Haplotype and ribotype diversity of Saxifraga cuneifolia s. l. (Saxifragaceae)

Saxifraga cuneifolia L. (sect. Gymnopera, Saxifragaceae) is a plant distributed in the main mountain ranges of southern Europe, from the eastern Pyrenees to the eastern Carpathian. Currently, two subspecies are recognized based on morphological characteristics: S. cuneifolia subsp. cuneifolia grows in the Maritime Alps and North Apennines and S. cuneifolia subsp. robusta is located in the remaining area of distribution. A more delicate form and a smaller number of flowers in S. cuneifolia subsp. cuneifolia are the morphological characteristics that differentiate this subspecies from the widespread S. cuneifolia subsp. robusta. To explore the genetic diversity and the subspecific geographic patterns of S. cuneifolia s. l. we conducted a molecular study of nuclear and plastid sequences. Samples of S. cuneifolia s. l. have been analysed throughout the distribution area of this species. Our results, based on nuclear (ITS) and plastid (rbcL, trnL–F, and psbA–trnH) markers, showed a genetic characterization of both subspecies presenting discriminant haplotypes and ribotypes that confirm the current subspecific systematics.     

Molecular phylogenetics of Kosteletzkya (Malvaceae,Hibisceae) reveals multiple independent and successive polyploid speciation events

Kosteletzkya s.s. is a genus of 17 species (excluding the endemic species of Madagascar), found in the New World, continental Africa, Madagascar, and Southeast Asia. Recent chromosome counts revealed diploid, tetraploid, and hexaploid species. To estimate the history of the genus, we sequenced nuclear and plastid loci for nearly all Kosteletzkya spp., in the majority of cases, with multiple accessions per species. The African species form a paraphyletic grade relative to a New World clade. Polyploidy has occurred only in some African species, resulting in the relatively ancient formation of one putative autotetraploid species (K. semota), one recent allotetraploid species (K. borkouana), two relatively ancient allotetraploid species (K. begoniifolia and K. rotundalata) and one recent allohexaploid species (K. racemosa). Our inferences regarding the hypothesized parentage of the polyploids mostly corroborate previous work based on chromosome‐pairing patterns in artificial hybrids, highlighting the utility of these complementary data sources. © 2015 The Linnean Society of London, Botanical Journal of the Linnean Society, 2015, 179 , 421–435.     

Chloroplast phylogenomics and the taxonomy of Saxifraga section Ciliatae (Saxifragaceae)

Comprising ca. 200 species, Saxifraga sect. Ciliatae is the most species-rich section of Saxifraga s.str., whose center of diversity is in the Tibeto-Himalayan region. The infra-sectional classification of sect. Ciliatae is still in debate due to the high level of species richness, as well as remarkable variations of habitat, morphology, physiology and life cycles. Subdivisions of this section proposed in various taxonomic systems have not been adequately tested in previous phylogenetic studies, partly due to low taxonomic sampling density, but also to the use of few DNA markers. In order to achieve a more robust infra-sectional classification of sect. Ciliatae, complete chloroplast genomes of 94 taxa from this section were analyzed, of which 93 were newly sequenced, assembled and annotated. The length of the 94 plastomes of sect. Ciliatae taxa range from 143,479 to 159,938 bp, encoding 75 to 79 unique protein-coding genes (PCGs). Analyses of the 94 plastomes revealed high conservation in structural organization, gene arrangement, and gene content. Gene loss and changes of IR boundaries were detected but in extremely low frequency. The molecular phylogenetic tree from concatenated PCGs and complete chloroplast genome sequences exhibited high resolution and support values and confirms that sect. Ciliatae is monophyletic. Three well-supported clades were revealed within the section that agree relatively well with the subsectional taxonomy of Gornall (1987), but some minor modifications should be made. Firstly, the monotypic subsection Cinerascentes should be abandoned and its constituent species, S. cinerascens, assigned to subsect. Gemmiparae. Secondly, subsections Rosulares and Serpyllifoliae should be merged and become subsect. Rosulares. Section Ciliatae thus comprises: subsect. Hirculoideae Engl. & Irmsch.; subsect. Rosulares Gornall; subsect. Gemmiparae Engl. & Irmsch.; subsect. Flagellares (C. B. Clarke) Engl. & Irmsch. and subsect. Hemisphaericae (Engl. & Irmsch.) Gornall.     

Incipient speciation revealed in Anastrepha fraterculus (Diptera; Tephritidae) by studies on mating compatibility, sex pheromones, hybridization, and cytology

It has long been proposed that the nominal species Anastrepha fraterculus is a species complex and earlier studies showed high levels of pre-zygotic isolation between two laboratory strains from Argentina and Peru. Further experiments were carried out on the same populations and on their reciprocal hybrids, including pre- and post-zygotic isolation studies, pheromone analysis, and mitotic and polytene chromosome analysis. A high level of pre-zygotic isolation had been maintained between the parental strains despite 3 years of laboratory rearing under identical conditions. The level of pre-zygotic isolation was reduced in matings with hybrids. There were also differences in other components of mating behaviour. There were quantitative and qualitative differences in the sex pheromone of the two strains with the hybrids producing a mixture. The pre-zygotic isolation barriers were complemented by high levels of post-zygotic inviability and sex ratio distortion, most likely not due to Wolbachia , although there was evidence of some cytoplasmic factor involved in sex ratio distortion. Analysis of polytene chromosomes revealed a high level of asynapsis in the hybrids, together with karyotypic differences between the parental strains. The combined results of the present study indicate that these two strains belong to different biological entities within the proposed A. fraterculus complex.  © 2009 The Linnean Society of London, Biological Journal of the Linnean Society , 2009, 97 , 152–165.     

Homoploid hybrid origin of Yucca gloriosa: intersectional hybrid speciation in Yucca (Agavoideae,Asparagaceae)

There is a growing appreciation for the importance of hybrid speciation in angiosperm evolution. Here, we show that Yucca gloriosa (Asparagaceae: Agavoideae) is the product of intersectional hybridization between Y. aloifolia and Y. filamentosa. These species, all named by Carl Linnaeus, exist in sympatry along the southeastern Atlantic coast of the United States. Yucca gloriosa was found to share a chloroplast haplotype with Y. aloifolia in all populations sampled. In contrast, nuclear gene‐based microsatellite markers in Y. gloriosa are shared with both parents. The hybrid origin of Y. gloriosa is supported by multilocus analyses of the nuclear microsatellite markers including principal coordinates analysis (PCO), maximum‐likelihood hybrid index scoring (HINDEX), and Bayesian cluster analysis (STRUCTURE). The putative parental species share only one allele at a single locus, suggesting there is little to no introgressive gene flow occurring between these species and Y. gloriosa. At the same time, diagnostic markers are segregating in Y. gloriosa populations. Lack of variation in the chloroplast of Y. aloifolia, the putative maternal parent, makes it difficult to rule out multiple hybrid origins of Y. gloriosa, but allelic variation at nuclear loci can be explained by a single hybrid origin of Y. gloriosa. Overall, these data provide strong support for the homoploid hybrid origin of Y. gloriosa.     

Phylogenetic and evolutionary insights into the Saxifraga pentadactylis complex (Saxifragaceae): variation in nrITS sequences

Variation in nrlTS sequences among seven members of a seemingly natural group of Saxifraga (the S. pentadactylis complex; series Pentadactyles ) is phylogenetically analyzed. The two most parsimonious trees indicate that the S. pentadactylis complex is not a monophyletic group, because 5. intricata is excluded and is most closely related to S. exarata (series Cespitosae ). A well-defined lineage includes, however, six of the seven members of the S. pentadactylis complex. The tree topology suggests that this remaining group of six taxa may have diverged in the northeastern part of the Iberian Peninsula. Two sublineages can be identified from the ITS phylogenetic reconstruction: S. losae-S.moncayensis and the three subspecies of S. pentadactylis (subspp. pentadactylis, willkommiana , and almanzorii ). The relationships between S. losae and S. moncayensis provide an example of north-south speciation along the Sistema Ibérico mountain range. The three subspecies of S. pentadactylis form a monophyletic group resolved into one clade containing subspp. willkommiana and almanzorii , sister to subsp. pentadactylis. The molecular evidence agrees with chorological, cytotaxonomical, chemosystematic, and reproductive data indicating two differentiation patterns within S. pentadactylis. Transition to predominant autogamy in subsp. almanzorii probably resulted in rapid reproductive isolation from the outcrossing subsp. willkommiana in part of the Sistema Central mountain range, as suggested by their two distinct floral types but similar ITS sequences. Allopatric separation of populations of subsp. willkommiana from subsp. pentadactylis (the Pyrenees) has resulted in molecular divergence and some morphological differentiation.     

Phylogenetic relationships and biogeographic history of the unique Saxifraga sect. Irregulares (Saxifragaceae) from eastern Asia

Saxifraga L. is the largest genus in Saxifragaceae and a characteristic component of the herbaceous flora of the temperate and alpine mountains in the Northern Hemisphere. Section Irregulares is a small group of 15–20 species, representing one of the early‐diverged lineages in the genus characterized with unique zygomorphic flowers. We used both nuclear internal transcribed spacer and chloroplast DNA regions (psbA‐trnH, trnL‐F, and matK) to reconstruct its species relationships, estimate divergence times, and infer its historical biogeography. Our phylogenetic results corroborate the monophyly of sect. Irregulares and its sister relationship to sect. Heterisia from North America. The section was well resolved into two lineages corresponding to their morphological features and biogeographic distributions. One represents ser. Stoloniferae including S. stolonifera Curtis and S. nipponica Makino with long‐creeping stolons/rhizomes and small petals with spots and the other comprises the remaining taxa (ser. Rufescentes) which lack long‐creeping rhizomes. Spots on leaves (abaxially spotted vs. abaxially without spots) and spots on petals (without spots vs. with spots) are inferred to be phylogenetically informative within ser. Rufescentes. Divergence time estimates and ancestral area analysis suggested a western North American origin of sect. Irregulares with migration into East Asia by way of the Bering land bridge in the Middle Oligocene. The development of drying and desertification belt in the late Miocene could have played an important role in the subsequent restriction and separation of the north and south lineages within eastern Asia.     

Allometry and chromosomal speciation of the casiraguas Proechimys (Mammalia, Rodentia)

Morphometric characters (linear measurements) of the skull and mandible of the rodent Proechimys occurring in Venezuela and Columbia were investigated through multivariate techniques in order to describe static allometry and to relate allometric patterns to the recent evolution of these taxa. At least five species originated during the recent Pleistocene period in the upper Orinoco basin, all characterized by different karyotypes, one of them (P. guairae) being a Rassenkreis of karyomorphs. Species are characterized by unique static allometric patterns and the study of these patterns suggests a phylogenetic rather than an ecogenetic origin for these patterns; modifications in the shape of the skull and the mandible have originated during phyletic speciation and there is no apparent sign of functional adaptation.     

Evidence of hybrid speciation in the North American primroses Primula suffrutescensP. parryiP. rusbyi and P. angustifolia (Primulaceae)

The genetic structure of tetraploid (4x = 44) North American species of Primula subgenus Auriculastrum: P. suffrutescens, P. parryi, P. rusbyi, and P. angustifolia was analyzed at seven enzyme loci and compared with that of the related diploid P. cuneifolia and P. nipponica. The studied tetraploid species showed fixed or almost fixed heterozygosity at various loci, indicating a hybrid origin. About half of their alleles were shared with Cuneifolia taxa sampled, suggesting that they arose from crosses involving a maternal Cuneifolia-like ancestor. A preliminary survey of their possible paternal species, as inferred from their genotypes, was carried out among different Primula groups. Several paternal alleles expected were observed in subgenus Aleuritia, particularly among taxa of sect. Crystallophlomis (e.g., P. chionantha, P. minor, and P. nivalis xanthobasis). However, none of these taxa proved to be a suitable paternal species. Hybridization events that originated P. suffrutescens, P. parryi, P. rusbyi, and P. angustifolia presumably occurred during Pleistocene secondary contacts in Beringia and involved a maternal Cuneifolia-like ancestor and at least two paternal species, for sect. Suffrutescens and Parryi, respectively. Further studies, involving a genetic survey of Aleuritia taxa from Siberia will be needed to detect such paternal species, if not extinct.     

Phyletic hot spots for B chromosomes in angiosperms

We determined whether supernumerary B chromosomes were nonrandomly distributed among major angiosperm lineages and among lineages within families, as well as the identity of lineages with unusually high B-chromosome frequencies (hot spots). The incidence of B chromosomes for each taxon was gathered from databases showing species with and without these chromosomes (among species with known chromosome numbers). Heterogeneity was found at all ranks above the species level. About 8% of monocots had B chromosomes versus 3% for eudicots; they were rare in nonmonocot basal angiosperms. Significant heterogeneity in B-chromosome frequency occurred among related orders, families within orders, and major taxa within families. There were many B-chromosome hot spots, including Liliales and Commelinales at the order level. At the family level, there was a trend suggesting that B-chromosome frequencies are positively correlated with genome size.     

On the gynodioecious polymorphism in Saxifraga granulata L. (Saxifragaceae)

Sexual and vegetative fitness components in hermaphrodite and female plants of the self-compatible, perennial herb Saxifraga granulata are compared using material derived from a gynodioecious population in northern England.
Females produced only 57% as many seeds as hermaphrodites, but their ovule offspring were 1.28 times as fit as those of hermaphrodites, and females were more vegetatively vigorous. The advantages to females in ovule offspring quality and in vegetative reproduction counteract their disadvantages in pollen and seed production and therefore probably play a role in the maintenance of the gynodioecious polymorphism. Pollination ecology, resource reallocation and inbreeding depression all appear to contribute to the observed sex differences in fitness.     

Phylogenetic and molecular evidence for allochronic speciation in gall-forming aphids (Pemphigus)

Sympatric populations can diverge when variation in phenology or life cycle causes them to mate at distinctly different times. We report patterns consistent with this process (allochronic speciation) in North American gall-forming aphids, in the absence of a host or habitat shift. Pemphigus populi-transversus Riley and P. obesinymphae Aoki form a monophyletic clade within the North American Pemphigus group. They are sympatric on the eastern cottonwood, Populus deltoides (Salicaceae), but have distinctly different life cycles, with sexual stages offset by approximately six months. Field evidence indicates that intermediate phenotypes do not commonly occur, and mitochondrial and bacterial endosymbiont DNA sequences show no maternal gene flow between the two species. Because a genetically distinct population of P. obesinymphae occurs in the southwestern United States on Populus fremontii, we consider the possibility of an initial allopatric phase in the divergence. We discuss the likely origins of the host use patterns in P. obesinymphae, and the larger sequence of evolutionary changes that likely led to the sympatric divergence of P. populi-transversus and P. obesinymphae. A plausible interpretation at this stage of investigation is that a shift in timing of the life cycle in an ancestral population, correlated with an underlying phenological complexity in its host plant, spurred divergence between the incipient species.     

Molecular genetic and quantitative trait divergence associated with recent homoploid hybrid speciation: a study of Senecio squalidus (Asteraceae)

Hybridization is increasingly seen as a trigger for rapid evolution and speciation. To quantify and qualify divergence associated with recent homoploid hybrid speciation, we compared quantitative trait (QT) and molecular genetic variation between the homoploid hybrid species Senecio squalidus and its parental species, S. aethnensis and S. chrysanthemifolius, and also their naturally occurring Sicilian hybrids. S. squalidus originated and became invasive in the United Kingdom following the introduction of hybrid plants from Mount Etna, Sicily, about 300 years ago. We recorded considerable molecular genetic differentiation between S. squalidus and its parents and their Sicilian hybrids in terms of both reduced genetic diversity and altered allele frequencies, potentially due to the genetic bottleneck associated with introduction to the United Kingdom. S. squalidus is also distinct from its parents and Sicilian hybrids for QTs, but less so than for molecular genetic markers. We suggest that this is due to resilience of polygenic QTs to changes in allele frequency or lack of selection for hybrid niche divergence in geographic isolation. While S. squalidus is intermediate or parental-like for most QTs, some trangressively distinct traits were observed, which might indicate emerging local adaptation in its invasive range. This study emphasizes the important contribution of founder events and geographic isolation to successful homoploid hybrid speciation.     

Evolution of oviposition strategies and speciation in the globeflower flies Chiastocheta spp. (Anthomyiidae)

Trollius europaeus (Ranunculaceae) is involved in an intimate interaction with several species of Chiastocheta flies (Anthomyiidae) that are both seed predators and pollinators. In this paper, we analyse the oviposition strategy of the six Chiastocheta species found to coexist on T. europaeus in 19 populations from the French Alps. We show that the species are not equivalent in their oviposition behaviour: C. rotundiventris usually deposits no more than one egg per flower in first-day flowers whereas C. dentifera aggregates its eggs on fruits and thus does not contribute to pollination at all; the four remaining species deposit eggs sequentially during the flowering period from the 2nd to the 7th day. Hence, the outcomes of the interaction in terms of net seed production for the plant greatly depend on the Chiastocheta species visiting it, ranging from a mutualistic to a purely parasitic interaction. We assessed mitochondrial divergence between Chiastocheta spp. by sequencing a 1320-bp mitochondrial DNA fragment. The low divergence observed between species (0–4.15%) suggests that genus diversification took place recently. Unlike in other plant–insect systems where diversification is usually thought to be driven by cospeciation or host shifts, we propose that Chiastocheta speciation took place within the host plant. Basal separation of a particularly mutualistic species provided favourable conditions for plant specialization on this seed-parasite as a pollinator early in the evolution of the association. The parasitic species ovipositing on fruits derived from a species ovipositing on flowers. Diversification of the intermediate strategies probably occurred in relation with the Pleistocene climatic events, reproductive isolation between species being reinforced by niche partitioning for oviposition and/or sexual selection.     

The promiscuous and the chaste: frequent allopolyploid speciation and its genomic consequences in American daisies (Melampodium sect. Melampodium; Asteraceae)

Polyploidy, an important factor in eukaryotic evolution, is especially abundant in angiosperms, where it often acts in concert with hybridization to produce allopolyploids. The application of molecular phylogenetic techniques has identified the origins of numerous allopolyploids, but little is known on genomic and chromosomal consequences of allopolyploidization, despite their important role in conferring divergence of allopolyploids from their parental species. Here, using several plastid and nuclear sequence markers, we clarify the origin of tetra- and hexaploids in a group of American daisies, allowing characterization of genome dynamics in polyploids compared to their diploid ancestors. All polyploid species are allopolyploids. Among the four diploid gene pools, the propensity for allopolyploidization is unevenly distributed phylogenetically with a few species apparently more prone to participate, but the underlying causes remain unclear. Polyploid genomes are characterized by differential loss of ribosomal DNA loci (5S and 35S rDNA), known hotspots of chromosomal evolution, but show genome size additivity, suggesting limited changes beyond those affecting rDNA loci or the presence of processes counterbalancing genome reduction. Patterns of rDNA sequence conversion and provenance of the lost loci are highly idiosyncratic and differ even between allopolyploids of identical parentage, indicating that allopolyploids deriving from the same lower-ploid parental species can follow different evolutionary trajectories.     

Chemotaxonomic importance of diarylheptanoids and phenylpropanoids in Saxifraga tangutica (Saxifragaceae)

A phytochemical investigation of Saxifraga tangutica led to the isolation of 11 compounds, including eight diarylheptanoids (1–6, 10 and 11) and three phenylpropanoids (7–9). The chemical structures were established by extensive analysis of their MS and NMR spectroscopic data or comparison with literature data. In the present research, we report the isolated compounds 1–11, for the first time, in the species S. tangutica. Moreover, compounds 1, 2 and 4–11 have not been reported from any species in Saxifragaceae family. Furthermore, we discuss the chemotaxonomic significance of the isolated compounds.