DNA sequence data reveal polyphyly of Brexioideae (Brexiaceae; Saxifragaceae sensu lato)

Previous molecular phylogenetic analyses have demonstrated that Saxifragaceae sensu lato are polyphyletic, with component lineages scattered throughout the eudicots. As part of our effort to elucidate the relationships of members of Engler and Prantl's Saxifragaceae s. l., we undertook a molecular systematic study of subfamily Brexioideae, which comprises three genera:Brexia, Ixerba, andRoussea. Not all taxonomic treatments have concurred, however, in placing these genera together. To elucidate relationships among these three genera as well as their relationships to other angiosperms we constructed large data sets ofrbcL, 18S rDNA, andrbcL + 18S rDNA sequences. Our phylogenetic analyses indicate clearly that Brexioideae are polyphyletic.Brexia is part of a celastroid clade that also includesParnassia, Lepuropetalon, and Celastraceae.Ixerba appears as sister to a large eurosid I clade;Roussea appears as part of Asterales. Molecular data, therefore, indicate that Brexioideae are a polyphyletic assemblage and component genera should ultimately be incorporated into other groups. Our studies continue to demonstrate the polyphyly not only Saxifragaceae s. l., but also of its constituent subfamilies.The first author would like to dedicate this paper to Kurt Schuchart, a good friend who passed away during this research.     

A Revaluation of the Systematic Positions of the Cercidiphyllaceae and Daphniphyllaceae Based on rbcL Gene Sequence Analysis,with Reference to the Relationship in the “Lower” Hamamelidae

The rbcL gene sequences of six species representing five subfamilies of the Hamamelidaceae and the Platanaceae were determined and used in the phylogenetic analysis on the “lower” Hamamelidae sensu Endress (1989) and its allies newly suggested. Four most parsimonious trees were obtained, all having 893 steps with CI = 0.558 and RI = 0.591. The families Cercidiphyllaceae, Daphniphyllaceae, Hamamelidaceae and Saxifragaceae are closely located, while the relationships among them remain unsolved even if more representatives of the Hamamelidaceae were further added in this parsimony analysis. Our results confirm the phylogenetic trees revealed by Chase et al. (1993) and Soltis et al. (1997), instead of those of Hoot and Crane (1996). Considering the morphological features they share, it is suggested that the Cercidiphyllaceae and Daphniphyllaceae be placed into the Hamamelidales. The relationship between the Platanaceae and the Hamamelidaceae shown in our analysis is not so closed as suggested by the cladistic analyses by using morphological characters only(e.g. Lu et al., 1991), while those among the Platanaceae, Trochodendraceae and Tetracentraceae are close as indicated by this study. The Eupteleaceae falls into the Ranunculales. The Eucommiaceae seems to show closer relationship with the Hamamelidaceae, the “core” family of the “lower” Hamamelidae, than with the other members except the Cercidiphyllaceae. The rbcL gene trees imply that the “lower” Hamamelidae is a heterogeneous group,composed of isolated ancient families.     

Determination of the evolutionary relationships in Rattus sensu lato (Rodentia : Muridae) using L1 (LINE-1) amplification events

We determined ∼215 bp of DNA sequence from the 3′-untranslated region (UTR) of 240 cloned L1 (LINE-1) elements isolated from 22 species of Rattus sensu lato and Rattus sensu stricto murine rodents. The sequences were sorted into different L1 subfamilies, and oligonucleotides cognate to them were hybridized to genomic DNA of various taxa. From the distribution of the L1 subfamilies in the various species, we inferred the partial phylogeny of Rattus sensu lato. The four Maxomys species comprise a well-defined clade separate from a monophyletic cluster that contains the two Leopoldamys and four Niviventer species. The Niviventer/Leopoldamys clade, in turn, shares a node with the clade that contains Berylmys, Sundamys, Bandicota, and Rattus sensu stricto. The evolutionary relationships that we deduced agree with and significantly extend the phylogeny of Rattus sensu lato established by other molecular criteria. Furthermore, the L1 amplification events scored here produced a unique phylogenetic tree, that is, in no case did a character (a given L1 amplification event) appear on more than one branch. The lack of homoplasy found in this study supports the robustness of L1 amplification events as phylogenetic markers for the study of mammalian evolution. Received: 8 November 1996 / Accepted: 11 April 1997     

Molecular and morphological phylogenetics of weevils (coleoptera,curculionoidea): do niche shifts accompany diversification?

The main goals of this study were to provide a robust phylogeny for the families of the superfamily Curculionoidea, to discover relationships and major natural groups within the family Curculionidae, and to clarify the evolution of larval habits and host-plant associations in weevils to analyze their role in weevil diversification. Phylogenetic relationships among the weevils (Curculionoidea) were inferred from analysis of nucleotide sequences of 18S ribosomal DNA (rDNA; approximately 2,000 bases) and 115 morphological characters of larval and adult stages. A worldwide sample of 100 species was compiled to maximize representation of weevil morphological and ecological diversity. All families and the main subfamilies of Curculionoidea were represented. The family Curculionidae sensu lato was represented by about 80 species in 30 "subfamilies" of traditional classifications. Phylogenetic reconstruction was accomplished by parsimony analysis of separate and combined molecular and morphological data matrices and Bayesian analysis of the molecular data; tree topology support was evaluated. Results of the combined analysis of 18S rDNA and morphological data indicate that monophyly of and relationships among each of the weevil families are well supported with the topology ((Nemonychidae, Anthribidae) (Belidae (Attelabidae (Caridae (Brentidae, Curculionidae))))). Within the clade Curculionidae sensu lato, the basal positions are occupied by mostly monocot-associated taxa with the primitive type of male genitalia followed by the Curculionidae sensu stricto, which is made up of groups with the derived type of male genitalia. High support values were found for the monophyly of some distinct curculionid groups such as Dryophthorinae (several tribes represented) and Platypodinae (Tesserocerini plus Platypodini), among others. However, the subfamilial relationships in Curculionidae are unresolved or weakly supported. The phylogeny estimate based on combined 18S rDNA and morphological data suggests that diversification in weevils was accompanied by niche shifts in host-plant associations and larval habits. Pronounced conservatism is evident in larval feeding habits, particularly in the host tissue consumed. Multiple shifts to use of angiosperms in Curculionoidea were identified, each time associated with increases in weevil diversity and subsequent shifts back to gymnosperms, particularly in the Curculionidae.     

Circumscription of the Malvales and relationships to other Rosidae: evidence from rbcL sequence data

The order Malvales remains poorly circumscribed, despite its seemingly indisputable core constituents: Bombacaceae, Malvaceae, Sterculiaceae, and Tiliaceae. We conducted a two-step parsimony analysis on 125 rbcL sequences to clarify the composition of Malvales, to determine the relationships of some controversial families, and to identify the placement of the Malvales within Rosidae. We sampled taxa that have been previously suggested to be within, or close to, Malvales (83 sequences), plus additional rosids (26 sequences) and nonrosid eudicots (16 sequences) to provide a broader framework for the analysis. The resulting trees strongly support the monophyly of the core malvalean families, listed above. In addition, these data serve to identify a broader group of taxa that are closely associated with the core families. This expanded malvalean clade is composed of four major subclades: (1) the core families (Bombacaceae, Malvaceae, Sterculiaceae, Tiliaceae); (2) Bixaceae, Cochlospermaceae, and Sphaerosepalaceae (Rhopalocarpaceae); (3) Thymelaeaceae sensu lato (s.l.); and (4) Cistaceae, Dipterocarpaceae s.l., Sarcolaenaceae (Chlaenaceae), and Muntingia. In addition, Neurada (Neuradaceae or Rosaceae) falls in the expanded malvalean clade but not clearly within any of the four major subclades. This expanded malvalean clade is sister to either the expanded capparalean clade of Rodman et al. or the sapindalean clade of Gadek et al. Members of Elaeocarpaceae, hypothesized by most authors as a sister group to the four core malvalean families, are shown to not fall close to these taxa. Also excluded as members of, or sister groups to, the expanded malvalean clade were the families Aextoxicaceae, Barbeyaceae, Cannabinaceae, Cecropiaceae, Dichapetalaceae, Elaeagnaceae, Euphorbiaceae s.l., Huaceae, Lecythidaceae, Moraceae s.l., Pandaceae, Plagiopteraceae, Rhamnaceae, Scytopetalaceae, Ulmaceae, and Urticaceae.     

Higher‐level phylogeny of diving beetles (Coleoptera: Dytiscidae) based on larval characters

A comprehensive higher‐level phylogeny of diving beetles (Dytiscidae) based on larval characters is presented. Larval morphology and chaetotaxy of a broad range of genera and species was studied, covering all currently recognized subfamilies and tribes except for the small and geographically restricted Hydrodytinae, where the larva is unknown. The results suggest several significant conclusions with respect to the systematics of Dytiscidae including the following: monophyly of all currently recognized subfamilies, although Dytiscinae when considered in a broad context is rendered paraphyletic by Cybistrinae; currently recognized tribes are monophyletic except for Agabini, Hydroporini and Laccornellini; inter‐subfamily and inter‐tribe relationships generally show weak support, except for a few well supported clades; three distinct clades are recognized within Dytiscinae [Dytiscini sensu lato (i.e. including the genera Dytiscus Linnaeus and Hyderodes Hope), Hydaticini sensu lato, and Cybistrini]; and recognition of Pachydrini as a distinct tribe. Other less robust results include: Methlini sister to the rest of Hydroporinae; relative basal position of Laccornini, Hydrovatini and Laccornellini within Hydroporinae; close relationship of Agabinae and Copelatinae; Matinae nested deep within Dytiscidae, as sister to a large clade including Colymbetinae, Coptotominae, Lancetinae and Dytiscinae sensu lato; the sister‐group relationship of Agabetini and Laccophilini is confirmed. The results presented here are discussed and compared with previous phylogenetic hypotheses based on different datasets, and the evolution of some significant morphological features is discussed in light of the proposed phylogeny. All suprageneric taxa are diagnosed, including illustrations of all relevant synapomorphies, and a key to separate subfamilies and tribes is presented, both in traditional (paper) format and as an online Lucid interactive identification key.     

Phylogenetic relationships of the enigmatic angiosperm family Podostemaceae inferred from 18S rDNA and rbcL sequence data

The phylogenetic relationships of some angiosperm families have remained enigmatic despite broad phylogenetic analyses of rbcL sequences. One example is the aquatic family Podostemaceae, the relationships of which have long been controversial because of major morphological modifications associated with their aquatic habit. Podostemaceae have variously been associated with Piperaceae, Nepenthaceae, Polygonaceae, Caryophyllaceae, Scrophulariaceae, Rosaceae, Crassulaceae, and Saxifragaceae. Two recent analyses of rbcL sequences suggest a possible sister-group relationship of Podostemaceae to Crassulaceae (Saxifragales). However, the branch leading to Podostemaceae was long, and use of different outgroups resulted in alternative placements. We explored the phylogenetic relationships of Podostemaceae using 18S rDNA sequences and a combined rbcL + 18S rDNA matrix representing over 250 angiosperms. In analyses based on 18S rDNA data, Podostemaceae are not characterized by a long branch; the family consistently appears as part of a Malpighiales clade that also includes Malpighiaceae, Turneraceae, Passifloraceae, Salicaceae, Euphorbiaceae, Violaceae, Linaceae, Chrysobalanaceae, Trigoniaceae, Humiriaceae, and Ochnaceae. Phylogenetic analyses based on a combined 18S rDNA + rbcL data set (223 ingroup taxa) with basal angiosperms as the outgroup also suggest that Podostemaceae are part of a Malpighiales clade. These searches swapped to completion, and the shortest trees showed enhanced resolution and increased internal support compared to those based on 18S rDNA or rbcL alone. However, when Gnetales are used as the outgroup, Podostemaceae appear with members of the nitrogen fixing clade (e.g., Elaeagnaceae, Ulmaceae, Rhamnaceae, Cannabaceae, Moraceae, and Urticaceae). None of the relationships suggested here for Podostemaceae receives strong bootstrap support. Our analyses indicate that Podostemaceae are not closely allied with Crassulaceae or with other members of the Saxifragales clade; their closest relatives, although still uncertain, appear to lie elsewhere in the rosids.     

Mitogenomic perspectives into iguanid phylogeny and biogeography: Gondwanan vicariance for the origin of Madagascan oplurines

Complete or nearly complete nucleotide sequences of mitochondrial genomes (mtDNAs) were determined from eight species which, together with previous mtDNA data for two other taxa, cover most subfamilies of Iguanidae sensu lato. These iguanid mtDNAs were found to be rather conservative with respect to gene arrangements and molecular evolutionary rates, which contrasts with mtDNAs of Acrodonta (Agamidae and Chamaeleonidae) in which several gene rearrangements and highly accelerated molecular evolutionary rates have been known. Phylogenetic analyses consistently suggested the earliest shoot-off of a Malagasy subfamily Oplurinae and an affinity of Polychrotinae and Tropidurinae sensu stricto. However, even with the ample molecular characters derived from complete mtDNA sequences, phylogenetic relationships between iguanid subfamilies were poorly resolved in general, presumably due to the rapid ancient cladogenesis. Divergence time estimation without assuming the molecular clock suggested the Late Triassic/Early Jurassic divergence of Iguanidae from acrodonts and the Middle/Late Jurassic divergence of Oplurinae from the other iguanids. Together with geological and paleontological evidence, these results led us to propose Gondwanan vicariance for the origin of Malagasy oplurines without invoking a land bridge connection between South America/Antarctica and drifting Madagascar/India.     

ITS sequence data support a single origin for North American Astereae (Asteraceae) and reflect deep geographic divisions in Aster s.l

The Astereae is the largest tribe of Asteraceae in North America. Morphological diversity suggests that the North American assemblage is polyphyletic as 12 endemic genera, as well as lineages of the genus Erigeron and Conyza (Conyzinae), have been hypothesized to represent at least five separate invasions of North America from Africa, Australia, Eurasia, and South America. This hypothesis was tested with a phylogenetic analysis of nucleotide sequence data from the internal transcribed spacers (ITS) of nuclear ribosomal DNA. Sequences for 62 taxa represent seven outgroup taxa and all major Northern and Southern Hemisphere groups of Astereae, including broad taxonomic and geographic sampling of Conyzinae and Aster s.l. (sensu lato). Parsimony analyses indicate that all North American Astereae are members of a strongly supported clade, and that a diverse group of predominantly woody taxa from Africa, Australia, and South America, are basal Astereae. Furthermore, Aster s.l. is deeply polyphyletic as Eurasian taxa, including Aster s.s. (sensu stricto), appear more closely related to Southern Hemisphere taxa than to North American Aster segregates. There is only low to moderate agreement between proposed higher level Astereae relationships based on ITS and those based either on morphology or chloroplast restriction site data.     

Phylogenetic structure in the grass family (Poaceae): evidence from the nuclear gene phytochrome B

Phylogenetic analyses of partial phytochrome B (PHYB) nuclear DNA sequences provide unambiguous resolution of evolutionary relationships within Poaceae. Analysis of PHYB nucleotides from 51 taxa representing seven traditionally recognized subfamilies clearly distinguishes three early-diverging herbaceous "bambusoid" lineages. First and most basal are Anomochloa and Streptochaeta, second is Pharus, and third is Puelia. The remaining grasses occur in two principal, highly supported clades. The first comprises bambusoid, oryzoid, and pooid genera (the BOP clade); the second comprises panicoid, arundinoid, chloridoid, and centothecoid genera (the PACC clade). The PHYB phylogeny is the first nuclear gene tree to address comprehensively phylogenetic relationships among grasses. It corroborates several inferences made from chloroplast gene trees, including the PACC clade, and the basal position of the herbaceous bamboos Anomochloa, Streptochaeta, and Pharus. However, the clear resolution of the sister group relationship among bambusoids, oryzoids, and pooids in the PHYB tree is novel; the relationship is only weakly supported in ndhF trees and is nonexistent in rbcL and plastid restriction site trees. Nuclear PHYB data support Anomochlooideae, Pharoideae, Pooideae sensu lato, Oryzoideae, Panicoideae, and Chloridoideae, and concur in the polyphyly of both Arundinoideae and Bambusoideae.     

Molecular phylogenetics reveals Leontodon (Asteraceae, Lactuceae) to be diphyletic

The plastid matK gene, trnL/F spacer, and nuclear rDNA ITS were sequenced for 36 species of Leontodon and 29 taxa of related genera of tribe Lactuceae. Phylogenetic relationships inferred from the independent and combined data are largely congruent and reveal that Leontodon sensu lato (s.l.) as presently defined is diphyletic: L. subgenus Leontodon forms a clade with Helminthotheca, Picris and Hypochaeris as sister genera, whereas L. subgenus Oporinia appears as a separate clade with strong bootstrap support and is thus better treated as a separate genus. Previous sectional classifications of Leontodon s.l. are considered in the light of DNA and additional morphological and karyological data. Support is presented for a core group of Hypochaeridinae sensu stricto (s.s.) with the two clades of Leontodon s.l., Helminthotheca, Picris, and Hypochaeris, whereas Urospermum, Hyoseris, Aposeris, and Rhagadiolus appear to be positioned more distantly.     

Molecular phylogenetics of Caryophyllales based on nuclear 18S rDNA and plastid rbcL, atpB, and matK DNA sequences

To study the inter- and infrafamilial phylogenetic relationships in the order Caryophyllales sensu lato (s.l.), ～930 base pairs of the matK plastid gene have been sequenced and analyzed for 127 taxa. In addition, these sequences have been combined with the rbcL plastid gene for 53 taxa and with the rbcL and atpB plastid genes as well as the nuclear 18S rDNA for 26 taxa to provide increased support for deeper branches. The red pigments of Corbichonia, Lophiocarpus, and Sarcobatus have been tested and shown to belong to the betacyanin class of compounds. Most taxa of the order are clearly grouped into two main clades (i.e., "core" and "noncore" Caryophyllales) which are, in turn, divided into well-defined subunits. Phytolaccaceae and Molluginaceae are polyphyletic, and Portulacaceae are paraphyletic, whereas Agdestidaceae, Barbeuiaceae, Petiveriaceae, and Sarcobataceae should be given familial recognition. Two additional lineages are potentially appropriate to be elevated to the family level in the future: the genera Lophiocarpus and Corbichonia form a well-supported clade on the basis of molecular and chemical evidence, and Limeum appears to be separated from other Molluginaceae based on both molecular and ultrastructural data.     

New evidence for the systematic significance of acylated spermidines and flavonoids in pollen of Higher Hamamelidae

New distributional recores of hydroxycinnamoyl spermidines (HCS), including novel trisubstituted HCSs and flavonol glycosides, in pollen of Higher Hamamelidae are presented. The 51 taxa analyzed by HPLC and TLC included members of the families Fagaceae (Castanoideae, Fagoideae, Quercoideae), Betulaceae, Juglandaceae, Myricaceae, Hamamelidaceae, Rosaceae, and Buxaceae (Simmondsia). The results support generic concepts in the Higher Hamamelidae derived from morphological and chloroplast DNA data and support a close evolutionary relationship between the Higher Hamamelidae and the Rosidae.     

Molecular data place Hydnoraceae with Aristolochiaceae

Utilization of molecular phylogenetic information over the past decade has resulted in clarification of the position of most angiosperms. In contrast, the position of the holoparasitic family Hydnoraceae has remained controversial. To address the question of phylogenetic position of Hydnoraceae among angiosperms, nuclear SSU and LSU rDNA and mitochondrial atp1 and matR sequences were obtained for Hydnora and Prosopanche. These sequences were used in combined analyses that included the above four genes as well as chloroplast rbcL and atpB (these plastid genes are missing in Hydnoraceae and were hence coded as missing). Three data sets were analyzed using maximum parsimony: (1) three genes with 461 taxa; (2) five genes with 77 taxa; and (3) six genes with 38 taxa. Analyses of separate and combined data partitions support the monophyly of Hydnoraceae and the association of that clade with Aristolochiaceae sensu lato (s.l.) (including Lactoridaceae). The latter clade is sister to Piperaceae and Saururaceae. Despite over 11 kilobases (kb) of sequence data, relationships within Aristolochiaceae s.l. remain unresolved, thus it cannot yet be determined whether Aristolochiaceae, Hydnoraceae, and Lactoridaceae should be classified as distinct families. In contrast to most traditional classifications, molecular phylogenetic analyses do not suggest a close relationship between Hydnoraceae and Rafflesiaceae. A number of morphological features is shared by Hydnoraceae and Aristolochiaceae; however, a more resolved phylogeny is required to determine whether these represent synapomorphies or independent acquisitions.     

The phylogenetic relationships of flies in the superfamily Empidoidea (Insecta: Diptera)

We conducted a molecular phylogenetic study of the Empidoidea, a diverse group of 10,000 species of true flies, with two major goals: to reconstruct a taxonomically complete and robustly supported phylogeny for the group and to use this information to assess several competing classifications for the clade. We amassed 3900+ nucleotides of coding data from the carbamoylphosphate synthase domain of the rudimentary locus (CAD) and 1200+ nucleotides from the large nuclear ribosomal subunit (28S) from 72 and 71 species, respectively, representing several orthorrhaphan and cyclorrhaphan families and all previously recognized empidoidean subfamilies. Independent and combined phylogenetic analyses of these data were conducted using parsimony, maximum likelihood, and Bayesian criteria. The combined matrix included 61 taxa for which both CAD and 28S sequences were obtained. Analyses of CAD first and second codon positions alone and when concatenated with 28S sequences yielded trees with similar and largely stable topologies. Analyses of 28S data alone supported many clades although resolution is limited by low sequence divergence. The following major empidoid clades were recovered with convincing support in a majority of analyses: Atelestidae, Empidoidea exclusive of Atelestidae, Hybotidae sensu lato, Dolichopodidae+Microphorinae (including Parathallassius), and Empididae sensu lato (including Brachystomatinae, Ceratomerinae, Clinocerinae, Empidinae, Hemerodromiinae, Oreogetoninae, and Trichopezinae). The branching arrangement among these four major clades was Atelestidae, Hybotidae, Dolichopodidae/Microphorinae, Empididae. Previously recognized subclades recovered with robust support included Hybotinae, Brachystomatinae, Tachydromiinae, Clinocerinae (in part), Hemerodromiinae, Empidinae, and Empidiini.     

A phylogeny of legumes (Leguminosae) based on analysis of the plastid matK gene resolves many well-supported subclades within the family

Phylogenetic analysis of 330 plastid matK gene sequences, representing 235 genera from 37 of 39 tribes, and four outgroup taxa from eurosids I supports many well-resolved subclades within the Leguminosae. These results are generally consistent with those derived from other plastid sequence data (rbcL and trnL), but show greater resolution and clade support overall. In particular, the monophyly of subfamily Papilionoideae and at least seven major subclades are well-supported by bootstrap and Bayesian credibility values. These subclades are informally recognized as the Cladrastis clade, genistoid sensu lato, dalbergioid sensu lato, mirbelioid, millettioid, and robinioid clades, and the inverted-repeat-lacking clade (IRLC). The genistoid clade is expanded to include genera such as Poecilanthe, Cyclolobium, Bowdichia, and Diplotropis and thus contains the vast majority of papilionoids known to produce quinolizidine alkaloids. The dalbergioid clade is expanded to include the tribe Amorpheae. The mirbelioids include the tribes Bossiaeeae and Mirbelieae, with Hypocalypteae as its sister group. The millettioids comprise two major subclades that roughly correspond to the tribes Millettieae and Phaseoleae and represent the only major papilionoid clade marked by a macromorphological apomorphy, pseudoracemose inflorescences. The robinioids are expanded to include Sesbania and members of the tribe Loteae. The IRLC, the most species-rich subclade, is sister to the robinioids. Analysis of the matK data consistently resolves but modestly supports a clade comprising papilionoid taxa that accumulate canavanine in the seeds. This suggests a single origin for the biosynthesis of this most commonly produced of the nonprotein amino acids in legumes.     

Phylogenetic analysis of the tribe Bovini (Mammalia: Artiodactyla)

A matrix of 57 (mainly cranial) characters and 32 taxa of fossil and Recent Bovini (buffaloes, bison and cattle) has been analysed using the parsimony program HENNIG86. Among the best established results are the exclusion of Parabos , polyphyly of Leptobos , monophyly of the Bos sensu lato + buffaloes group (a clade including all Recent Bovini), probable monophyly of the Bubalina and Syncerina, and the close relationship between bison and yak. Some other interesting questions raised include the apparent absence of a close link between Pliocene African bovines (except "Leptobos" syrticus ) and later African buffaloes, and the possible monophyly of Pelorovis oldowayensis+Bos sensu lato .     

A molecular phylogeny of the Old World stingless bees (Hymenoptera: Apidae: Meliponini) and the non-monophyly of the large genus Trigona

Abstract.  We examined the inter- and infrageneric relationships of Old World Meliponini with a near-complete sampling of supra-specific taxa. DNA sequences for the taxa were collected from four genes (mitochondrial 16S rRNA, nuclear long-wavelength rhodopsin copy 1 (opsin), elongation factor-1α copy F2 and arginine kinase). Additional sampling of New World taxa indicated that Trigona sensu lato is not monophyletic: Trigona from the Indo-Malayan/Australasian Regions forms a large clade distantly related to the Neotropical Trigona . A separate clade comprises the Afrotropical meliponines, and includes the 'minute' species found in the Afrotropical, Indo-Malayan and Australasian Regions. The Neotropical genus Melipona , by contrast with previous investigations, is not the sister lineage to the remaining stingless bees, but falls within the strongly supported Neotropical clade. These results constitute the framework for a revised classification and ongoing biological investigations of Meliponini. A single taxonomic change, Heterotrigona bakeri stat.n. , is proposed on the basis of sequence divergence.     

Phylogenetic relationships of the Gomphales based on nuc-25S-rDNA, mit-12S-rDNA, and mit-atp6-DNA combined sequences

Phylogenetic relationships among Geastrales, Gomphales, Hysterangiales, and Phallales were estimated via combined sequences: nuclear large subunit ribosomal DNA (nuc-25S-rDNA), mitochondrial small subunit ribosomal DNA (mit-12S-rDNA), and mitochondrial atp6 DNA (mit-atp6-DNA). Eighty-one taxa comprising 19 genera and 58 species were investigated, including members of the Clathraceae, Gautieriaceae, Geastraceae, Gomphaceae, Hysterangiaceae, Phallaceae, Protophallaceae, and Sphaerobolaceae. Although some nodes deep in the tree could not be fully resolved, some well-supported lineages were recovered, and the interrelationships among Gloeocantharellus, Gomphus, Phaeoclavulina, and Turbinellus, and the placement of Ramaria are better understood. Both Gomphus sensu lato and Ramaria sensu lato comprise paraphyletic lineages within the Gomphaceae. Relationships of the subgenera of Ramaria sensu lato to each other and to other members of the Gomphales were clarified. Within Gomphus sensu lato, Gomphus sensu stricto, Turbinellus, Gloeocantharellus and Phaeoclavulina are separated by the presence/absence of clamp connections, spore ornamentation (echinulate, verrucose, subreticulate or reticulate), and basidiomal morphology (fan-shaped, funnel-shaped or ramarioid). Gautieria, a sequestrate genus in the Gautieriaceae, was recovered as monophyletic and nested with members of Ramaria subgenus Ramaria. This agrees with previous observations of traits shared by these two ectomycorrhizal taxa, such as the presence of fungal mats in the soil. Clavariadelphus was recovered as a sister group to Beenakia, Kavinia, and Lentaria. The results reaffirm relationships between the Geastrales, Gomphales, Hysterangiales, and the Phallales, suggesting extensive convergence in basidiomal morphology among members of these groups. A more extensive sampling that focuses on other loci (protein-coding genes have been shown to be phylogenetically informative) may be useful to answer questions about evolutionary relationships among these fungal groups.