Reticulate evolution in the Acrolophus subgroup (Centaurea L., Compositae) from the western Mediterranean: origin and diversification of section Willkommia Blanca

Section Willkommia (Centaurea, Compositae) is endemic to the east-central portion of the Iberian Peninsula and northwestern Africa. The section has been included with sections Acrolophus and Phalolepis in the informal subgroup Acrolophus. We have used a molecular phylogenetic approach to test the hypothesis proposed by earlier authors that the diversification of section Willkommia involved a schizoendemic process from an ancestral syngameon. Comparative analysis of the transcribed spacer sequences of the nuclear ribosomal DNA (ITS and 3'ETS) regions reveals the presence of three different types of ribosomal sequences in the Acrolophus subgroup (referred to here as the Willkommia, Acrolophus-Phalolepis and Simulans ribotypes) which show a sectional-independent geographic structure. This evidence, together with the presence of additive polymorphic sites in the Willkommia sequences which agree with the geographic distribution of the taxa, suggests that members of section Willkommia and the western Mediterranean taxa of sections Acrolophus and Phalolepis fit a reticulate evolution model.     

A new species of Centaurea (sect. Phalolepis, Compositae: Cardueae) from eastern Peloponnisos, Greece

A new species of Centaurea L. , Centaurea leonidia Kalpoutz. & Constantin. , from two localities west and south-west of the town of Leonidio in eastern Peloponnisos, Greece, is described and illustrated. It belongs to C . sect. Phalolepis , and taxonomically its closest relatives are C. heldreichii Halácsy , a very localized species from south-west Sterea Ellas (Greece) and, surprisingly, C. niederi Heldr., which belongs to sect. Acrolophus. The new species is currently known from two populations of less than 100 individuals each, growing on almost inaccessible cliffs close to the convent of Agios Nikolaos Sintzas (St. Nicolas of Sintza) and the slopes of Poundes summit. Several other Greek endemic species are found in the same areas. Centaurea leonidia is scientifically important as it belongs to a small group of taxa, which, although they are members of sect. Phalolepis , have close allies in sect. Acrolophus. The chromosome number of C. leonidia , 2 n  = 18, counted in root tips, is also reported and illustrated.  © 2004 The Linnean Society of London, Botanical Journal of the Linnean Society , 2004, 146 , 375–383.     

Pollen Studies in Subtribe Centaureinae (Asteraceae): The Carthamus Complex and the Genus Aegialophila Analyzed with Electron Microscopy

Abstract: Recent molecular and karyologic studies have deeply modified the delimitation of the genera of the Carthamus complex, and have led to a new classification of the group in four genera ( Carduncellus, Carthamus, Femeniasia and Phonus ). Molecular studies have confirmed the position of the group among the derived genera of the subtribe Centaureinae, and have suggested a faint relationship between the Carthamus complex and the small genus Aegialophila. However, despite the importance of pollen evolution in the subtribe, a comprehensive study of the pollen of the involved genera with electron microscopy was lacking. Therefore, we have carried out a survey of pollen morphology and ultrastructure in a wide sample of the genera, using both scanning and transmission electron microscopy. Our results suggest that pollen type of the Carthamus complex is homogeneous and should be classified as a new pollen type in the classification of Wagenitz. Pollen type of Aegialophila shows strong similarities with the Centaurea scabiosa pollen type of Wagenitz, but there are slight differences in shape and in ultrastructure of the exine. These differences are evaluated, together with morphological and molecular evidence; the authors conclude that similarities are the result of parallel evolution and that pollen of Aegialophila could be considered a new pollen type. Some considerations are made on the placement of the new types in the cadre of pollen and molecular evolution in the subtribe Centaureinae.     

Satellite-DNA diversification and the evolution of major lineages in Cardueae (Carduoideae Asteraceae)

In a previous work, we characterized the HinfI satellite DNA family in the subtribe Centaureinae (Cardueae) demonstrating that a “library” of eight HinfI subfamilies would exist in the common ancestor of all Centaureinae, which were differentially amplified in different lineages. Now, we extend our study by analyzing a total of 219 additional repeats from fifteen species belonging to Carlininae, Echinopsinae and Carduinae, and comparing them to those of Centaureinae. Most HinfI sequences belonged to the subfamily II, although a few sequences of other subfamilies were detected in some species. Additionally, a new subfamily characteristic of several Carduinae species was discovered. Although phylogenetic trees grouped sequences by subfamily affinity instead of species provenance, when comparing repeats of the same subfamily, the degree of divergence between any pair of sequences was related to the evolutionary distance between the species compared in most cases. Exceptions were in comparisons between sequences of some Centaureinae species, and between sequences of some Carduinae species and those of Centaureinae. Our results demonstrate that: (1) At least nine HinfI subfamilies would exist in the common ancestor of Cardueae, each one differentially amplified in different lineages; (2) After differential spreading, sequences of each subfamily evolved concertedly through molecular drive, resulting in the gradual divergence of repeats between different species; (3) The rate to which concerted evolution occurred was different between lineages according to the evolutionary history of each one.     

New chromosome counts in the Centaurea Jacea group (Asteraceae, Cardueae) and some related taxa

Twenty-seven chromosome counts are reported in 23 species of the genus Centaurea , mostly eastern endemic species of the Jacea group, which has become the core of the re-defined genus Centaurea . Twenty reports are new, one is a correction of a previous count, one is a confirmation of limited previous data and one represents a new basic number in the Centaureinae. The prevalence of the basic chromosome number x  = 9 among the Eastern sections of the Jacea group is confirmed, together with the close correlation between karyological data and classification of the genus. Two alternative hypotheses on the aberrant chromosome number (for the Centaureinae) found in C. behen are proposed. One of them, if verified, would confirm that a cycle of polyploidy and descending dysploidy is a key mechanism in the speciation of the group.  © 2004 The Linnean Society of London, Botanical Journal of the Linnean Society , 2004, 145 , 345–352.     

Karyology, generic delineation and dysploidy in the genera Carduncellus, Carthamus and Phonus (Asteraceae)

Within the Mediterranean complex Carduncellus Carthamus Phonus , taxonomic classification has proven problematical. A recent molecular analysis has clarified the generic delineation, while a revision of the abundant karyological data has suggested that correlation of taxonomic classification and karyology would be of great interest. In this paper, a confirmation of chromosome numbers in the complex is offered, with 44 populations of 30 taxa studied. Six of the counts are new. A short analysis of the correlation between base chromosome numbers and generic classification follows. The main conclusion is that descending dysploidy is the main mechanism of karyological evolution in the complex, as has been the case in other genera of the subtribe.     

Pollen studies in subtribe Centaureinae (Asteraceae): the Jacea group analysed with electron microscopy

Although it has been recognized for many years that the genus Centaurea L. is an artificial assemblage of taxa, its partition into more natural affiliations has been impossible due to its incredible complexity. One of the most reliable characteristics for establishing the phylogeny within this group is the type of pollen. Most of the classification difficulties centre in the Jacea group, which has a characteristic Jacea pollen type. Recent molecular studies indicate that this assemblage is probably polyphyletic. Specifically, previous DNA sequence analyses indicate that Centaurea pulchella and the genera Oligochaeta and Zoegea represent different lineages. This finding prompted an investigation of their pollen types, using scanning electron microscopy, and for some species, transmission microscopy. For a rigorous comparison, the study also included a wide representation of other species across the entire Jacea group. Results showed that both Oligochaeta and Zoegea , but not C. pulchella , can be clearly distinguished from the Jacea group on the basis of pollen morphology. The genus Oligochaeta has a peculiar pollen type that may represent a simplified form of the Serratula pollen type, and the genus Zoegea has Serratula pollen type.     

Centaurea serpentinica sp. nov. (Asteraceae) from the central and south Anatolia transition zone, Turkey

A new species, Centaurea serpentinica A. Duran & B. Doğan (Asteraceae) in sect. Acrolophus (Cass.) DC., is described and illustrated from Anatolia, Turkey. The species grows on eroded serpentine stony slopes and in open Pinus brutia Ten. forest in the Yahyalı district (C5 Kayseri Province) in the central and south Anatolia transition zone. It is morphologically similar to Centaurea kilaea Boiss. Diagnostic morphological characters from closely similar taxa are discussed and arranged in a key. Ecology, conservation status and biogeography of the species is also presented. In addition, the geographical distribution of the new species and other related species is mapped.     

Karyotaxonomy of Greek serpentine angiosperms

The chromosome numbers are given for 20 angiosperm taxa, most of which grow predominately or exclusively on serpentine in Greece, and the karyotype morphology is illustrated in all cases but one. Chromosome data are provided for the first time for ten taxa ( Alyssum pogonocarpum, Centaurea charrellii, C. vlachorum, Cephalaria fanourii, Matricaria tempskyana, Onosma stridii, Scorzonera doriae, Silene fabarioides, S. salamandra, Trinia glauca ssp. pindica ) and for the endemic monospecific genus Leptoplax . A new number is reported for Thymus teucrioides ssp. candilicus . An unexpected dysploid number is recorded for a population of Leontodon hispidus ssp. hispidus. Chromosome number and karyotype details from Greek populations are presented for the rest of the taxa. Chromosomal evidence supports close relationships among members of Onosma subsect. Asterotricha . The unusual chromosome number of Centaurea vlachorum supports its placement either in C. sect. Jacea or C . sect. Cyanus . The evolution of taxa in sections Vierhapperia, Pulvinares , and Nervosae of Scorzonera appears to be connected with particular chromosomal rearrangements and dysploidy. Leptoplax does not share the same chromosome number with Peltaria but with Bornmuellera instead, something that facilitates infrageneric hybridization. Further issues of taxonomy, distribution, evolution and conservation of serpentine species are briefly discussed where appropriate. © 2002 The Linnean Society of London , Botanical Journal of the Linnean Society , 2002, 139 , 109–124.     

Centaurea vlachorum sp. nov. (subgen. Jacea) from NW Greece Materials for the Mountain Flora of Greece, 8

Centaurea vlachorum Hartvig is described from alpine meadows on ophiolithic substratum on Mt. Milea in N Pindhos, Greece. It is a very distinct species related to sect. Leptoranthus within subgen. Jacea.     

SatDNA Analyzer: a computing tool for satellite-DNA evolutionary analysis

satDNA Analyzer is a program, implemented in C++, for the analysis of the patterns of variation at each nucleotide position considered independently amongst all units of a given satellite-DNA family when comparing it between a pair of species. The program classifies each site accordingly as monomorphic or polymorphic, discriminates shared from non-shared polymorphisms and classifies each non-shared polymorphism according to the model proposed by Strachan et al. in six different stages of transition during the spread of a variant repeat unit toward its fixation. Furthermore, this program implements several other utilities for satellite-DNA analysis evolution such as the design of the average consensus sequences, the average base pair contents, the distribution of variant sites, the transition to transversion ratio and different estimates of intra-specific variation and inter-specific variation. Aprioristic hypotheses on factors influencing the molecular drive process and the rates and biases of concerted evolution can be tested with this program. Additionally, satDNA Analyzer generates an output file containing a sequence alignment without shared polymorphisms to be used for further evolutionary analysis by using different phylogenetic softwares. AVAILABILITY: satDNA Analyzer is freely available at http://satdna.sourceforge.net/. SatDNA Analyzer has been designed to operate on Windows, Linux and Mac OS X.     

Taxonomic problems in Carthamus (Asteraceae): RAPD markers and sectional classification

Recent molecular studies have clarified the problem of the generic limits of Carthamus . However, taxonomic problems remain in the sectional classification: section Carthamus was confirmed as a natural group, but molecular phylogenies based on DNA sequences did not resolve the other sections, resulting in a confusing conglomerate. A survey based on RAPD markers has been carried out in this conflicting group of sections, with the aim of evaluating the usefulness of these markers at the section and species levels. On the basis of the results, correlated with morphological and karyological characters, some recommendations are made in relation to the taxonomy of Carthamus . The number of sections is reduced from five to two: section Thamnacanthus is currently classified as a different genus, Phonus ; section Carthamus s.s. is retained in its present delimitation, and section Atractylis is redefined, including current sections Atractylis , Lepidopappus and Odontagnathius . The commonly accepted treatment of some taxa as subspecies is not well founded, and C. alexandrinus , C. creticus , C. tenuis and C. turkestanicus should be considered as independent species. Our results confirm that methodological problems posed by RAPD markers can be avoided by careful laboratory procedures and appropriate data analyses; they also suggest that this kind of marker is useful at low taxonomic levels and is, furthermore, complementary to DNA sequence analysis.  © 2005 The Linnean Society of London, Botanical Journal of the Linnean Society , 2005, 147 , 375–383.     

Phylogeny and molecular evolution of the tribe Harpalini (Coleoptera, Carabidae) inferred from mitochondrial cytochrome-oxidase I

The tribe Harpalini is a group of ground beetles with a world-wide distribution that comprises approximately 2000 species and about 238 genera and subgenera. Hypotheses about the phylogenetic relationships of the subtribes of Harpalini are implicit within the systematic criteria put forward by different authors. A 759 bp fragment of the mitochondrial COI was sequenced in 119 specimens (107 species) of 52 genera and subgenera that represent the main lineages of Harpalines, and 3 species of other tribes used as outgroups. A hierarchical study of sequence divergence (under uncorrected and corrected models) and ts:tv ratio pattern analyses were carried out at different taxonomic levels. A low saturation rate was detected at first and second codon positions, whereas A+T richness causes a low transitions:transversions ratio, which suggests--a priori--a high rate of saturation at the third codon position. A progressive accumulation of sequence divergence and a decreasing ts:tv ratio were found from lower to higher taxonomic levels. MP strict consensus, ML, and minimum evolution distance (under ts+tv and tv only schemes) trees showed similar major clades within the tribe. The subtribe Ditomina is a monophyletic lineage with close affinities to the subtribe Harpalina. Harpalina is a polyphyletic lineage as the genus Daptus is always related to members of the subtribe Stenolophina, and the Selenophorines resulted a polyphyletic group related to the subtribe Anisodactylina. Main lineages proposed by Noonan [Quaest. Entomol. 9 (1973) 266] within the subtribe Anisodactylina have been corroborated in this study. The Australian genus Phorticosomus is not related to Ditomina but to the Australian Notiobioids lineage. Most taxa of the subtribe Stenolophina are always included in the same clade, together with taxa of the subtribe Pelmatellina, which might be considered as a lineage of Stenolophina related to Bradycellus and Dicheirotrichus. The subtribe Amblystomina lacks a well-supported relationship to the other subtribes of Harpalini and could not be consistently related to any of them.     

Effect of location,organization, and repeat-copy number in satellite-DNA evolution

Here, we analyze the evolutionary dynamics of a satellite-DNA family in an attempt to understand the effect of factors such as location, organization, and repeat-copy number in the molecular drive process leading to the concerted-evolution pattern found in this type of repetitive sequences. The presence of RAE180 satellite-DNA in the dioecious species of the plant genus Rumex is a noteworthy feature at this respect, as RAE180 satellite repeats have accumulated differentially, showing a distinct distribution pattern in different species. The evolution of dioecious Rumex gave rise to two phylogenetic clades: one clade composed of species with an ancestral XX/XY sex chromosome system and a second, derived clade of species with a multiple sex–chromosome system XX/XY₁Y₂. While in the XX/XY dioecious species, the RAE180 satellite-DNA is located only in a small autosomal locus, the RAE180 repeats are present also in a small autosomal locus and additionally have been massively amplified in the Y chromosomes of XX/XY₁Y₂ species. Here, we have found that the RAE180 repeats of the autosomal locus of XX/XY species are characterized by intra-specific sequence homogeneity and inter-specific divergence and that the comparison of individual nucleotide positions between related species shows a general pattern of concerted evolution. On the contrary, both in the autosomal and the Y-linked loci of XX/XY₁Y₂ species, ancestral variability has remained with reduced rates of sequence homogenization and of evolution. Thus, this study demonstrates that molecular mechanisms of non-reciprocal exchange are key factors in the molecular drive process; the satellite DNAs in the non-recombining Y chromosomes show low rates of concerted evolution and intra-specific variability increase with no inter-specific divergence. By contrast, freely recombining loci undergo concerted evolution with genetic differentiation between species as occurred in the autosomal locus of XX/XY species. However, evolutionary periods of rapid sequence change might alternate with evolutionary periods of stasis with variability remaining by the reduced action of molecular mechanisms of non-reciprocal exchange as occurred in XX/XY₁Y₂ species, which could depend on repeat-copy number and the processes involved in their amplification.     

Phylogeny of the Spiny African Daisies (Compositae, tribe Arctotideae, subtribe Gorteriinae) based on trnL-F, ndhF, and ITS sequence data

The tribe Arctotideae (African Daisies), of the flowering plant family Compositae (Asteraceae), is a diverse and interesting group with a primarily southern African distribution (ca. 13 genera, 215 species) and many species in the Cape Floristic Region. It is divided into two subtribes: Arctotidinae (ca. 5 genera, 85 species) and Gorteriinae (ca. 8 genera, 130 species). The monophyly of the genera within the subtribe Gorteriinae and their relationship to one another was investigated using 71 samples/212 sequences including 64/141 of which are newly reported from three phylogenetic markers, two from chloroplast DNA (trnL-F and ndhF) and one from the nuclear genome (ITS). The outgroup was composed of seven members from the sister subtribe. Results show the subtribe Gorteriinae to be divided into three monophyletic groups, the Gazania-Hirpicium-Gorteria group, the Didelta group, and the Berkheya-Cullumia group. Within these three groups are 13 sub-groups, one of which has sub-clades. The genus Berkheya Ehrh. is paraphyletic, falling into five different sub-groups. The two monotypic genera, Cuspidia and Heterorhachis are not nested within any of the Berkheya clades. Hirpicium and Cullumia each have most of their taxa in a monophyletic group, but they also have one or two taxa associated with other clades. Four of the five sub-groups of Berkheya have morphologically recognizable shared characters, such as habit and spines that have been recognized by past studies. However, the grouping of one species with Didelta is difficult to explain. Support for the major clades and most of the sub-groups is strong but the relationships among some of the terminal taxa are variable.     

Concerted evolution of satellite DNA in Sarcocapnos: a matter of time

SarkOne is a genus-specific satellite-DNA family, isolated from the genomes of the species of the genus Sarcocapnos. This satellite DNA is composed of repeats with a consensus length of 855 bp and a mean G+C content of 52.5%. We have sequenced a total of 189 SarkOne monomeric repeats belonging to a total of seven species of the genus Sarcocapnos. The comparative analysis of these sequences both at the intraspecific and the interspecific levels have revealed divergence patterns between species are proportional to between-species divergence according to the phylogeny of the genus. Our study demonstrates that the molecular drive leading to the concerted-evolution pattern of this satellite DNA is a time-dependent process by which new mutations are spreading through genomes and populations at a gradual pace. However, time is a limiting factor in the observation of concerted evolution in some pairwise comparisons. Thus, pairwise comparisons of species sharing a recent common ancestor did not reveal nucleotide sites in transitional stages higher than stage III according to the Strachan's model. By contrast, there was a gradation in the percentage of upper transition stages (IV, V, VI) the more phylogenetically distant the species were. In addition, closely related species shared a high number of polymorphic sites, but these types of sites were not common when comparing more distant species. All these data are discussed in the light of current life-cycle models of satellite-DNA evolution.     

Differential spreading of HinfI satellite DNA variants during radiation in Centaureinae

Background and Aims

Subtribe Centaureinae appears to be an excellent model group in which to analyse satellite DNA and assess the influence that the biology and/or the evolution of different lineages have had on the evolution of this class of repetitive DNA. Phylogenetic analyses of Centaureinae support two main phases of radiation, leading to two major groups of genera of different ages. Furthermore, different modes of evolution are observed in different lineages, reflected by morphology and DNA sequences.

Methods

The sequences of 502 repeat units of the HinfI satellite DNA family from 38 species belonging to ten genera of Centaureinae were isolated and compared. A phylogenetic reconstruction was carried out by maximum likelihood and Bayesian inference.

Key Results

Up to eight different HinfI subfamilies were found, based on the presence of a set of diagnostic positions given by a specific mutation shared by all the sequences of one group. Subfamilies V–VIII were mostly found in older genera (first phase of radiation in the subtribe, late Oligocene–Miocene), although some copies of these types of repeats were also found in some species of the derived genera. Subfamilies I–IV spread mostly in species of the derived clade (second phase of radiation, Pliocene to Pleistocene), although repeats of these subfamilies exist in older species. Phylogenetic trees did not group the repeats by taxonomic affinity, but sequences were grouped by subfamily provenance. Concerted evolution was observed in HinfI subfamilies spread in older genera, whereas no genetic differentiation was found between species, and several subfamilies even coexist within the same species, in recently radiated groups or in groups with a history of recurrent hybridization of lineages.

Conclusions

The results suggest that the eight HinfI subfamilies were present in the common ancestor of Centaureinae and that each spread differentially in different genera during the two main phases of radiation following the library model of satellite DNA evolution. Additionally, differential speciation pathways gave rise to differential patterns of sequence evolution in different lineages. Thus, the evolutionary history of each group of Centaureinae is reflected in HinfI satellite DNA evolution. The data reinforce the value of satellite DNA sequences as markers of evolutionary processes.     

Phylogenetic relationships of the enigmatic species Serratula chinensis and Serratula forrestii (Asteraceae - Cardueae)

The phylogenetic relationships of the Chinese species Serratula forrestii and S. chinensis within the subtribe Centaureinae (Asteraceae – Cardueae) were investigated based on nuclear ribosomal DNA external and internal transcribed spacer sequences. Results indicated that Serratula s. l. is clearly polyphyletic, none of the two species showing close affinities to either Serratula s. str. or Klasea, a genus traditionally included in Serratula. Serratula forrestii has a basal position within the subtribe and has retained most plesiomorphic character states. Serratula chinensis is related to the genera of the Rhaponticum group. Its chromosome number was determined as 2n = 26, and the relationship between this species and the Rhapon-ticum group is discussed from a morphological and karyological point of view.