Hybridity as a main evolutionary force in the genus Gagea Salisb. (Liliaceae)

Abstract

The important role of hybridity in the evolution of the genus Gagea is becoming clear, through morphological, karyological and molecular evidences. Several species were recently inferred or hypothesized to be of hybrid origin; especially in sect. Didymobulbos, sect. Fistulosae and sect. Gagea. Representative case studies, such as G. luberonensis J.-M. Tison, G. polidorii J.-M. Tison and G. pomeranica Ruthe, are presented and discussed.

Since many Gagea species show very reduced or null sexual reproduction vs. a massive vegetative propagation, there are several problems in distinguishing hybrids from hybridogenous species in this genus. The actual trend is to consider them at specific level because of their ability to stabilize, at least through vegetative propagation by bulblets and/or bulbils.     

Hybridization drives speciation in Gagea (Liliaceae)

Hybridization seems to play an important role in speciation of Gagea Salisb., a genus which is characterised by polyploid taxa lines and in which diploids (2n = 24) appear only to be common in basal sections. Hybrid detection was applied utilising direct and cloning nrDNA ITS data (ITS1, 5.8S rDNA, ITS2) combined with neighbour and ribotype networks and discussed in connection with previously published cpDNA, morphological and karyological data of the authors. We have evidence of the hybrid origin of taxa within the section Gagea (G. pomeranica, G. megapolitana) and the monophyletic clade of sections Didymobulbos and Fistulosae (G. microfistulosa, G. polidorii, G. cf. bohemica). Morphologically and karyologically differentiated Gagea megapolitana and G. pomeranica, adapted to synanthropic habitats, represent both hybrids of G. pratensis × G. lutea. Gagea microfistulosa represents a hybrid of G. villosa × G. fragifera; Gagea polidorii could represent the reverse hybrid. G. glacialis is also closely related to the latter complex.     

Morphological and molecular investigations of <Emphasis Type="Italic">Gagea</Emphasis> (Liliaceae) in southeastern Kazakhstan with special reference to putative altitudinal hybrid zones

The most important center of speciation in the genus Gagea is thought to be in Central Asia. Here, we focus on species diversity in southeastern Kazakhstan (around Almaty, Ili-Alatau range of the Western Tian-Shan mountains). We studied an elevational transect, reaching from lowland steppes to the alpine zone (500–2750 m a. s. l.), and carried out detailed morphological and molecular investigations for populations of Gagea spp. Nine species were identified in different altitudinal zones; one of these (Gagea almaatensis) is described as new to science. We could detect two altitudinal contact zones between closely related species: G. filiformis and G. granulosa (sect. Minimae), and G. almaatensis and G. kuraminica (sect. Gagea). Morphological and molecular investigations (ITS data and cpDNA networks) indicate ongoing hybridization of co-occurring G. filiformis into G. granulosa and putative bidirectional hybridization events between G. almaatensis and G. kuraminica.     

A molecular phylogeny of the genus Gagea (Liliaceae) in Germany inferred from non-coding chloroplast and nuclear DNA sequences

The systematics of the mainly yellow flowered Gagea species complex (Liliaceae) has long been considered difficult because only a few phenotypic features within this genus and as a result of hypothesized interspecific hybridisation. A molecular phylogenetic study of seven Gagea species (G. bohemica, G. lutea, G. minima, G. pomeranica, G. pratenis, G. spathacea and G. villosa) from Germany has been undertaken, based on plastid DNA sequences (trnL(UAA)-trnF(GAA), psbA-trnH) and on the nuclear ribosomal internal transcribed spacer (ITS). Sequence divergence within the Gagea species ranges up to 15.5% for psbA-trnH, 22.0% for trnL-trnF and 23.7% for ITS (ITS1 + 5.8S rRNA + ITS2). Two subspecies of Gagea bohemica: G. bohemica subsp. saxatilis and G. bohemica subsp. bohemica are characterized by trnL-trnF data and morphological features. Analysis of the ITS region shows that G. pomeranica represents a hybrid of G. pratensis and G. lutea. Lloydia serotina was initially used as an outgroup species, but it was placed within the investigated Gagea species in the psbA-trnH and the trnL-trnF phylogenetic tree.     

Cladistic relationships of extant and fossil hominoids

There is general agreement that the hominoid primates form a monophyletic group, that the extant great apes and humans form a second clade within that group with the gibbons as the sister group, and that the African apes and humans form a third clade. Although it has recently been proposed that humans and orang utans are sister taxa and also that the great apes form a clade to the exclusion of humans, our analysis, particularly of the molecular evidence, supports the existence of an African ape and human clade. The major problem in hominoid phylogeny at present is the relationships of the species within this clade: morphological data generally support the existence of an African ape clade which is the sister group to humans; some molecular data also support this conclusion, but most molecular evidence indicates the existence of a chimpanzee/human clade. We have cladistically re-analysed the DNA and protein sequence data for which apomorphic character states can be assessed. It is clear that there is a high degree of homoplasy whichever branching pattern is produced, with some characters supporting the existence of a chimpanzee/human clade and others supporting an African ape clade. When the cladistic analyses of morphological and molecular data are combined we believe that the most parsimonious interpretation of the data is that the African apes form a clade which is the sister taxon of the human (i.e., Australopithecus, Homo and Paranthropus) clade.This paper is not intended as a survey of all hominoid fossils but as a study of branching points in hominoid evolution and fossils are included which are relevant to this branching pattern. The analysis of fossil taxa in this study leads us to conclude that Proconsul is the sister taxon to the later Hominoidea. A number of middle Miocene forms such as Dryopithecus, Kenyapithecus, Heliopithecus and Afropithecus are shown to share derived characters with great apes and humans and provide evidence for the divergence of that clade from the gibbon lineage prior to 18 Ma. The position that Sivapithecus represents the sister group of the orang utan clade is supported here and shows that the orang utan lineage had diverged from the African ape and human lineage prior to 11·5 Ma. There is unfortunately no definitive fossil cvidence on branching sequences within the African ape and human clade, although a new specimen from Samburu, Kenya may be related to the gorilla.     

Two newly recognized species of Hemidactylus (Squamata,Gekkonidae) from the Arabian Peninsula?and Sinai,Egypt

A recent molecular phylogeny of the Arid clade of the genus Hemidactylus revealed that the recently described H. saba and two unnamed Hemidactylus species from Sinai, Saudi Arabia and Yemen form a well-supported monophyletic group within the Arabian radiation of the genus. The name ‘Hemidactylus saba species group’ is suggested for this clade. According to the results of morphological comparisons and the molecular analyses using two mitochondrial (12S and cytb) and four nuclear (cmos, mc1r, rag1, rag2) genes, the name Hemidactylus granosus Heyden, 1827 is resurrected from the synonymy of H. turcicus for the Sinai and Saudi Arabian species. The third species of this group from Yemen is described formally as a new species H. ulii sp. n. The phylogenetic relationships of the members of ‘Hemidactylus saba species group’ are evaluated and the distribution and ecology of individual species are discussed.     

Phylogenetic Relationships of a Distinct Species of Globodera from Portugal and Two Punctodera Species

Evolutionary relationships based on ribosomal DNA (rDNA) sequence data for a previously unknown species of Globodera from Portugal, Punctodera chalcoensis from Mexico, and P. punctata from Estonia, plus previously published sequences, support the following relationships: (((Cactodera weissi, G. artemisiae, C. milleri), ((G. sp. Bouro, G. sp. Canha, G. sp. Ladoeiro), ((G. pallida, G. rostochiensis), (P. chalcoensis, P. punctata)))), Heterodera avenae). Globodera sp. from Portugal, which can be confused with potato cyst nematodes by phytosanitary services when the identification is based only on morphological characters, is clearly different based on our molecular data. In addition, the rDNA data show the Globodera sp. to be only distantly related to other European Globodera species that parasitize Asteraceae. Punctodera chalcoensis and P. punctata form a sister clade to the G. pallida + G. rostochiensis clade.     

Euptychia boulleti (Le Cerf) n. comb. (Lepidoptera: Nymphalidae: Satyrinae), a Rare and Endangered Butterfly from Southeastern Brazil

This paper discusses the systematic position of the rare and endangered satyrine butterfly Caenoptychia boulleti Le Cerf, the only included species in Caenoptychia (type species), based on adult morphology and molecular data. The results showed that Caenoptychia Le Cerf belongs to the Euptychia Hübner clade, and the genus is synonymized with Euptychia, new synonymy. Euptychia boulleti (Le Cerf) is a new combination. The male genitalia of E. boulleti showed at least one important synapomorphy with the other species of Euptychia, which is the presence of a posterior projection of the tegumen above the uncus. Molecular data reinforces the position of Caenoptychia within the genus Euptychia.     

Molecular systematics, character evolution, and pollen morphology of Cistus and Halimium (Cistaceae)

Pollen analysis and parsimony-based phylogenetic analyses of the genera Cistus and Halimium, two Mediterranean shrubs typical of Mediterranean vegetation, were undertaken, on the basis of cpDNA sequence data from the trnL-trnF, and trnS-trnG regions, to evaluate limits between the genera. Neither of the two genera examined formed a monophyletic group. Several monophyletic clades were recognized for the ingroup. (1) The ??white and whitish pink Cistus??, where most of the Cistus sections were present, with very diverse pollen ornamentations ranging from striato-reticulate to largely reticulate, sometimes with supratectal elements; (2) The ??purple pink Cistus?? clade grouping all the species with purple pink flowers belonging to the Macrostylia and Cistus sections, with rugulate or microreticulate pollen. Within this clade, the pink-flowered endemic Canarian species formed a monophyletic group, but with weak support. (3) Three Halimium clades were recovered, each with 100% bootstrap support; all Halimium species had striato-reticulate pollen. Two Halimium clades were characterized by yellow flowers, and the other by white flowers.     

Molecular phylogeny of Plumbaginaceae with emphasis on Acantholimon Boiss. based on nuclear and plastid DNA sequences in Iran

The present study represents phylogenetic analyses of Plumbaginaceae with emphasis on Acantholimon from Iran using nrDNA ITS and plastid trnY-T sequences. The analyses support the monophyly and the close relationship of Limonium, Armeria and Psylliostachys. This is the first report of the close relationship between Acantholimon and Cephalorhizum. The data for the position of Cephalorhizum is unclear. The Shimodaira–Hasegawa test of nrDNA ITS and the combined datasets indicated that Acantholimon and Cephalorhizum are distinct genera. The molecular data revealed that the traditionally recognized multi-specific Acantholimon sections (Acantholimon, Acmostegia, Glumaria, Microstegia, Staticopsis and Tragacanthina) are not monophyletic. Their members are intermixed with each other and scattered across the Acantholimon clade, but the smaller sections including Platystegia and Pterostegia, each comprising two species, are monophyletic.     

Phellinus castanopsidis sp. nov. (Hymenochaetaceae) from southern China, with preliminary phylogeny based on rDNA sequences

Phellinus castanopsidis sp. nov. is described and illustrated from southern China. This species is characterized by resupinate, annual basidiomata, a dimitic hyphal system, hooked hymenial setae, and ovoid to broadly ellipsoid basidiospores that are colorless, thick-walled, weakly dextrinoid, and moderately cyanophilous. Most of these morphological features are shared by Fomitiporia ellipsoidea, P. gabonensis, and P. caribaeo-quercicolus, although in the two latter species, the basidiospores are not dextrinoid. In a phylogenetic perspective, parsimony inferences based on LSU and ITS DNA sequence data show that these four species are closely related, forming a monophyletic clade. Furthermore, this clade is more closely related to the Phellinus ignarius clade (Phellinus s.s.) than to the Fomitiporia clade. Hence, F. ellipsoidea is transferred to Phellinus, and a new combination P. ellipsoideus is proposed also.     

Phylogenetic estimation of Sciaenidae in the East China Sea inferred from nuclear EPIC DNA sequence variation

Here we describe a phylogenetic analysis of sciaenids of the East China Sea based on nuclear exon-primed intron-crossing genes (EPIC markers) and a mitochondrial gene (CO1). Separate analyses of the two data partitions resulted in mostly congruent trees. Although there were some differences in the classification of these species, the main difference between trees obtained by the mitochondrial gene (CO1) and nuclear DNA sequences was the position of Miichthys miiuy and Johnius belangerii. In the mitochondrial phylogeny, Johnius belangerii was placed at the most basal position forming an individual clade, while other species formed another large cluster. Miichthys miiuy formed an independent basal sub-clade grouped with Larimichthys and Collichthys. Collichthys lucidus was grouped with Larimichthys crocea and Larimichthys polyactis. Trees based on the nuclear genes differed somewhat from those based on the CO1 mitochondrial gene. In this analysis, two groups resulted, the Larimichthys and Collichthys clade, and another clade including a total of five species: Johnius belangerii, Nibea albiflora, Pennahia argentata, Sciaenops ocellatus, and Argyrosomus japonicus; Johnius belangerii clustered with Nibea albiflora. Miichthys miiuy was placed at the basal position of the other cluster because it was an independent basal sub-clade grouped with Johnius belangerii, Nibea albiflora, Pennahia argentata, Sciaenops ocellatus, and Argyrosomus japonicus. Many aspects of the phylogeny of the Sciaenidae remain unresolved, and further analysis based on more molecular information and extensive taxon sampling is necessary to elucidate the phylogenetic relationships among the major lineages within Sciaenidae.     

Molecular phylogeny and host use evolution of the genus Exorista Meigen (Diptera: Tachinidae)

Members of the genus Exorista are parasitoids of a diverse array of insect hosts in the orders, Lepidoptera, Hymenoptera, Mantodea and Orthoptera. Phylogenetic relationships among subgenera and species of Exorista were inferred using four nuclear (Tpi, white, 18S and 28S) and four mitochondrial DNA (16S, 12S, ND5 and CO1) genes in maximum parsimony (MP), maximum likelihood (ML) and Bayesian Markov chain Monte Carlo (MCMC) analyses. Separate trees based on different sets of genes (mt DNA, nuclear, ribosomal, etc.) were compared and found to be nearly concordant. According to the molecular tree generated from the concatenated sequence data, the genus Exorista is paraphyletic. The phylogenetic analyses indicate the existence of two major clades of Exorista, including two genera Parasetigena and Phorocera. Morphological traits supporting clades indicated by molecular analyses within this genus are evaluated. Evolutionary patterns of the host use and host shifts are examined by optimizing host information using maximum likelihood on the molecular phylogeny. The ancestral host group of the tribe Exoristini (excluding Ctenophorinia and Phorinia) appears to be the order Lepidoptera, although hosts of some species are unknown. A major host shift to the Hymenoptera occurred in the clade of subgenus Adenia, and the ancestral state of subgenus Spixomyia is equivocal because there is little information available on the hosts in members of a subclade of this group (subclade A: Exorista hyalipennis group).     

Hoffmannoscypha, a novel genus of brightly coloured, cupulate Pyronemataceae closely related to Tricharina and Geopora

The rare apothecial, cupulate fungus Geopora pellita (Pyronemataceae) is characterized by a uniquely bright yellow-orange excipulum. We here re-examine its affiliations by use of morphological, molecular phylogenetic and ultrastructural analyses. G. pellita appears as phylogenetically rather isolated, being the sister group of a clade comprising Phaeangium, Picoa, the majority of the Tricharina species, and the remaining Geopora species. Based on its phylogenetic position and its unique combination of morphological characters, we assign G. pellita to Hoffmannoscypha, gen. nov., as H. pellita, comb. nov. As in a previous study, analyses of both large subunit (LSU) and internal transcribed spacer (ITS) ribosomal DNA suggest that the remaining genus Geopora is paraphyletic, with the hypogeous, ptychothecial type species more closely related to Picoa and Phaeangium than to the greyish-brownish cupulate and apothecial Geopora spp., indicating that the latter should be reassigned to the genus Sepultaria. The current study also shows that ITS confirm LSU data regarding the polyphyly of Tricharina.     

MOLECULAR PHYLOGENY OF GRACILARIA SPECIES INFERRED FROM MOLECULAR MARKERS BELONGING TO THREE DIFFERENT GENOMES1

The nucleotide sequence data of molecular markers 18S rRNA, RUBISCO spacer, and cox2‐3 intergenic spacer were integrated to infer the phylogeny of Gracilaria species, collected from the western coast of India, reducing the possibility of misidentification and providing greater phylogenetic resolution. A phylogenetic tree was constructed using cox2‐3 and RUBISCO spacer sequences, exhibiting the same clustering but differing slightly from that of the rRNA‐based phylogenetic tree. The phylogeny inferred from the combined data set confers an analogous pattern of clustering, compared with those of trees constructed from individual data sets. The combined data set resulted in a phylogeny with better resolution, which supported the clade with higher consistency index, retention index, and bootstrap values. It was observed that Gracilaria foliifera (Forssk.) Børgesen is closer to G. corticata (J. Agardh) J. Agardh varieties, while G. salicornia (C. Agardh) E. Y. Dawson and G. fergusonii J. Agardh both originated from the same clade. The position of G. textorii (Suringar) De Toni faltered and toppled between G. salicornia and G. dura (C. Agardh) J. Agardh; however, G. gracilis (Stackh.) M. Steentoft, L. M. Irvine et W. F. Farnham was evidently distant from the rest of the species.     

Molecular Phylogeny of Asian Meconopsis Based on Nuclear Ribosomal and Chloroplast DNA Sequence Data

The taxonomy and phylogeny of Asian Meconopsis (Himalayan blue poppy) remain largely unresolved. We used the internal transcribed spacer (ITS) region of nuclear ribosomal DNA (nrDNA) and the chloroplast DNA (cpDNA) trnL-F region for phylogenetic reconstruction of Meconopsis and its close relatives Papaver, Roemeria, and Stylomecon. We identified five main clades, which were well-supported in the gene trees reconstructed with the nrDNA ITS and cpDNA trnL-F sequences. We found that 41 species of Asian Meconopsis did not constitute a monophyletic clade, but formed two solid clades (I and V) separated in the phylogenetic tree by three clades (II, III and IV) of Papaver and its allies. Clade V includes only four Asian Meconopsis species, with the remaining 90 percent of Asian species included in clade I. In this core Asian Meconopsis clade, five subclades (Ia–Ie) were recognized in the nrDNA ITS tree. Three species (Meconopsis discigera, M. pinnatifolia, and M. torquata) of subgenus Discogyne were imbedded in subclade Ia, indicating that the present definition of subgenera in Meconopsis should be rejected. These subclades are inconsistent with any series or sections of the present classifications, suggesting that classifications of the genus should be completely revised. Finally, proposals for further revision of the genus Meconopsis were put forward based on molecular, morphological, and biogeographical evidences.