common with Convolvulus, most Macaronesian groups have sister groups distributed in the near-continent (i.e., western Mediterranean). Disjunct sister group relationships (including Eastern Mediterranean disjunctions) occur in only 18% of groups.

The phylogeny of Gaura (Onagraceae) based on ITS, ETS, and trnL-F sequence data

Gaura (Onagraceae: Onagreae) is a small North American genus of 21 species consisting mostly of night-blooming, moth-pollinated annuals and perennials. The current infrageneric classification based on differences in habit, floral symmetry, and fruit morphology recognizes eight sections within the genus. We examine the phylogenetic relationships of all 21 species of Gaura using DNA sequence data from the internal transcribed spacer region (ITS), the external transcribed spacer region (ETS), and the plastid trnL-F region. Combined analysis of these regions indicate Gaura is monophyletic only if it includes Stenosiphon, a monotypic genus comprised of S. linifolius. Within Gaura, our studies indicate that sections Gauridium, Schizocarya, Campogaura, Stipogaura, Xenogaura, and Gaura are monophyletic, but sections Xerogaura and Pterogaura are not and should be reevaluated. In addition, molecular data provide support for the hypothesis that G. sinuata and G. drummondii arose via interspecific hybridization followed by genome doubling; their influence on phylogenetic reconstruction is discussed.

Molecular systematic analysis reveals cryptic tertiary diversification of a widespread tropical rain forest tree

The broad geographic range of many Neotropical rain forest tree species implies excellent dispersal abilities or range establishment that preceded the formation of current dispersal barriers. In order to initiate historical analyses of such widespread Neotropical trees, we sequenced the nuclear ribosomal spacer (ITS) region of Symphonia globulifera L. f. (Clusiaceae) from populations spanning the Neotropics and western Africa. This rain forest tree has left unmistakable Miocene fossils in Mesoamerica (15.5-18.2 Ma) and in South America ( approximately 15 Ma). Although marine dispersal of S. globulifera is considered improbable, our study establishes three marine dispersal events leading to the colonization of Mesoamerica, the Amazon basin, and the West Indies, thus supporting the paleontological data. Our phylogeographic analysis revealed the spatial extent of the three Neotropical S. globulifera clades, which represent trans-Andes (Mesoamerica+west Ecuador), cis-Andes (Amazonia+Guiana), and the West Indies. Strong phylogeographic structure found among trans-Andean populations of S. globulifera stands in contrast to an absence of ITS nucleotide variation across the Amazon basin and indicates profound regional differences in the demographic history of this rain forest tree. Drawing from these results, we provide a historical biogeographic hypothesis to account for differences in the patterns of beta diversity within Mesoamerican and Amazonian forests.

The influence of the Miocene Mediterranean desiccation on the geographical expansion and genetic variation of Androcymbium gramineum (Cav.) McBride (Colchicaceae)

Chloroplast DNA (cpDNA) restriction site and isozyme data were combined to explore the spatial-temporal influence of the Messinian desiccation in the Mediterranean on the disjunct distribution of Androcymbium gramineum in Almería and Morocco (north and south of the straits of Gibraltar, respectively). Lack of evidence for different selective pressures, divergence time estimates based on the calibration of the isozyme molecular clock with the cpDNA data, the basal position of Almerian populations in the A. gramineum clade, and the much higher isozyme polymorphism in Almería suggest that (i) only a southern European range of A. gramineum existed before the Messinian [ approximately 11.2 million years ago (Ma), in the middle Miocene] and (ii) the desiccation of the Mediterranean basin about 5.5-4.5 Ma induced the migration of A. gramineum from Almería to Morocco (between 4.9 and 4.6 Ma, according to our time estimates). After the split into two allopatric units following the refilling of the Mediterranean, the major influence of drift associated with Plio-Pleistocene recurrent glaciation cycles and range expansions/contractions probably fostered the substantial interpopulation genetic differentiation observed within Almería (CGST = 0.41, average DNei = 0.185) and, to a lesser extent, within Morocco (CGST = 0.24, average DNei = 0.089), but did not hinder the maintenance of considerable levels of genetic variation in either geographical area (A = 2.14, HE = 0.230 and A = 1.90, HE = 0.213, respectively).

Phylogenetics of the grass genus Ehrharta: evidence for radiation in the summer-arid zone of the South African Cape

Climatic and geological change may play a key role in stimulating biological radiations. Here, we use phylogenetic data to test whether the comparatively high diversity of ehrharteoid grasses in the Cape region of South Africa is the result of rapid radiation associated with the onset of a seasonally arid climate during the late Miocene. A phylogenetic hypothesis based on morphological and nucleotide sequence (nuclear ITS1 and plastid trnL-F) data confirms the monophyly of the African Ehrharta species and shows that the diversification of this lineage was centered in the Cape region. Sequence divergence data (ITS1 + trnL-F) indicate a pulse of rapid speciation, which may explain poor phylogenetic resolution within the African Ehrharta clade. Alternative calibrations yield a broad range of time estimates for the start and end of this radiation, most of which indicate a radiation inside the last 11 million years. A calibration based on the age of Ehrhartoideae suggests that radiation started 9.82 +/- 0.20 million years ago and ended 8.74 +/- 0.21 million years ago. Under alternative calibrations, estimated speciation rates during the period of radiation range between 0.87 and 4.18 species per million years. Parsimony optimization of habitat parameters reveals that radiation was correlated with the occupation of seasonally arid succulent karoo environments, wet heathy (fynbos) environments being ancestral. These data support earlier suggestions that late Miocene climatic change stimulated floristic radiation at the Cape, and highlight the potential importance of environmental change in powering diversification in continental floras.

Chloroplast and nuclear evidence for multiple origins of polyploids and diploids of Hedera (Araliaceae) in the Mediterranean basin

Chloroplast (trnT-L) and nuclear rDNA (ITS) sequence analyses of the Araliaceae provide strong molecular evidence for the monophyly of the genus Hedera. Phylogenetic reconstructions suggest multiple origins and an active polyploidization process not only in the formation of tetraploids (2n = 96), hexaploids (2n = 144), and octoploids (2n = 192), but also of diploids (2n = 48). A high basic chromosome number of x = 24, extensive polyphyly in widespread diploids, and terminal placement of Hedera in phylogenies of the Araliaceae reveal that extant diploid taxa may be, in fact, assemblages of ancestral polyploids from plants of n = 12. Four major lineages containing four types of chloroplast (chlorotypes I, II, III, and IV), which are defined by different trnT-L nucleotide substitutions and two large insertions (50- and 30-bp), provide evidence for evolutionary processes and historical biogeography in Hedera. We propose a scenario where an initial colonization in the Mediterranean basin by Asian ancestors (carrying the ancestral Araliaceae chlorotype I) is followed by differentiation into the four chlorotypes of the Mediterranean region, and then recolonization of Asia and northern Europe only by chlorotype III. The Macaronesian taxa (Hedera azorica, Hedera maderensis ssp. maderensis, and Hedera canariensis) appear to have originated from a single-colonization event to each archipelago with no further contact either with continental or insular species.

Origin of Macaronesian Sideritis L. (Lamioideae: Lamiaceae) inferred from nuclear and chloroplast sequence datasets

Sideritis L. (Lamiaceae) comprises approximately 150 species of annuals and perennials distributed chiefly in the Mediterranean region. The majority of the species belong to the continental subgenus Sideritis which is divided into two perennial (Sideritis and Empedoclea) and two annual (Hesiodia and Burgsdorfia) sections. Twenty-three species are woody perennials endemic to the Macaronesian archipelagos of Madeira and the Canary Islands. In an effort to determine the continental origin of the insular group, we constructed independent phylogenies comprising sequence data from both chloroplast and nuclear markers. Sampling included 7 island taxa drawn from the Macaronesian subgenus Marrubiastrum and 25 continental taxa representing all four sections of subgenus Sideritis. Subgenus Marrubiastrum and the two continental perennial sections form well-supported monophyletic groups in both individual and combined analyses. The annual sections are not monophyletic in any analysis; further sampling of annual taxa is needed to resolve these relationships. All analyses identified Sideritis cossoniana, an annual species from Morocco, as the closest continental relative of the Macaronesian group. This contrasts with the hypothesis of earlier workers who suggested that the insular taxa were most closely related to eastern Mediterranean species of the genus. The phylogenies also demonstrate a distinct increase in woodiness among the Macaronesian species relative to their continental congeners, providing further support for the secondary nature of woodiness in island plants.

Coding of insertion-deletion events of the chloroplastic intergene atp beta-rbcL for the phylogeny of the Valerianeae tribe (Valerianaceae)

A preliminary analysis of the sequence alignment of the chloroplast intergene atp beta-rbcL in tribe Valerianeae reveals that insertion-deletion evolutionary events ('indels'), combined with nucleotide substitutions, have occurred in large zones in some of the studied taxa. Due to the frequent occurrence and large size of indels within this tribe, intergene length varies from 531 to 788 base pairs within the studied species. This situation poses gap coding problems that we had to tackle before phylogenetic analysis. Four methods of gap coding were used: elimination of gapped sites ('complete omission'), 'missing data', 'fifth base' and Barriel's coding method, which translates indels into new multistate characters in the data matrix. After application of these four methods of data treatment, phylogenetic analyses (maximum parsimony) did not lead to very different results. Three robust clades emerged in each case, corresponding to the Centranthinae subtribe (genus Centranthus), the Fediinae subtribe (genera Fedia and Valerianella), and the American species of Valeriana. The theoretical basis and biological significance of these four methods are discussed in order to apply the best ones in future studies.

Rapid diversification of a species-rich genus of neotropical rain forest trees

Species richness in the tropics has been attributed to the gradual accumulation of species over a long geological period in stable equatorial climates or, conversely, to speciation in response to late Tertiary geological events and unstable Pleistocene climates. DNA sequence data are consistent with recent diversification in Inga, a species-rich neotropical tree genus. We estimate that speciation was concentrated in the past 10 million years, with many species arising as recently as 2 million years ago. This coincides with the more recent major uplifts of the Andes, the bridging of the Isthmus of Panama, and Quaternary glacial cycles. Inga may be representative of other species-rich neotropical genera with rapid growth and reproduction, which contribute substantially to species numbers in the world's most diverse flora.

Evolution and biogeography of Alectryon (Sapindaceae)

Phylogenetic analysis of nucleotide sequences from four plastid loci (matK, partial trnK-matK introns, rps16 intron) and one nuclear locus (the internal transcribed spacer of rDNA; ITS-1) was conducted for 14 species of Alectryon and five related genera in Sapindaceae. Both matK and rps16 intron provide few informative characters within Alectryon, whereas ITS-1 provides the largest number of parsimony-informative characters and has the greatest sequence divergence between taxa. Support for branches in cladograms produced in PAUP increased markedly upon inclusion of ITS-1 data to matK and rps16 intron data. Analyses of each region alone or combined produced congruent results, suggesting that the regions are complementary. Phylogenetic analysis indicates that there are two main lineages within Alectryon, with A. subcinereus sister to the remaining sampled Alectryon taxa. Two morphological characters, presence/absence of petals and aril patterning, are congruent with the molecular phylogeny. One robustly supported clade is characterized by smooth arils and petals, in contrast to the taxa in the other major clade which have patterned arils and an absence of petals. These analyses also support a number of revised subgeneric groupings for Alectryon. The decision to submerge Heterodendrum in Alectryon is supported, although taxa belonging to Heterodendrum do not form a clade. The majority of the Australian Alectryon appear to belong to the tropical monsoonal/arid flora with species from both lineages being found in representative vine thickets across northern Australia. It appears that the seasonally dry rainforest communities comprise a number of elements that do not share common evolutionary histories within this genus.

Why nuclear ribosomal DNA spacers (ITS) tell different stories in Quercus

The molecular systematics of Quercus (Fagaceae) was recently assessed by two teams using independently generated ITS sequences. Although the results disagreed in several remarkable features, the phylogenetic trees for either hypothesis were highly supported by bootstrap resampling. We have reanalyzed the ITS sequences used by both teams (eight taxa) to reveal the underlying patterns of this divergence. Within species, conspicuous length and G + C% divergence were evident in most sequence comparisons. In addition, a high rate of substitutions and deletions involving highly conserved motifs in both ITS spacers were present in a set of sequences. This was coupled with a less thermodynamic stability in the RNA structure, lacking conserved hairpins that are putatively involved in the processing of the RNA transcripts. Compelling evidence suggests that the divergent ITS alleles reported by one team are pseudogenes, i.e., nonfunctional paralogous loci. The hypothesis that the contrasting phylogenetic histories drawn from Quercus using ITS data are not strictly related to technical differences between laboratories, but that they have rather been generated from the analysis of paralogous sequences, best reconciles the available data. The risk of incorporating ITS paralogues in plant evolutionary studies which can distortion the phylogenetic signal should caution molecular systematists. Without a detailed inspection of some basic features of the sequence, including the integrity of the conserved motifs and the thermodynamic stability of the secondary structures of the RNA transcripts, errors in evolutionary inferences could be easily overlooked.

The colonization history of Olea europaea L. in Macaronesia based on internal transcribed spacer 1 (ITS-1) sequences, randomly amplified polymorphic DNAs (RAPD), and intersimple sequence repeats (ISSR)

Phylogenetic relationships in the Olea europaea complex and the phylogeography of 24 populations of the Macaronesian olive (O. europaea ssp. cerasiformis) were assessed by using three molecular markers: nuclear ribosomal internal transcribed spacer 1 (ITS-1) sequences, randomly amplified polymorphic DNAs (RAPD), and intersimple sequence repeats (ISSR). Parsimony analysis of the ITS-1 sequences and Neighbour-joining (NJ) analyses of RAPD and ISSR banding variation revealed four major lineages in the O. europaea complex: (1) ssp. cuspidata; (2) ssp. cerasiformis from Madeira; (3) ssp. laperrinei; and (4) ssp. cerasiformis from the Canary Islands plus ssp. europaea. These results provide unequivocal support for two independent dispersal events of Olea to the Madeira and Canary Islands. Molecular and morphological evidence led to recognition of two separate olive taxa in Macaronesia, to date included in ssp. cerasiformis. NJ analyses of the combined RAPD and ISSR data suggest that the colonization of the Canaries by O. europaea may have followed an east to west stepping-stone model. An interisland dispersal sequence can be recognized, starting from the continent to Fuerteventura, Gran Canaria, Tenerife, La Gomera, and finally La Palma. High dispersal activity of the lipid-rich Olea fruits by birds in the Mediterranean region is congruent with multiple dispersal of olives to Macaronesia and successive colonization of the archipelagos. The observation of strong genetic isolation between populations of different islands of the Canary Islands suggests, however, that subsequent interisland dispersal and establishment has been very rare or may not have occurred at all.

Phylogeny and biogeography of Juglans (Juglandaceae) based on matK and ITS sequence data

We investigated phylogenetic and biogeographic relationships within Juglans (walnuts), a Tertiary disjunct genus, using 15 species of Juglans and related (Juglandaceae) outgroups. The relationships were analyzed using nucleotide sequences of the chloroplast gene matK and its flanking spacers and of the internal transcribed spacers (ITS) and 5.8S gene of the nuclear ribosomal DNA. The DNA sequences provided 246 informative characters for parsimony analysis. ITS data supported as monophyletic groups the four generic sections, Cardiocaryon, Dioscaryon, Rhysocaryon, and Trachycaryon. Within Rhysocaryon, the temperate black walnuts and the tropical black walnuts were supported as monophyletic groups. When the two data sets were combined, J. cinerea was nested within Cardiocaryon. Combined analysis with published nuclear DNA restriction site data placed J. cinerea in a monophyletic group with Cardiocaryon. These analyses consistently supported Juglans as a monophyletic group and as the sister group to the genus Pterocarya. The results of this work are consistent with the known geological history of Juglans. The fossil record suggests that the butternuts had evolved by the early Oligocene in North America. The presence of butternuts in Eurasia could be the result of migration from North America to Eurasia during the warming trend of the mid Oligocene.