Phylogenetic analyses of 18s rdna sequences reveal a new coccoid lineage of the prasinophyceae (Chlorophyta)

Phylogenetic analyses of 18S rDNA sequences from 25 prasinophytes, including 10 coccoid isolates, reveals that coccoid organisms are found in at least three prasinophyte lineages. The coccoid Ostreococcus tauri is included in the Mamiellales lineage and P ycnococcus provasolii is allied with the flagellate P seudoscourfieldia marina. A previously undescribed prasinophyte lineage is comprised of the coccoid Prasinococcus cf. capsulatus (CCMP 1407) and other isolates tentatively identified as Prasinococcus sp. (CCMP 1202, CCMP 1614, and CCMP 1194), as well as three unnamed coccoids (CCMP 1193, CCMP 1413, and CCMP 1220). No flagellate organisms are known from this lineage. Organisms of this new lineage share some characteristics of both the Pycnococcaceae and the Mamiellales, although relationships among these separate lineages were not supported by bootstrap analyses. An additional unnamed coccoid isolate (CCMP 1205) is separate from all major prasinophyte lineages. The analyses did not resolve the relationships among the major prasinophyte lineages, although they support previous conclusions that the Prasinophyceae are not monophyletic.     

Pollination system of the Pilosocereus leucocephalus columnar cactus (tribe Cereeae) in eastern Mexico

It has been suggested that there is a geographic dichotomy in the pollination systems of chiropterophilous columnar cacti: in intra‐tropical areas they are pollinated almost exclusively by bats, whereas in extratropical areas they are pollinated by bats, birds and bees. However, currently the studies are clumped both taxonomically (mainly Pachycereeae species) and geographically (mainly in the Tehuacan Valley and the Sonoran Desert). This clumping limits the possibility of generalising the pattern to other regions or cactus tribes. Only four of the 36 chiropterophilous cacti in Pilosocereus have been studied. Despite the tropical distribution of two Pilosocereus species, bees account for 40–100% of their fruit set. We examined how specialised is the pollination system of P. leucocephalus in eastern Mexico. As we studied tropical populations, we expected a bat‐specialised pollination system. However, previous studies of Pilosocereus suggest that a generalised pollination system is also possible. We found that this cactus is mainly bat‐pollinated (bats account for 33–65% of fruit set); although to a lesser degree, diurnal visitors also caused some fruit set (7–15%). Diurnal visitors were more effective in populations containing honeybee hives. P. leucocephalus is partially self‐compatible (14–18% of fructification) but unable to set fruit without visitors. Despite the variation in pollination system, P. leucocephalus shows more affinity with other columnar cacti from tropical regions than with those from extratropical regions. Although we report here that a new species of tropical Pilosocereus is relatively bat‐specialised, this Cereeae genus is more flexible in its pollination system than the Pachycereeae genera.     

Cross-species amplification of microsatellites reveals incongruence in the molecular variation and taxonomic limits of the Pilosocereus aurisetus group (Cactaceae)

The Pilosocereus aurisetus group contains eight cactus species restricted to xeric habitats in eastern and central Brazil that have an archipelago-like distribution. In this study, 5–11 microsatellite markers previously designed for Pilosocereus machrisii were evaluated for cross-amplification and polymorphisms in ten populations from six species of the P. aurisetus group. The genotypic information was subsequently used to investigate the genetic relationships between the individuals, populations, and species analyzed. Only the Pmac101 locus failed to amplify in all of the six analyzed species, resulting in an 88?% success rate. The number of alleles per polymorphic locus ranged from 2 to 12, and the most successfully amplified loci showed at least one population with a larger number of alleles than were reported in the source species. The population relationships revealed clear genetic clustering in a neighbor-joining tree that was partially incongruent with the taxonomic limits between the P. aurisetus and P. machrisii species, a fact which parallels the problematic taxonomy of the P. aurisetus group. A Bayesian clustering analysis of the individual genotypes confirmed the observed taxonomic incongruence. These microsatellite markers provide a valuable resource for facilitating large-scale genetic studies on population structures, systematics and evolutionary history in this group.     

Phylogenetic systematics of Erythronium (Liliaceae): morphological and molecular analyses

For a nearly complete set of species of Erythronium (Liliaceae), we examined two plastid loci (the rps16 intron and the 5′ trnK intron, excluding the matK exon), one nuclear locus (nrITS) and morphology to evaluate species relationships and that of Erythronium to Amana, the putatively most closely allied genus. A matrix of morphological characters was developed through observation of around 900 living and herbarium specimens; evolution of these was examined using character optimization on the combined (total‐evidence) tree. Parsimony methods were used to examine the morphological and molecular data sets produced, both separately and in combination, with Bayesian methods also used on the molecular data sets. These established that the genus is probably sister to Amana (although most analyses placed Amana inside Erythronium) and that Tulipa is sister to the pair of Erythronium and Amana. Within Erythronium, there are three strongly supported geographically distinct clades: (1) Eurasian and (2) eastern and (3) western North American. Separation of species in these three clades is less clear, particularly among the western North American taxa. © 2012 The Linnean Society of London, Botanical Journal of the Linnean Society, 2012, ●●, ●●–●●.     

Phylogenetic analysis based on structural and combined analyses of Rhus s.s. (Anacardiaceae)

Structural data were combined with trnL‐F and internal transcribed spacer sequences from other studies and with new sequences representing ten additional species to clarify the phylogenetic relationships of Rhus s.s. These data indicate that Rhus s.s and both subgenera, Rhus and Lobadium, are monophyletic. The genus Rhus is supported as monophyletic by the presence of red glandular hairs on the berries and inflorescence axis, cilia on the sepals and glands on the leaf blades. Subgenus Rhus can be identified by the presence of more than seven resin channels in the petiole, weakly percurrent tertiary veins and a type I vascular system in the mid‐vein. Subgenus Lobadium is characterized by the presence of short bracteoles and pedicels. This subgenus is divided into four sections, Lobadium, Rhoeidium, Styphonia and Terebinthifolia. Section Lobadium has trifoliate leaves; section Rhoeidium is monotypic, including only Rhus microphylla; section Styphonia is supported by five synapomorphies, including an incomplete marginal vein, fibres in the petiole, a thick cuticle, two layers of palisade parenchyma and prismatic crystals in the mesophyll; and section Terebinthifolia has gelatinous xylary fibres in the petiole. Hypotheses about the evolutionary changes of these characters are presented based on the cladograms. © 2014 The Linnean Society of London, Botanical Journal of the Linnean Society, 2014, 176 , 452–468.     

Phylogeny in Echinocereus (Cactaceae) based on combined morphological and molecular evidence: taxonomic implications

Echinocereus is a morphologically diverse genus that includes 64 species grouped into eight taxonomic sections based on morphological traits. In previous molecular phylogenetic analyses, the relationships amongst Echinocereus species were not entirely revealed and useful characters to recognize clades were not provided. The inclusion of several sources of evidence in a phylogenetic analysis is likely to produce more supported hypotheses. Therefore, we performed a combined phylogenetic analysis with a set of 44 morphological characters and six chloroplast DNA sequences. Topologies from parsimony and Bayesian analyses were mostly congruent. However, the relationships of E. poselgeri were not consistent between analyses. A second Bayesian analysis using a long-branch extraction test resulted in a topology with the morphological position of E. poselgeri congruent with that in parsimony analysis. Parsimony and Bayesian analyses corroborated the monophyly of Echinocereus, which included eight monophyletic groups. The combined phylogeny integrated into different clades those taxa that were not determined in previous analyses and changed the relationships of some recognized clades. The clades did not recover the recent infrageneric classification. In the present study, a new sectional classification for Echinocereus is proposed based on the eight recovered clades, which is supported by a combination of morphological and molecular characters. An identification key for sections in the genus is included.     

Phylogenetic analyses reveal reliable morphological markers to classify mega‐diversity in Onthophagini dung beetles (Coleoptera: Scarabaeidae: Scarabaeinae)

Based largely on homoplastic characters of external morphology, the current systematics of the tribe Onthophagini and allied dung beetle lineages is unstable, contradictory, and thus inefficient. A number of recently proposed molecular phylogenies conflict strongly with each other and with formal classification, and none of them provides new tools for the improvement of dung beetle systematics. We explored the source of these inconsistencies by performing an independent, morphology‐based phylogenetic analysis of the “Serrophorus complex”, one of the most systematically confusing knots among the onthophagines, that involves 52 species from various genera of Onthophagini and allied tribes. The phylogenetic pattern revealed conflicts with existing classifications and with most of the earlier molecular phylogenies. However, it was largely congruent with the molecular phylogeny (Evolution 2005, 59 , 1060), using the largest gene sampling thus far. All current competing phylogenetic hypotheses were evaluated against each other, and the degree of their biogeographic plausibility was used as an additional evaluative criterion. Of the 91 morphological characters involved in our analyses, traits belonging to the endophallic sclerites of the aedeagus had a very strong phylogenetic signal. Terminology of these endophallic characters was established and their morphology was studied in detail, illustrated, and presented as a tool for further practical use. The enormous variety of shapes of the lamella copulatrix within the Onthophagini and allies present a methodological problem in character coding for phylogenetic analyses. Based on the performance of alternative coding approaches, it is argued that a seemingly less informative absence/presence coding scheme would be a better choice. The phylogenetic structure of the Serrophorus complex has been largely resolved, and some taxonomic changes improving its systematics are recommended.
© The Willi Hennig Society 2011.     

Phylogenetic analyses of Tolpis Adans. (Asteraceae) reveal patterns of adaptive radiation,multiple colonization and interspecific hybridization

The plant genus Tolpis (Asteraceae) has been the subject of several investigations on the evolution of oceanic island plants. Its insular species were utilized in studies of artificial hybrid fertility, testing the validity of Baker’s law, the application of DNA barcodes, and the phylogenetic utility of inter‐simple sequence repeat markers. Despite this considerable interest in Tolpis, little is known about its phylogenetic history. Past investigations were unable to resolve most of the interspecific relationships, especially within the Canary Islands, where the genus is particularly diverse. Incomplete taxon sampling, the use of ambiguous outgroups and the limited utility of slowly evolving chloroplast DNA markers precluded detailed reconstructions. The present investigation presents a comprehensive molecular phylogeny of Tolpis. By utilizing highly variable nuclear DNA markers and a comprehensive taxon set, we have resolved the majority of interspecific relationships in the genus. Evaluations of competing tree topologies and ancestral area reconstructions complemented the analyses. Our results highlight the presence of three dominant mechanisms of island plant evolution—island colonization, adaptive radiation and interspecific hybridization—in Tolpis: (i) the extant distribution of the genus is the result of two independent colonization pathways, (ii) Tolpis has colonized at least one archipelago multiple times, (iii) the present insular diversity is the product of adaptive radiation, (iv) potential hybridization was detected between species now inhabiting different islands and archipelagoes, indicating sympatric historical distributions, and (v) several undescribed species await taxonomic recognition.     

Seed germination of Pilosocereus arrabidae (Cactaceae) from a semiarid region of south‐east Brazil

We evaluated the effect of temperature regimes (six constant and four alternating temperatures), light qualities (five red : far red ratios) and water potentials (ΨW; seven NaCl and polyethylene glycol 6000 [PEG] solutions) on the percentage and germination rate, as well as the post‐seminal development morphology, that allow Pilosocereus arrabidae seeds to germinate in a hot semiarid climate on the south‐eastern Brazilian coast. The results showed that seeds germinated similarly between constant and alternating temperatures, with an optimal germination at 25/20°C and 20°C. Pilosocereus arrabidae seeds were photoblastic positive and the final germination percentage was inhibited at low red : far red ratios. Maximum germination was obtained in distilled water (0 MPa) and decreases of Ψ_W in the solutions reduced the germination, which was lower in NaCl than in iso‐osmotic PEG solutions. Germination inhibition appears to be osmotic because the recovery response was high when non‐germinated seeds from both iso‐osmotic solutions were transferred to water. Seeds of P. arrabidae are small and germination is phaneroepigeal. Despite the slow growth typically seen in seedlings and adults of Cactaceae, germination in this species depends on the ability of the seeds to appropriately sense and react to environmental cues that correlate with times and places under low‐risk growth conditions.     

Phylogenetic analyses of Andromedeae (Ericaceae subfam. Vaccinioideae)

Phylogenetic relationships within the Andromedeae and closely related taxa were investigated by means of cladistic analyses based on phenotypic (morphology, anatomy, chromosome number, and secondary chemistry) and molecular (rbcL and matK nucleotide sequences) characters. An analysis based on combined molecular and phenotypic characters indicates that the tribe is composed of two major clades—the Gaultheria group (incl. Andromeda, Chamaedaphne, Diplycosia, Gaultheria, Leucothoe¨, Pernettya, Tepuia, and Zenobia) and the Lyonia group (incl. Agarista, Craibiodendron, Lyonia, and Pieris). Andromedeae are shown to be paraphyletic in all analyses because the Vaccinieae link with some or all of the genera of the Gaultheria group. Oxydendrum is sister to the clade containing the Vaccinieae, Gaultheria group, and Lyonia group. The monophyly of Agarista, Lyonia, Pieris, and Gaultheria (incl. Pernettya) is supported, while that of Leucothoe¨ is problematic. The close relationship of Andromeda and Zenobia is novel and was strongly supported in the molecular (but not morphological) analyses. Diplycosia, Tepuia, Gaultheria, and Pernettya form a well-supported clade, which can be diagnosed by the presence of fleshy calyx lobes and methyl salicylate. Recognition of Andromedeae is not reflective of our understanding of geneological relationships and should be abandoned; the Lyonia group is formally recognized at the tribal level.     

Phylogenetic analyses reveal deeply divergent species lineages in the genus Sphaerobolus (Phallales: Basidiomycota)

Phylogenetic analyses of 27 artillery fungus (Sphaerobolus sp.) isolates were conducted to identify species boundaries in the genus Sphaerobolus. Multiple gene genealogies inferred from maximum likelihood, Bayesian, and maximum-parsimony analyses of sequence data from individual loci (mtSSU, ITS, EF 1-alpha, and LSU) and a combined dataset (mtSSU, ITS, and EF 1-alpha) concordantly indicate the existence of three deeply divergent lineages in the genus Sphaerobolus, each representing a phylogenetic species. These three phylogenetic species correspond to two known species: Sphaerobolus iowensis and Sphaerobolus stellatus, and a newly discovered species. Suprageneric phylogenetic analyses of the mtSSU and LSU datasets containing representatives of related genera of the gomphoid-phalloid clade of Homobasidiomycetes suggested that the undescribed taxon likely is more closely related to S. stellatus than to S. iowensis.     

Phylogenetic relationships among Bombycidae s.l. (Lepidoptera) based on analyses of complete mitochondrial genomes

The family Bombycidae (sensu Minet, 1994) is a diverse group of species belonging to the superfamily Bombycoidea. It is an economically important group of moth species, containing well‐known silk‐producing insects, as well as many pests of agriculture and forestry. The morphology‐based hypothesis of Minet (1994) on the composition of Bombycidae is in conflict with subsequent phylogenetic hypotheses for the superfamily based on nuclear genes. In this paper, the complete mitochondrial genomes of nine species of Bombycidae are presented for the first time. Based on these genomes, four dataset partitions and three gblocks parameter settings, phylogenetic relationships among Bombycidae were reconstructed using maximum likelihood and Bayesian inference methods. Bombycidae was confirmed as a polyphyletic group, with the traditional subfamilies Prismostictinae and Oberthueriinae forming a single well‐supported clade that is distant to Bombycinae. The phylogenetic relationships within Bombycoidea were supported as ((((Bombycinae, Sphingidae), Saturniidae), (Prismostictinae, Oberthueriinae)), Eupterotidae).     

芍药属牡丹组基于形态学证据的系统发育关系分析

对芍药属牡丹组Paeonia L.sect.Moutan DC.（全部野生种）40个居群进行了基于形态学证据的系统学分析,试图建立组内种间的系统发育关系。利用PAUP （4.0）计算机程序分别构建了建立在25个形态学性状基础上的所有研究类群的距离树（UPGMA、NJ）和最大简约树（MP）。所得树的拓扑结构基本一致,差异只发生在距离树和简约树之间,在由形态和细胞学关系都很近的5个种（牡丹P.suffruticosa、矮牡丹P.jishanensis、卵叶牡丹P.qiui、紫斑牡丹P.rockii和凤丹P.o     

Phylogenetic analysis of ecological and morphological diversification in Hispaniolan trunk-ground anoles (Anolis cybotes group)

Abstract Anolis lizards in the Greater Antilles partition the structural microhabitats available at a given site into four to six distinct categories. Most microhabitat specialists, or ecomorphs, have evolved only once on each island, yet closely related species of the same ecomorph occur in different geographic macrohabitats across the island. The extent to which closely related species of the same ecomorph have diverged to adapt to different geographic macro-habitats is largely undocumented. On the island of Hispaniola, members of the Anolis cybotes species group belong to the trunk-ground ecomorph category. Despite evolutionary stability of their trunk-ground microhabitat, populations of the A. cybotes group have undergone an evolutionary radiation associated with geographically distinct macrohabitats. A combined phylogeographic and morphometric study of this group reveals a strong association between macrohabitat type and morphology independent of phylogeny. This association results from long-term morphological evolutionary stasis in populations associated with mesic-forest environments ( A. c. cybotes and A. marcanoi ) and predictable morphometric changes associated with entry into new macrohabitat types (i.e., xeric forests, high-altitude pine forest, rock outcrops). Phylogeographic analysis of 73 new mitochondrial DNA sequences (1921 aligned sites) sampled from 68 geographic populations representing 12 recognized species and subspecies diagnoses 16 allopatric or parapatric groupings of populations differing from each other by 5–18% sequence divergence. At least some of these groupings appear to have attained species-level divergence from others. Evolutionary specialization to different macrohabitat types may be a major factor in the evolutionary diversification of Greater Antillean anoles.     

Phylogenetic origins of Lophocereus (Cactaceae) and the senita cactus-senita moth pollination mutualism

Recent ecological research has revealed that the Sonoran Desert columnar cactus Lophocereus and the pyralid moth Upiga virescens form an obligate pollination mutualism, a rare but important case of coevolution. To investigate the phylogenetic origins of this unusual pollination system, we used molecular sequence data to reconstruct the phylogeny of the four taxa within the genus Lophocereus and to determine the phylogenetic position of Lophocereus within the North American columnar cacti (tribe Pachycereeae). Our analysis included Lophocereus, six Pachycereus species, Carnegiea gigantea, and Neobuxbaumia tetetzo within the subtribe Pachycereinae, and Stenocereus thurberi as an outgroup within the Stenocereinae. Extensive screening of chloroplast and mitochondrial genomes failed to reveal sequence variation within Lophocereus. At a deeper phylogenetic level, however, we found strong support for the placement of Lophocereus within Pachycereus as sister group to the hummingbird-pollinated P. marginatus. We discuss possible hypotheses that may explain the transition from bat pollination (ancestral) to moth and hummingbird pollination in Lophocereus and P. marginatus, respectively. Additional phylogenetic analyses suggest that the genus Pachycereus should be expanded to include Lophocereus, Carnegiea, Neobuxbaumia, and perhaps other species, whereas P. hollianus may need to be excluded from this clade. Future study will be needed to test taxonomic distinctions within Lophocereus, to test for parallel cladogenesis between phylogroups within Lophocereus and Upiga, and to fully delineate the genus Pachycereus and relationships among genera in the Pachycereinae.