Divergence time analyses have become increasingly popular over the past several decades, partly due to the proliferation of molecular data, but also because of the development of methods that do not assume a strict molecular clock. In this review, I provide a brief background to the topic, then highlight several methods for “relaxing” the assumptions of a strict molecular clock. I discuss the pros and cons of many of these methods. Finally, I discuss the various techniques for incorporating fossils in molecular studies to estimate absolute ages of clades.

Aligning multiple nucleotide sequences is a prerequisite for many if not most comparative sequence analyses in evolutionary biology. These alignments are often recognized as representing the homology relations of the aligned nucleotides, but this is a necessary requirement only for phylogenetic analyses. Unfortunately, existing computer programs for sequence alignment are not based explicitly on detecting the homology of nucleotides, and so there is a notable gap in the existing bioinformatics repertoire. If homology is the goal, then current alignment procedures may be more art than science. To resolve this issue, I present a simple conceptual scheme relating the traditional criteria for homology to the features of nucleotide sequences. These relations can then be used as optimization criteria for nucleotide sequence alignments. I point out the way in which current computer programs for multiple sequence alignment relate to these criteria, noting that each of them usually implements only one criterion. This explains the apparent dissatisfaction with computerized sequence alignment in phylogenetics, as any program that truly tried to produce alignments based on homology would need to simultaneously optimize all of the criteria.

The suborder Jungermanniineae of the Jungermanniales is a major lineage of leafy liverworts, recognized in recent classifications to include 15 families. Gametophytes within the suborder are morphologically diverse, but commonly anisophyllous to distichous, usually with succubous, rarely transverse or incubuous, leaf insertions. Sporophytes are frequently, but not universally, enclosed by stemderived perigynia or coelocaules, often accompanied by perianth reduction or loss and some level of geocauly or marsupial development. We herein provide the first comprehensive molecular phylogeny of this geographically widespread suborder, using sequences generated from one nuclear (rpb2), two mitochondrial (nad1 and rps3), and seven plastid (atpB, psbA, psbT-H, rbcL, rps4, trnG and trnL) loci, sampled from 279 accessions representing 163 species in 57 genera. Ancestral states were reconstructed for 14 morphological characters generally considered taxonomically diagnostic for families in the suborder. Our phylogenetic analyses support the return of Leiomylia (=Mylia anomala) to the Myliaceae, removal of Myliaceae from the Jungermanniineae, and validation of the monogeneric suborder Myliineae subord. nov. to house it. Eighteen families are recognized within the Jungermanniineae, nine of which are monogeneric; namely, Endogemmataceae, Harpanthaceae, Gyrothyraceae, Arnelliaceae, Saccogynaceae, Geocalycaceae, Jackiellaceae, Notoscyphaceae stat. nov., and Trichotemnomaceae. The generic compositions of other families are modified as follows: Saccogynidium is transferred from Geocalycaceae to a newly named subfamily of Acrobolbaceae, Acrobolbaceae subf. Saccogynidioideae, and one other subfamily of the Acrobolbaceae is validated, Acrobolbaceae subf. Austrolophozioideae; Hygrobiella is included in Antheliaceae (previously in Cephaloziaceae or its own family); Jungermanniaceae is broadened to include Mesoptychiaceae and Delavayellaceae; Cryptocoleopsis and Nardia are transferred from Solenostomataceae to Gymnomitriaceae; Gottschelia, Herzogobryum, and Nothogymnomitrion are excluded from the Jungermanniineae; Solenostomataceae is recognized to include Solenostoma, Arctoscyphus, Cryptocolea, and Diplocolea. Additional nomenclatural changes include recognizing Horikawaella as a synonym of Solenostoma and Apomarsupella as a synonym of Gymnomitrion, establishing two new subgenera of Solenostoma, Solenostoma subg. Metasolenostoma and Solenostoma subg. Eucalyx, and transferring Jungermannia conchata to Cephalozia. Morphological character state reconstructions identify dioecious inflorescences, gametangia on leading stems, flagelliform or stoloniferous branches absent, dorsal leaf insertions not overlapping the stem midline, large underleaves, and lack of gemmae as ancestral within the Jungermanniineae. All morphological characters appear to be moderately to highly homoplasious within the suborder.

Elaphoglossum is comprised almost entirely of epiphytic species with simple and entire leaves. Elaphoglossum section Squamipedia is intriguing because four of its species have dissected leaves. To generate a phylogenetic hypothesis of the relationships among all taxa belonging to section Squamipedia, we assembled a three-locus plastid dataset that included all recognized species in the section plus taxa representing all other sections of Elaphoglossum and three bolbitidoid genera. Our results support section Squamipedia as monophyletic. The species belonging to section Squamipedia are recovered in two well supported clades. The first clade includes two species endemic to Madagascar, whereas the second includes 16 species endemic to the Neotropics. Echinulate spores are synapomophic for the Neotropical species of section Squamipedia. Other characters that characterize most species of section Squamipedia are long-creeping rhizomes and absence of phyllopodia; however, two species of section Squamipedia (E. nidusoides and E. nidiforme) have phyllopodia and short-creeping rhizomes. The four species with dissected leaves belong to different clades and had independent origins from ancestors with simple, entire leaves. Dissected leaves have evolved at least six times during the history of Elaphoglossum. Elaphoglossum lloense and E. squamipes, two species defined on the basis of morphology, are not supported by our molecular analyses, being recovered in three and two different clades, respectively.

Anticlea vaginata (Melanthiaceae) is a rare and endemic plant species restricted to hanging gardens in low-elevation desert regions of the Colorado Plateau. Its more widespread congener, A. elegans, is morphologically similar, but occurs in montane forests that encompass and extend beyond the natural range of A. vaginata. Here, we use morphometric and genetic analyses to investigate the biogeographic origin, population structure, and taxonomic classification of A. vaginata relative to A. elegans. Our results demonstrate that A. vaginata is closely related to and morphologically indistinguishable from A. elegans and likely represents remnant populations of A. elegans derived from a Pleistocene vicariance event. We conclude that A. vaginata warrants treatment as Anticlea elegans subsp. vaginata, since it exhibits a similar level of differentiation from A. elegans subsp. elegans as subsp. glaucus. Since A. vaginata occupies an ecologically unique niche, exhibits a distinct flowering period and harbors unique alleles, we suggest separate conservation management in order to protect this subspecies and its fragile habitat, which is currently threatened by climate change and the potential for groundwater development.

A new species, Alstroemeria marticorenae (Alstroemericaceae), from central Chile is described and illustrated. Diagnostic morphological characters that allow the distinction of A. marticorenae from similar taxa are presented. It differs from these in its flower shape, size, and color. The plants are small, reaching up to 35 cm tall, the flowers are pink, the upper inner tepals are rhomboidal and narrow, with a yellow stripe and a pattern of purple lines in the two upper tepals, varying from yellow to white in the basal portion; the anthers are yellow. It grows in hard, reddish soils, never in dunes. It is endemic to the Valparaíso Region of central Chile. A comparative cytological analysis of other sympatric species of Alstroemeria was conducted. The most important karyotypic characteristic for A. marticorenae is the presence of a submetacentric chromosome 3.

A new species of Pleurothallis from Valle del Cauca, Colombia, is described and illustrated. Pleurothallis ottocari is similar to the Ecuadorian P. scoparum, but differs in the widely elliptic leaf, the smaller flowers, the incurved dorsal sepal, the purplish-tinted petals, which are conspicuously curved downwards above the middle, and the basally sub-truncate lip. Brief comments are given as to the reason for not using the generic names Ancipitia and Colombiana, to which the new species would otherwise belong.

Campylocentrum insulare is a new species of Campylocentrum section Dendrophyllopsis from Santa Catarina, southern Brazil, a group of species characterised by the aphyllous condition. It is the smallest species known from this subtribe in the Neotropics, and is morphologically related to species of the Campylocentrum fasciola complex. It differs by its small size, an inflorescence and ovary that are minutely pubescent, a lip that is distinctly three-lobed, and a conic spur. A distribution map, illustrations, and an identification key that includes species of this genus from southern Brazil are provided.

A new species, Reichantha jorge-warneri, from the Atlantic plains of Nicaragua and Costa Rica is described and illustrated. The species is similar to Reichantha tonduzii, but can be distinguished by its reddish inflorescence and ovary, glabrous sepals that are stained with red at the base and are distinctly shorter, lateral sepals with parallel tails, and the trullate-acuminate apex of the lip.

Notes on the Cyrtochilum serratum alliance are presented together with the description of two new species from Colombia, C. orozcoi and C. renisepalum. Information about the ecology of the new species and their distribution maps are presented together with illustrations of their perianth segments. Taxonomic affinities of the new species are discussed.

Scelochilus schmidt-mummii, a new orchid species, is described and illustrated based on Colombian material. It is similar to S. tuerckheimii and S. stenochilus, but differs from both taxa, especially in the shape of the lip hypochile and epichile and the form of the lip appendages. A key to the identification of Colombian Scelochilus species is provided.

Rapid radiations are notoriously difficult to resolve, yet understanding phylogenetic patterns in such lineages can be useful for investigating evolutionary processes associated with bursts of speciation and morphological diversification. Here we present an expansive molecular phylogeny of Costus L. (Costaceae Nakai) with a focus on the Neotropical species within the clade, sampling 47 of the known 51 Neotropical species and including five molecular markers for phylogenetic analysis (ITS, ETS, rps16, trnL-F, and CaM). We use the phylogenetic results to investigate shifts in pollination syndrome, with the intention of addressing potential mechanisms leading to the rapid radiation documented for this clade. Our ancestral reconstruction of pollination syndrome presents the first evidence in this genus of an evolutionary toggle in pollination morphologies, demonstrating both the multiple independent evolutions of ornithophily (bird pollination) as well as reversals to melittophily (bee pollination). We show that the ornithophilous morphology has evolved at least eight times independently with four potential reversals to melittophilous morphology, and confirm prior work showing that neither pollination syndrome defines a monophyletic lineage. Based on the current distribution for the Neotropical and African species, we reconstruct the ancestral distribution of the Neotropical clade as the Pacific Coast of Mexico and Central America. Our results indicate an historic dispersal of a bee-pollinated taxon from Africa to the Pacific Coast of Mexico/Central America, with subsequent diversification leading to the evolution of a bird-pollinated floral morphology in multiple derived lineages.

Of the eight subfamilies currently recognized in Bromeliaceae, Bromelioideae is perhaps the most poorly understood. Generic circumscriptions are unclear, and an exceptionally diverse morphology coupled with an unusually low rate of sequence divergence within Bromeliaceae has made it difficult to resolve phylogenetic relationships within the subfamily. Although recent molecular studies have begun elucidating relationships among species in Bromeliaceae, most have not sampled deeply and/or broadly across Bromelioideae. The purpose of this study was to conduct a phylogenetic analysis within subfamily Bromelioideae using three chloroplast DNA regions (matK, psbA-trnH, and trnL-trnF), with the inclusion of multiple species from a broad sampling of bromelioid genera. Ochagavia, Deinacanthon, Fascicularia, Bromelia and Fernseea diverged relatively early in the history of the subfamily, with the remaining taxa being placed in a large and poorly resolved eubromelioid clade. Bromelia and Cryptanthus were found to be monophyletic, while 13 other genera were polyphyletic. Aechmea, the most morphologically diverse genus within the subfamily, was highly polyphyletic, with species distributed among 12 different lineages, with little support for subgeneric circumscriptions.

In this contribution the rediscovery of the bromeliad Dyckia excelsa in Mato Grosso do Sul state, central-western Brazil, is reported. This species was first described based on a single individual from a particular collection in 1993 with no precise locality. Illustrations and a brief discussion on the leaf anatomy of the species are provided. One additional species, Dyckia gracilis, which has been overlooked by previous authors, is included in the list of Bromeliaceae of Mato Grosso do Sul State. An updated key for Dyckia species from the region of D. excelsa is presented. The status of D. excelsa in Mato Grosso do Sul State, Brazil, is discussed, and recommendations for its conservation are offered.

Comanthera consists of 41 species grouped in two subgenera. Both subgenera are restricted to South America and include most of the species of Eriocaulaceae used commercially as everlasting plants. Molecular and morphological phylogenies have revealed the genus and both its subgenera as monophyletic, but relationships among species have yet to be investigated. The last revision of Comanthera subg. Thysanocephalus is more than one century old, and the recognition and circumscription of taxa are still poorly understood. The present work aims, therefore, to study the taxonomy of C. subg. Thysanocephalus. Herein, descriptions of the genus and subgenus are provided along with identification keys for the subgenera and species. This taxonomic treatment proposes 17 new synonyms, excludes three taxa, and designates four lectotypes. One new species, Comanthera dimera, is described and illustrated, one variety is elevated to species status, C. angustifolia, and one species is resurrected with a new combination, C. tricostata. Nine species are accepted with no sub-specific ranks, yielding a total of 35 species in the genus Comanthera. Comments on phenology, habitat, and distribution, along with diagnoses, taxonomic notes, and distribution maps are provided.

New species of the caesalpinioid legume genus Hymenaea (Detarieae s. str. clade) have not been discovered in the last 40 yr. This study describes and illustrates the striking new species Hymenaea fariana from the few known collections made in the Atlantic Forest biome of the Brazilian state of Espírito Santo. The new species has close morphological affinities to H. altissima, from which it is readily distinguished by the mainly shrubby to small tree habit and lanceolate to oblanceolate petals with a well-differentiated petal claw. An updated identification key to the Atlantic Forest species of Hymenaea is also provided.

A new species of Chamaecrista was found in the Chapada dos Veadeiros region, in the state of Goiás, Brazil, during an expedition to study the taxonomy of this genus. Chamaecrista floribunda is herein described, illustrated, and assigned to Chamaecrista sect. Absus subsect. Absus ser. Rigidulae. Comments about the ecology, distribution, and conservation status of the new species, as well as its morphological relationships, are provided. Additionally, a key to the species of Chamaecrista sect. Absus subsect. Absus ser. Rigidulae occurring in the Chapada dos Veadeiros region is presented.

During a floristic survey of Croton in montane areas of the Cerrado biome of Central Brazil, a new species, Croton gracilirameus, was discovered and is herein described, illustrated, and compared to its putative closest relatives, C. agoensis and C. catariae. The new species most likely belongs to Croton section Geiseleria due to its stellate trichomes, leaves with glands at the apex of the petiole and margins, thyrses with a brief interruption between the pistillate and staminate flowers, and pistillate flowers with valvate sepals. A key to Croton gracilirameus and allied species, a synonymization of C. chaetocalyx under C. catariae, and new occurrence records of C. arirambae are also provided.

A new species of Manihot from Brazil was discovered in the course of revising the taxonomy of species of the genus with unlobed or very shortly lobed leaves. Manihot appanii is herein described and illustrated. Its relationships with M. stricta and M. saxatilis, the morphologically most similar species, are discussed, as well as its geographical distribution and conservation status. A key to the species of Manihot with unlobed or shortly lobed leaves is also provided.

Rinorea is a pantropical genus of shrubs and small trees within the family Violaceae. The genus is particularly diverse in Africa where species are ecologically important as they are often abundant or even dominant in particular forest types and act as larval host plants for highly specialized Cymothoe butterflies. Despite their importance, species identification of African Rinorea is difficult and a taxonomic revision is needed. Previous phylogenetic studies have suggested that neotropical taxa are sister to a palaeotropical clade, with multiple independent dispersals to Madagascar, but these were based on plastid data only. We therefore present an updated phylogeny of Rinorea with increased sampling of African taxa, using plastid as well as nuclear DNA sequences. Phylogenetic relationships inferred from nuclear DNA data were generally congruent with those based on evidence from plastid haplotypes from earlier studies. Our increased taxonomic sampling also revealed previously undiscovered African Rinorea clades, some of which warrant further taxonomic study. Ancestral state reconstructions refute previous hypotheses about the evolution of morphological characters traditionally used for Rinorea infrageneric classification. In addition, some widespread species may comprise species complexes. It is clear that African Rinorea require comprehensive taxonomic revision; our contribution to understanding Rinorea infrageneric relationships will facilitate this task.

A new species, Pleurophora pulchra, is described, illustrated, and compared with the two other species of Pleurophora occurring in Brazil. Pleurophora pulchra was found on the mountain ranges Serra do Livramento, Serra do Bendó, and Serrote in Negreiros National Park, Pernambuco, Brazil, and is the second species of the genus from the Caatinga region. It differs from other Pleurophora by a combination of a sterile ventral ovary locule, an unusually enlarged floral tube, and conspicuous, relatively large red petals. A key to the species of subgenus Anisotes to which P. pulchra belongs is provided.

Dwarf mistletoes (Arceuthobium spp., Viscaceae) are ecologically and economically important parasitic flowering plants. Despite detection of morphological and host specialization differences, ribosomal DNA and plastid sequence information have not resolved genetic differentiation among the dwarf mistletoes parasitizing white pines (Pinus subgenus Strobus) in the western U. S. A. We assessed the effectiveness of integrating amplified fragment length polymorphism and morphometric analyses in the delineation of three closely related and morphologically similar species of white pine dwarf mistletoes. Using amplified fragment length polymorphism data for 995 loci, we quantified intra- and inter-specific genetic variation, tested for geographic isolation-by-distance, and visualized genetic patterns using Bayesian-based structure analyses, neighbor-joining tree reconstruction, and principal coordinate analysis ordination. A total of 19 morphological characters were also analyzed using standard statistical methods and discriminant analysis. We found that 13% of the total genetic variation (p = 0.0001) was due to among-species differences, and species were distinguished by tree and ordination plots. Species also differed in estimates of genetic diversity and differentiation, and the degree of isolation-by-distance in genetic structuring. Amplified fragment length polymorphism and morphometric analyses both demonstrated that the dwarf mistletoes examined are well-differentiated genetically and morphologically, and therefore, should be considered distinct species.

The presence of Dianthus roseoluteus Velen. species in Turkey is based on specimens collected from Antalya province. After the publication of Flora of Turkey, many specimens have been collected from Thrace (Kırklareli and Edirne provinces) that belong to this species. A comparison of the specimens collected from Antalya and Thrace revealed that they were morphologically different. The literature survey verified that the specimens collected from Thrace were Dianthus roseoluteus. The species collected from Antalya province is a new species, Dianthus macroflorus Hamzaoglu, and its description, pictures, distribution, habitat, and threatened categories are given. Its general morphology and seed micromorphology are compared with the related species, Dianthus roseoluteus. In addition to phylogenetic relationships between some closely related Dianthus species that belong to section Dentati in Turkey, Dianthus macroflorus and 13 additional Dianthus species sequences obtained from GenBank were examined with DNA sequence data from the nuclear ribosomal ITS region. These analyses were supported with morphological data.

A new, non-climbing species from the Guiana Shield is described and illustrated: Matelea graciliflora (Apocynaceae, Asclepiadeae, Gonolobinae). The new species is morphologically similar to M. herbacea and M. palustris (together the only other erect species of Gonolobinae in the Guianas), but can be differentiated by a number of characters, including perianth and corona dimensions and corolla color. A synopsis of the erect members of the Matelea palustris complex in the Guianas and northern Brazil is provided.

Swertia perennis s. l. ranges discontinuously across Eurasia to the mountains of western North America in a series of geographic isolates sometimes recognized as distinct taxa. We sequenced the chloroplast trnL intron, the trnL-trnF intergenic spacer, and the trnH-psbA spacer from 26 North American populations of S. perennis, two Altai populations, and ten outgroup taxa, and analyzed these data with previously published sequences. Combined data from trnL, trnL-trnF, and trnH-psbA yielded 11 distinct haplotypes from North America and two from the Altai. Phylogenetic analyses resolve rooted phylogenies of chloroplast lineages within North American S. perennis. In our sample, some lineages have well-characterized, non-overlapping geographic ranges. Further sampling will likely reveal additional haplotypes and polymorphism within populations or geographic areas, but this study lays a foundation for investigations of phylogenetic biogeography in S. perennis and co-distributed species.

Pedicularis is a genus of over 600 species distributed throughout tundra and alpine habitats of the Northern Hemisphere. Phylogenetic relationships of North American species to Asian species were reconstructed by sampling sequences from nuclear ribosomal internal transcribed spacer (ITS) regions and the plastid matK region of 28 North American species, collected in the field or sampled from herbarium specimens, and 134 accessions of 102 Asian and three European species, obtained from GenBank. Maximum parsimony (PAUP) and Bayesian (MrBayes) analyses of ITS and combined ITS and matK data reveal two robustly supported monophyletic North American clades derived from Asian ancestors. Biogeographic analysis (S-DIVA) suggests Asia plus Japan, the Cascade Range, or Rocky Mountains as highly probable ancestral areas without involving Beringia for one clade. In the other clade, Asia plus the Rocky Mountains is specified as the most probable ancestral area, but less probable alternatives also include Asia plus Europe, Japan, or Beringia. Once established in North America, dispersal/divergence throughout North America occurred out of Rocky Mountain and/or Cascade Range ancestral centers of distribution. Beringian and European species are derived from North American centers rather than being part of ancestral areas for North American species.

Pedaliaceae and Martyniaceae are Old World and New World families occurring primarily in arid environments with some taxa exhibiting similar adaptations to dispersal by large animals. Their taxonomic histories have also been intertwined, since they have often been combined as one family (e.g. Pedaliaceae). The temperate Asian aquatic plant Trapella was also assigned to Pedaliaceae, based on fruits with similar dispersal traits. With expanded sampling of both families, including Trapella, and data from ndhF, trnLF, and ETS sequences, this study confirms that the two families are distinct lineages, identifies a new placement for Trapella in tribe Gratioleae (Plantaginaceae s. 1), and shows that the two families exhibit a combination of shared floral morphology due to their proximity in Lamiales, and convergent functional morphology for dispersal. The phylogeny indicates the three tribes of Pedaliaceae are monophyletic, but that Sesamum is not.

Cuscuta (dodders, Convolvulaceae) is one of the largest and most economically important lineages of parasitic plants. The genus has a sub-cosmopolitan distribution with more than 75% of the species diversifying in the New World. The last monograph, published by Truman George Yuncker in 1932, provided a solid species-level taxonomic foundation. However, as revealed by recent phylogenetic studies, its infrageneric classification has been in great need of a taxonomic reappraisal, mainly because the morphological characters used in the previous classifications have been greatly affected by convergent evolution. Several recent phylogenetic and character evolution studies with broad sampling, as well as species-level revisions, have illustrated the deficiencies of previous classifications and provided an explicit and robust phylogenetic framework. Here we propose a new phylogenetic classification that places all 194 currently accepted species of Cuscuta into four subgenera and 18 sections. Sections have a strong morphological and biogeographical predictive value and include from one to 31 species. Thirteen section names are new or applied for the first time at the sectional rank: Babylonicae (Yunck.) M. A. García, Subulatae (Engelm.) Costea & Stefanović, Obtusilobae (Engelm.) Costea & Stefanović, Prismaticae (Yunck.) Costea & Stefanović, Ceratophorae (Yunck.) Costea & Stefanović, Umbellatae (Yunck.) Costea & Stefanović, Gracillimae Costea & Stefanović, Californicae (Yunck.) Costea & Stefanović, Indecorae (Yunck.) Costea & Stefanović, Oxycarpae (Engelm. ex Yunck.) Costea & Stefanović, Racemosae (Yunck.) Costea & Stefanović, Partitae Costea & Stefanović, and Denticulatae (Yunck.) Costea & Stefanović. An identification key to sections is included together with an overview of morphology, geographical distribution, taxonomic notes, and lists of included species.

A phylogenetic hypothesis of American Vernonieae based on three molecular regions (ITS, ndhF, rpl32-trnL) and on a morphological dataset reveals the existence of four main lineages. Three of these lineages correspond, with a few adjustments, to subtribes Chrestinae, Lychnophorinae, and Vernoniinae. The fourth lineage, which has never been recognized at a taxonomic rank due to the lack of morphological characterization, is mainly composed of taxa usually included in Lepidaploinae and Elephantopinae as well as a number of genera traditionally placed in other subtribes (Chrestinae, Piptocarphinae, and Vernoniinae). The relationships between these lineages are still not satisfactorily resolved. In order to keep the Lychnophorinae monophyletic, two small subtribes (Centratherinae, Sipolisiinae) and three monotypic genera (Albertinia, Blanchetia, and Gorceixia) have to be transferred to Lychnophorinae, which has the presence of heliangolide in aerial parts as a synapomorphy. Even though syncephaly has been historically used to delimit the subtribe Lychnophorinae, our results show that this character probably appeared independently three or four times in the evolution of American Vernonieae. The formation of the syncephalium, in each case, seems to be related to different biological functions: attractive (Chrestinae), disseminative (Rolandrinae), or protective and, to a lesser extent, attractive (Lychnophorinae).

The subtribe Lychnophorinae (Asteraceae: Vernonieae) comprises approximately 100 species and 18 genera distributed mostly in the Cerrado Domain of the Brazilian Central Plateau. Phylogenetic analyses of Lychnophorinae based on four molecular regions (ETS, ITS, ndhF, rpl32-trnL) and a morphological dataset were performed, aiming to delimit monophyletic genera, to confirm or refute the generic assignment of several species, to achieve a better understanding of the relationships between the genera, and to identify morphological characters and synapomorphies for major clades within the subtribe. Our analyses recovered several clades that represent currently recognized genera or genera that have been recognized in the past. All clades recovered are characterized by a combination of morphological characters. However, Lychnophora (35 species), the richest genus of the subtribe, emerged as polyphyletic. Albertinia, Blanchetia and Gorceixia were the first lineages to diversify, whereas Eremanthus plus Lychnophora sensu stricto emerged as the most derived clade. Relationships among other clades remained partially unresolved. Some incongruence in the placement of species of Eremanthus, Paralychnophora, and Piptolepis in the nuclear and chloroplast phytogenies provided additional evidence for the occurrence of two putative intergeneric hybrids in the wild. Biogeographic reconstruction suggests that the diversification and expansion range of most Lychnophorinae clades in the campos rupestres, from an ancestor in tropical seasonl forests, occurred previously to the conquest of the cerrado s. s. areas performed by only a few clades.

Chuquiraga is a genus of evergreen shrubs endemic to the arid and semiarid regions of the Andes and southern South America. The genus has been classified into two sections based on its variation in leaf morphology: Chuquiraga and Acanthophylla. Within section Chuquiraga, two series, Chuquiraga and Parviflorae, have been recognized based on variation in size of flower heads. The objectives of this study were to test this classification and to assess the monophyly of Chuquiraga and its intergeneric relationships with the closely related genera Doniophyton and Duseniella. The phylogenetic relationships of 24 of the 27 species and/or subspecies of Chuquiraga (19 of its 22 recognized species), plus 14 species representing seven of the remaining eight genera of Barnadesioideae, and two species of non-barnadesioid Asteraceae were inferred using sequence data from the chloroplast DNA psbA-trnH, rps16-trnK, trnL-rpl32, and/or nuclear ribosomal DNA ITS regions. The plastid and nuclear data sets were analyzed individually and combined, using maximum parsimony, maximum likelihood, and Bayesian inference methods. The phylogenetic results show that Chuquiraga, Duseniella, and Doniophyton form a well-supported monophyletic group, but the relationships among these genera and the monophyly of Chuquiraga are still uncertain. The phylogenies obtained support the monophyly of the sections and reject the monophyly of the series. Section Chuquiraga is divided into two subclades: one includes all species of Chuquiraga series Parviflorae, plus Chuquiraga calchaquina and C. longiflora (of Chuquiraga series Chuquiraga), and the other subclade includes all remaining species of Chuquiraga series Chuquiraga.

Primers from a recently published study that identified a set of low-copy nuclear genes (LCNG) in multiple angiosperms were used to obtain sequence data from three LCNG (Chlp, Agt1, and Hmgs) for phylogenetic inference at the species level. The phylogenetic utility of each of these markers was compared to ITS and seven chloroplast loci (trnL, trnG-S, ycf5, accD, rpoC1, trnK intron, psbM-trnD intergenic spacer) widely used in phylogenetic analyses. Here we use Valerianaceae as an example for two reasons: 1) the group has a well-supported “backbone” phylogeny based on numerous molecular markers; and 2) there are several species groups (e.g. the South American taxa) that have been particularly difficult to resolve, potentially due to a rapid or recent radiation. Although these new markers added nucleotide characters, they did not provide significant phylogenetic information to resolve relationships among closely related species of Valerianaceae. Likewise, relationships among some of the major clades of Valerianaceae are still not resolved with much certainty. This study indicates that several of these nuclear markers provide a significant increase in phylogenetic signal compared to traditional chloroplast markers, but information content within these regions is most useful at broader-scale phylogenetic levels. Advances in “next-generation” sequencing technologies may ultimately make their utility obsolete.

Previous mapping studies have revealed that the frequency and large size of inverted repeat junction shifts in Apiaceae plastomes are unusual among angiosperms. To further examine plastome structural organization and inverted repeat evolution in the Apiales (Apiaceae Araliaceae), we have determined the complete plastid genome sequences of five taxa, namely Anthriscus cerefolium (154,719 base pairs), Crithmum maritimum (158,355 base pairs), Hydrocotyle verticillata (153,207 base pairs), Petroselinum crispum (152,890 base pairs), and Tiedemannia filiformis subsp. greenmanii (154,737 base pairs), and compared the results obtained to previously published plastomes of Daucus carota subsp. sativus and Panax schin-seng. We also compared the five Apiaceae plastomes to identify highly variable noncoding loci for future molecular evolutionary and systematic studies at low taxonomic levels. With the exceptions of Crithmum and Petroselinum, which each demonstrate a ∼1.5 kilobase shift of its LSC-IR_B junction (J_LB), all plastomes are typical of most other non-monocot angiosperm plastid DNAs in their structural organization, gene arrangement, and gene content. Crithmum and Petroselinum also incorporate novel DNA in the LSC region adjacent to the LSC-IR_A junction (J_LA). These insertions (of 1,463 and 345 base pairs, respectively) show no sequence similarity to any other region of their plastid genomes, and BLAST searches of the Petroselinum insert resulted in multiple hits to angiosperm mitochondrial genome sequences, indicative of a mitochondrial to plastid transfer of DNA. A comparison of pairwise sequence divergence values and numbers of variable and parsimony-informative alignment positions (among other sequence characteristics) across all introns and intergenic spacers >150 base pairs in the five Apiaceae plastomes revealed that the rpl32-trnL, trnE-trnT, ndhF-rpl32, 5′rps16-trnQ, and trnT-psbD intergenic spacers are among the most fast-evolving loci, with the trnD-trnY-trnE-trnT combined region presenting the greatest number of potentially informative characters overall. These regions are therefore likely to be the best choices for molecular evolutionary and systematic studies at low taxonomic levels. Repeat analysis revealed direct and inverted dispersed repeats of 30 base pairs or more that may be useful in population-level studies. These structural and sequence analyses contribute to a better understanding of plastid genome evolution in the Apiales and provide valuable new information on the phylogenetic utility of plastid noncoding loci, enabling further molecular evolutionary and phylogenetic studies on this economically, ecologically, and medicinally important group of flowering plants.

The morphologically and phylogenetically anomalous genus Hermas is revised and nine perennial species are recognized, all endemic to mountain slopes within the Cape Floristic Region of South Africa. The new combination Hermas lanata is instated as the correct name for H. pillansii, based on the oldest available basionym. The latter species is also shown to be a very narrow endemic of the Cape Peninsula (Table Mountain to Noordhoek), not extending into the Jonkershoek Mountains as previously reported. The genus is characterized by fruits with woody endocarps, rhomboidal crystals, and pseudo-wings, all features shared with subfamily Azorelloideae, but recent phylogenetic analyses suggest that Hermas is an isolated lineage in the family, possibly sister to subfamily Apioideae s. l. An isolated position for Hermas is supported further by the unique floral morphology, viz. petaloid sepals and filiform petals, both of which are recovered as generic synapomorphies. The species may be distinguished on the basis of their habits, the size, shape, and vestiture of the leaves and involucral bracts, the synflorescence structure, the colour and venation of the sepals and petals, and the morphology and anatomy of the fruits. Species relationships are assessed in the form of a cladistic analysis of 11 morphological characters, resulting in a well-resolved phylogenetic hypothesis. A comprehensive taxonomic treatment is presented, including a key to the species, updated nomenclature, typification, descriptions, and geographical distributions.