Unique floral structures and iterative evolutionary themes in Asparagales: Insights from a morphological cladistic analysis

A morphological cladistic analysis is presented of the lilioid order Asparagales, with emphasis on relationships within the “lower” asparagoids, in the context of recent new data on both floral and vegetative structures. The analysis retrieved a monophyletic “lower” asparagoid clade, in contrast to molecular analyses, in which lower asparagoids invariably form a grade. However, limited outgroup sampling in the current analysis is a significant factor in this “inside-out” topology; if the morphological tree is rerooted with Orchidaceae as the outgroup, the result is a topology broadly similar to the molecular one. The relatively low resolution of the “lower” asparagoid clade identified here is a result of high homoplasy in several characters, which could be regarded as iterative evolutionary themes within Asparagales, notably (among floral characters) epigyny and zygomorphy. Close relationships between some family pairs were inferred, including Orchidaceae and Hypoxidaceae, Boryaceae and Blandfordiaceae, Asphodelaceae and Hemerocallidaceae, and Iridaceae and Doryanthaceae. The small South African genusPauridia, which differs from other Hypoxidaceae in that it lacks the outer stamen whorl, was placed as sister to Orchidaceae rather than being embedded in Hypoxidaceae as in molecular analyses, because despite some significant similarities with other Hypoxidaceae (e.g., mucilage canals), it shares some characters with Orchidaceae, notably the presence of a gynostemium and pontoperculate pollen.Xanthorrhoea andLanaria were wild-card taxa in the context of this analysis, with characters in common with more than one different group.     

Floral structure and development and systematic aspects of some 'lower' Asparagales

 Floral structure and development of representatives of Asteliaceae, Blandfordiaceae, Boryaceae, Doryanthaceae, and Hypoxidaceae, all members of the `lower' Asparagales, were studied comparatively. The results are discussed in the light of new molecular systematic studies, but also with regard to established morphological characters in related groups. Stamen shape varies considerably within and between taxa: the shape of anthers is from X-shaped, sagittate to non-sagittate, they are either latrorse or introrse, basifixed, centrifixed or dorsifixed. Gynoecia are syncarpous up to the stigmatic region in all taxa. Ovaries of Doryanthaceae and Hypoxidaceae are inferior, but they are superior in Asteliaceae, Blandfordiaceae and Boryaceae. All ovaries have at least a short synascidiate zone. With the exception of Astelia alpina (Asteliaceae), the ovaries are trilocular. Ovaries of Asteliaceae contain mucilage, which is secreted from trichomes on the funicle and on the placenta. Although flowers are polysymmetric at anthesis, they are monosymmetric in earliest stages with a developmental gradient from adaxial to abaxial. Perianth organs arise individually from either a concave (taxa with inferior ovary) or convex (taxa with superior ovary) apex. Hypoxidaceae have pollen flowers with free stamens. One species, Curculigo capitulata, has Solanum-type flowers with postgenitally united stamens. It is most probably pollinated by buzzing bees. All other taxa have nectariferous flowers with internal or external septal nectaries. Received February 5, 2001 Accepted June 20, 2001     

Molecular phylogenetics of Hypoxidaceae--evidence from plastid DNA data and inferences on morphology and biogeography

Phylogenetic relationships of the monocot family Hypoxidaceae (Asparagales), which occurs mainly in the Southern Hemisphere, were reconstructed using four plastid DNA regions (rbcL, trnL intron, trnL-F intergenic spacer, and trnS-G intergenic spacer) for 56 ingroup taxa including all currently accepted genera and seven species of the closely related families Asteliaceae, Blandfordiaceae, and Lanariaceae. Data were analyzed by applying parsimony, maximum likelihood and Bayesian methods. The intergenic spacer trnS-G--only rarely used in monocot research--contributed a substantial number of potentially parsimony informative characters. Hypoxidaceae consist of three well-supported major clades, but their interrelationships remain unresolved. Our data indicate that in the Pauridia clade one long-distance dispersal event occurred from southern Africa to Australia. Long-distance dispersal scenarios may also be likely for the current distribution of Hypoxis, which occurs on four continents. In the Curculigo clade, the present distribution of Curculigo s.s. on four continents could support a Gondwanan origin, but the level of divergence is too low for this hypothesis to be likely. The main clades correspond well with some floral characters, habit and palynological data, whereas chromosomal data exhibit plasticity and probably result from polyploidization and subsequent dysploidy and/or aneuploidy. Evolutionary flexibility is also suggested by the number of reported pollination syndromes: melittophily, myophily, sapromyophily, and cantharophily. Based on our phylogenetic results, we suggest cautious nomenclatural reorganization to generate monophyly at the generic level.     

Phylogenetic position of Apostasia and Neuwiedia (Orchidaceae)

JUDD, W. S., STERN, W. L. & CHEADLE, V. I. 1993. Phylogenetic position of Apostasia and Neuwiedia (Orchidaceae). Cladistic analyses of the phylogenetic relationships of selected orchid taxa were conducted in order to assess the phylogenetic position of Apostasia and Neuwiedia (Orchidaceae: Apostasioideae). These analyses employed newly available anatomical characters, along with several morphological features that had been used in recent phylogenetic analyses of Orchidaceae. Our analyses indicate that Apostasia is more closely related to Neuwiedia than it is to Cypripedioideae. The two genera comprise an apostasiad clade; this clade is the sister-group to a clade including Cypripedioideae and monandrous orchids. The apostasiad clade is diagnosed by the derived features of operculate pollen colpi, Apostasia-type seeds, and vessel members with simple perforation plates. Of these, the presence of simple perforation plates is considered to be the most significant phylogenetically. Therefore, the apostasiads should not be considered ancestral to the remaining orchid groups. Vessel members of the monandrous orchids, as well as the cypripediads, are multiperforate–the hypothesized ancestral state based on the condition in Hypoxidaceae.     

The discovery of polyandry in Curculigo (Hypoxidaceae): implications for androecium evolution of asparagoid monocotyledons

BACKGROUND AND AIMS: Individual flowers of the monocot Curculigo racemosa (Hypoxidaceae, Asparagales) are regularly polyandrous. To evaluate the significance of this almost unique character among Asparagales for flower evolution of asparagoid monocots, flowers of C. racemosa were studied comparatively. METHODS: Anthetic flowers as well as early floral developmental stages were studied by light and scanning electron microscopy. KEY RESULTS: Despite the polyandry, floral development is similar to that of other Asparagales with a developmental gradient from adaxial to abaxial. Stamens initiate simultaneously and the diameter of staminal primordia is about half of that in species with six anthers. The number of stamens is not fixed (12-26) and varies within the same inflorescence. Surprisingly, the gynoecium can be four- or six-locular, besides the normal trimerous state. CONCLUSIONS: The discovery of a polyandrous Curculigo reveals plasticity of stamen number at the base of Asparagales. Orchidaceae - sister to all other Asparagales - has a reduced stamen number (three, two or one), whereas in Hypoxidaceae - part of the next diverging clade - either the normal monocot stamen number (six), polyandry (this study) or the loss of three anthers (Pauridia) occurs. However, at present it is impossible to decide whether the flexibility in stamen number is autapomorphic for each group or whether it is a synapomorphy. The small size of stamen primordia of Curculigo is conspicuous. It allows more space for additional androecial primordia. Stamens are initiated as independent organs, and filaments are not in bundles, hence C. racemosa is not secondarily polyandrous as may be the case in the distantly related Gethyllis of asparagoid Amaryllidaceae. The increase in carpel number is a rare phenomenon in angiosperms. A possible explanation for the polyandry of C. racemosa is that it is a natural SUPERMAN-deficient mutant, which shows an increase of stamens, or ULTRAPETALA or CARPEL FACTORY mutants, which are polyandrous and changed in carpel number.     

The Nucellus and Chalaza in monocotyledons: Structure and systematics

The majority of monocotyledons are crassinucellate, including some early-branching taxa (sensu Chase et al., 1995a, 1995b) such asTofieldia, although Araceae are predominantly tenuinucellate. The tenuinucellate condition occurs in a taxonomically wide range of monocotyledons, and there is some congruence between this character and existing monocot topologies at higher levels. For example, present evidence indicates a few tenuinucellate asparagoid clades, including Alliaceae sensu stricto and Hypoxidaceae, possibly two tenuinucellate lilioid lineages, and at least two tenuinucellate commelinoid lineages. Proximal nucellar structures arise from a multi-layered region of the ovule and include hypostase, enlarged dermal cells and conducting passage (Zuleitungsbahn), haustoria, postaments, podia, and perisperm. In some cases they may represent the same tissues at different developmental stages; in general the last three are seed structures. For example, a postament may be a resistant conducting passage from which the surrounding dermal cells have degenerated, or alternatively a resistant hypostase, although both are nucellar in origin. Such terminological confusions cause problems in establishing homologies. Several characters relating to the nucellus are outlined.     

Apostasiads, systematic anatomy, and the origins of Orchidaceae

Anatomical study of several species of the putatively primitive orchids Apostasia and Neuiviedia was based on specimens of leaves, stems and rootS. Research was carried out in the hope of providing objective information from anatomy towards unravelling the relationships of these plants, and especially towards answering the question of whether extant orchids evolved from these two genera, or from plants like them. The morphology of Apostasia and Neuwiedia has evoked the dogma of primitiveness because of the two or three anthers borne on separate filaments and the free style and stigma which characterize the flowerS. In most other orchids there is only one anther and filaments and styles are fused to form the column (gynostemium). The general anatomical structure of apostasiads shows features present in other orchids; none is restricted to Apostasia and Neuwiedia. Tracheary anatomy, however, shows vessels in roots, but not in any part of the shoot system. Vessel members are characterized by chiefly simple perforation plates in contrast with other orchids where scalariform perforation plates predominate in vessel members of the root. These phenomena, considered from the phylogenetic standpoint, would cast serious doubt on the possibility that plants with scalariform perforation plates, the ancestral, or primitive condition, could have arisen from plants with simple perforation plates, the derived, or advanced condition. On this basis the apostasiads could not have given rise to the di- and monandrous orchidS. Of the several suggested origins for orchids, Hypoxidaceae, or plants similar to them, whether in Asparagales, Liliales or Haemadorales of different authors, could have been the progenitors of orchids as a group, including the apostasiadS. Because of the unique combination of floral features in the apostasiads, their predominantly simple perforation plates, and their overall anatomical similarity to orchids in general, it would appear appropriate to consider them as a subfamily, Apostasioideae, of Orchidaceae sensu lato.     

Mycoheterotrophic germination of Pyrola asarifolia dust seeds reveals convergences with germination in orchids

Dust seeds that germinate by obtaining nutrients from symbiotic fungi have evolved independently in orchids and 11 other plant lineages. The fungi involved in this 'mycoheterotrophic' germination have been identified in some orchids and non-photosynthetic Ericaceae, and proved identical to mycorrhizal fungi of adult plants. We investigated a third lineage, the Pyroleae, chlorophyllous Ericaceae species whose partial mycoheterotrophy at adulthood has recently attracted much attention. We observed experimental Pyrola asarifolia germination at four Japanese sites and investigated the germination pattern and symbiotic fungi, which we compared to mycorrhizal fungi of adult plants. Adult P. asarifolia, like other Pyroleae, associated with diverse fungal species that were a subset of those mycorrhizal on surrounding trees. Conversely, seedlings specifically associated with a lineage of Sebacinales clade B (endophytic Basidiomycetes) revealed an intriguing evolutionary convergence with orchids, some of which also germinate with Sebacinales clade B. Congruently, seedlings clustered spatially together, but not with adults. This unexpected transition in specificity and ecology of partners could support the developmental transition from full to partial mycoheterotrophy, but probably challenges survival and distribution during development. We discuss the physiological and ecological traits that predisposed to the repeated recruitment of Sebacinales clade B for dust seed germination.     

Roles of synorganisation,zygomorphy and heterotopy in floral evolution: the gynostemium and labellum of orchids and other lilioid monocots

A gynostemium, comprising stamen filaments adnate to a syncarpous style, occurs in only threc groups of monocots: the large family Orchidaceae (Asparagales) and two small genera Pauridia (Hypoxidaceae: Asparagales) and Corsia (Corsiaceae, probably in Liliales), all epigynous taxa. Pauridia has actinomorphic (polysymmetric) flowers, whereas those of Corsia and most orchids are strongly zygomorphic (monosymmetric) with a well-differentiated labellum. In Corsia the labellum is formed from the outer median tepal (sepal), whereas in orchids it is formed from the inner median tepal (petal) and is developmentally adaxial (but positionally abaxial in orchids with resupinate flowers). Furthermore, in orchids zygomorphy is also expressed in the stamen whorls, in contrast to Corsia. In Pauridia a complete stamen whorl is suppressed, but the 'lost' outer whorl is fused to the style. The evolution of adnation and zygomorphy are discussed in the context of the existing phylogenetic framework in monocotyledons. An arguably typological classification of floral terata is presented, focusing on three contrasting modes each of peloria and pseudopeloria. Dynamic evolutionary transitions in floral morphology are assigned to recently revised concepts of heterotopy (including homeosis) and heterochrony, seeking patterns that delimit developmental constraints and allow inferences regarding underlying genetic controls. Current evidence suggests that lateral heterotopy is more frequent than acropetal heterotopy, and that full basipetal heterotopy does not occur. Pseudopeloria is more likely to generate a radically altered yet functional perianth, but is also more likely to cause acropetal modification of the gynostemium. These comparisons indicate that there are at least two key genes or sets of genes controlling adnation, adaxial stamen suppression and labellum development in lilioid monocots; at least one is responsible for stamen adnation to the style (i.e. gynostemium formation), and another controls adaxial stamen suppression and adaxial labellum formation in orchids. Stamen adnation to the style may be a product of over-expression of the genes related to epigyny (i.e. a form of hyper-epigyny). If, as seems likely, stamen-style adnation preceded zygomorphy in orchid evolution, then the flowers of Pauridia may closely resemble those of the immediate ancestors of Orchidaceae, although existing molecular phylogenetic data indicate that a sister-group relationship is unlikely. The initial radiation in Orchidaceae can be attributed to the combination of hyper-epigyny, zygomorphy and resupination, but later radiations at lower taxonomic levels that generated the remarkable species richness of subfamilies Orchidoideae and Epidendroideae are more likely to reflect more subtle innovations that directly influence pollinator specificity, such as the development of stalked pollinaria and heavily marked and/or spur-bearing labella.     

Rangewide analysis of fungal associations in the fully mycoheterotrophic Corallorhiza striata complex (Orchidaceae) reveals extreme specificity on ectomycorrhizal Tomentella (Thelephoraceae) across North America

Fully mycoheterotrophic plants offer a fascinating system for studying phylogenetic associations and dynamics of symbiotic specificity between hosts and parasites. These plants frequently parasitize mutualistic mycorrhizal symbioses between fungi and trees. Corallorhiza striata is a fully mycoheterotrophic, North American orchid distributed from Mexico to Canada, but the full extent of its fungal associations and specificity is unknown. Plastid DNA (orchids) and ITS (fungi) were sequenced for 107 individuals from 42 populations across North America to identify C. striata mycobionts and test hypotheses on fungal host specificity. Four largely allopatric orchid plastid clades were recovered, and all fungal sequences were most similar to ectomycorrhizal Tomentella (Thelephoraceae), nearly all to T. fuscocinerea. Orchid-fungal gene trees were incongruent but nonindependent; orchid clades associated with divergent sets of fungi, with a clade of Californian orchids subspecialized toward a narrow Tomentella fuscocinerea clade. Both geography and orchid clades were important determinants of fungal association, following a geographic mosaic model of specificity on Tomentella fungi. These findings corroborate patterns described in other fully mycoheterotrophic orchids and monotropes, represent one of the most extensive plant-fungal genetic investigations of fully mycoheterotrophic plants, and have conservation implications for the >400 plant species engaging in this trophic strategy worldwide.     

A phylogenetic analysis of Diurideae (Orchidaceae) based on plastid DNA sequence data

DNA sequence data from plastid matK and trnL-F regions were used in phylogenetic analyses of Diurideae, which indicate that Diurideae are not monophyletic as currently delimited. However, if Chloraeinae and Pterostylidinae are excluded from Diurideae, the remaining subtribes form a well-supported, monophyletic group that is sister to a "spiranthid" clade. Chloraea, Gavilea, and Megastylis pro parte (Chloraeinae) are all placed among the spiranthid orchids and form a grade with Pterostylis leading to a monophyletic Cranichideae. Codonorchis, previously included among Chloraeinae, is sister to Orchideae. Within the more narrowly delimited Diurideae two major lineages are apparent. One includes Diuridinae, Cryptostylidinae, Thelymitrinae, and an expanded Drakaeinae; the other includes Caladeniinae s.s., Prasophyllinae, and Acianthinae. The achlorophyllous subtribe Rhizanthellinae is a member of Diurideae, but its placement is otherwise uncertain. The sequence-based trees indicate that some morphological characters used in previous classifications, such as subterranean storage organs, anther position, growth habit, fungal symbionts, and pollination syndromes have more complex evolutionary histories than previously hypothesized. Treatments based upon these characters have produced conflicting classifications, and molecular data offer a tool for reevaluating these phylogenetic hypotheses.     

A Phylogenetic Analysis of the Plastid matK Gene with Emphasis on Melanthiaceae sensu lato

Abstract: The presented mat K tree primarily agrees well with the previously presented rbc L tree and combined rbc L + atp B + 18SrDNA tree. According to the mat K tree, the monocotyledons are monophyletic with 100 % bootstrap support. Acorus diverges first from all other monocotyledons (90 % bootstrap support) in which two major clades are recognized: one (89 %) consisting of Alismatanae and Tofieldia (Nartheciaceae), and the other (< 50 %) comprising Lilianae, Commelinanae and Nartheciaceae other than Tofieldia. Within the latter major clade, Petrosavia and Japonolirion (Nartheciaceae) (82 %) diverge first from the remaining taxa (< 50 %) in which two clades are formed: one (81 %) consisting of Pandanales, Dioscoreales and Nartheciaceae-Narthecioideae, and the other (< 50 %) comprising Liliales, Asparagales and Commelinanae. In the former clade, Dioscoreales and Narthecioideae are grouped together (88 %). In the latter clade, Asparagales and Commelinanae are grouped together (< 50 %). Differences between the mat K and rbc L tree topologies appear in the positions of Tricyrtis (Calochortaceae) and Dracaenaceae. Differences between the mat K and combined rbc L + atp B + 18SrDNA tree topologies exist in the positions of the Petrosavia-Japonolirion pair (Nartheciaceae) and Pandanales. The stop codon position of the mat K gene appears to be highly variable among the monocotyledons, especially in the Liliales.     

Mycorrhizal fungi of Vanilla: diversity, specificity and effects on seed germination and plant growth

Mycorrhizal fungi are essential for the germination of orchid seeds. However, the specificity of orchids for their mycorrhizal fungi and the effects of the fungi on orchid growth are controversial. Mycorrhizal fungi have been studied in some temperate and tropical, epiphytic orchids, but the symbionts of tropical, terrestrial orchids are still unknown. Here we study diversity, specificity and function of mycorrhizal fungi in Vanilla, a pantropical genus that is both terrestrial and epiphytic. Mycorrhizal roots were collected from four Vanilla species in Puerto Rico, Costa Rica and Cuba. Cultured and uncultured mycorrhizal fungi were identified by sequencing the internal transcribed spacer region of nuclear rDNA (nrITS) and part of the mitochondrial ribosomal large subunit (mtLSU), and by counting number of nuclei in hyphae. Vanilla spp. were associated with a wide range of mycorrhizal fungi: Ceratobasidium, Thanatephorus and Tulasnella. Related fungi were found in different species of Vanilla, although at different relative frequencies. Ceratobasidium was more common in roots in soil and Tulasnella was more common in roots on tree bark, but several clades of fungi included strains from both substrates. Relative frequencies of genera of mycorrhizal fungi differed significantly between cultured fungi and those detected by direct amplification. Ceratobasidium and Tulasnella were tested for effects on seed germination of Vanilla and effects on growth of Vanilla and Dendrobium plants. We found significant differences among fungi in effects on seed germination and plant growth. Effects of mycorrhizal fungi on Vanilla and Dendrobium were similar: a clade of Ceratobasidium had a consistently positive effect on plant growth and seed germination. This clade has potential use in germination and propagation of orchids. Results confirmed that a single orchid species can be associated with several mycorrhizal fungi with different functional consequences for the plant.     

The duplicated B-class MADS-box genes display dualistic characters in orchid floral organ identity and growth

Orchidaceae are an excellent model to examine perianth development because of their sophisticated floral architecture. In this study, we identified 24 APETALA3 (AP3)-like and 13 PISTILLA (PI)-like genes from 11 species of orchids and characterized them into four AP3- and two PI-duplicated homologs. The first duplication event in AP3 homologs occurring in the early evolutionary history of the Orchidaceae gave rise to AP3A and AP3B clades. Further duplication events resulted in four subclades, namely AP3A1, AP3A2, AP3B1 and AP3B2, during the evolution of Orchidaceae. The AP3 paralogous genes were expressed throughout inflorescence and floral bud development. From the in situ hybridization results, we noticed that the transition timings from ubiquitous to constrained expression in floral organs for both clades are different. The transition point of expression of the AP3A clade (clades 3 and 4) was at the late floral organ primordia stage. In contrast, that for the AP3B clade (clades 1 and 2) was not observed until the late inflorescence and floral bud stages. In addition, the AP3 orthologous genes revealed diverse expression patterns in various species of orchids, whereas the PI homologs were uniformly expressed in all floral whorls. AP3A2 orthologs play a noticeable role in lip formation because of their exclusive expression in the lip. Further evidence comes from the ectopic expression of AP3A2 detected in the lip-like petals extending from the lip in four sets of peloric mutants. Finally, a Homeotic Orchid Tepal (HOT) model is proposed, in which dualistic characters of duplicated B-class MADS-box genes are involved in orchid perianth development and growth.     

Types of pollen dispersal units in orchids,and their consequences for germination and fertilization

The various pollen dispersal units (PDU) found in orchids are discussed together with possible evolutionary trends and the consequences for germination and fertilization. Orchids with monad and tetrad pollen form more complex dispersal units by means of pollenkitt, elastoviscin, a callosic wall, common walls or a combination of these. Evolutionary trends include (1) from pollenkitt to elastoviscin; (2) from monad to tetrads and multiples of tetrads; (3) from partially dehydrated (<30 %) to partially hydrated (>30 %) pollen; and (4) from monad pollen to PDUs with many pollen grains. The biological consequences concern both male and female reproductive systems. Some features of the male side are present in all orchids irrespective of the pollen dispersal unit, whereas other characters are found only in orchids with pollinia; the same applies for the female counterpart. Pollen grains of orchids with pollinia germinate at least 24 h after pollination because the pollen grains/tetrads must swell and make space for the growth of pollen tubes.     

The position of Cetacea within mammalia: phylogenetic analysis of morphological data from extinct and extant taxa

Knowledge of the phylogenetic position of the order Cetacea (whales, dolphins, and porpoises) within Mammalia is of central importance to evolutionary biologists studying the transformations of biological form and function that accompanied the shift from fully terrestrial to fully aquatic life in this clade. Phylogenies based on molecular data and those based on morphological data both place cetaceans among ungulates but are incongruent in other respects. Morphologists argue that cetaceans are most closely related to mesonychians, an extinct group of terrestrial ungulates. They have disagreed, however, as to whether Perissodactyla (odd-toed ungulates) or Artiodactyla (even-toed ungulates) is the extant clade most closely related to Cetacea, and have long maintained that each of these orders is monophyletic. The great majority of molecule-based phylogenies show, by contrast, not only that artiodactyls are the closest extant relatives of Cetacea, but also that Artiodactyla is paraphyletic unless cetaceans are nested within it, often as the sister group of hippopotamids. We tested morphological evidence for several hypotheses concerning the sister taxon relationships of Cetacea in a maximum parsimony analysis of 123 morphological characters from 10 extant and 30 extinct taxa. We advocate treating certain multistate characters as ordered because such a procedure incorporates information about hierarchical morphological transformation. In all most-parsimonious trees, whether multistate characters are ordered or unordered, Artiodactyla is the extant sister taxon of Cetacea. With certain multistate characters ordered, the extinct clade Mesonychia (Mesonychidae + Hapalodectidae) is the sister taxon of Cetacea, and Artiodactyla is monophyletic. When all fossils are removed from the analysis, Artiodactyla is paraphyletic with Cetacea nested inside, indicating that inclusion of mesonychians and other extinct stem taxa in a phylogenetic analysis of the ungulate clade is integral to the recovery of artiodactyl monophyly. Phylogenies derived from molecular data alone may risk recovering inconsistent branches because of an inability to sample extinct clades, which by a conservative estimate, amount to 89% of the ingroup. Addition of data from recently described astragali attributed to cetaceans does not overturn artiodactyl monophyly.     

Data set incongruence and correlated character evolution: an example of functional convergence in the hind-limbs of stifftail diving ducks

The unwitting inclusion of convergent characters in phylogenetic estimates poses a serious problem for efforts to recover phylogeny. Convergence is not inscrutable, however, particularly when one group of characters tracks phylogeny and another set tracks adaptive history. In such cases, convergent characters may be correlated with one or a few functional anatomical units and readily identifiable by using comparative methods. Stifftail ducks (Oxyurinae) offer one such opportunity to study correlated character evolution and function in the context of phylogenetic reconstruction. Morphological analyses place stifftail ducks as part of a large clade of diving ducks that includes the sea ducks (Mergini), Hymenolaimus, Merganetta, and Tachyeres, and possibly the pochards (Aythyini). Molecular analyses, on the other hand, place stifftails far from other diving ducks and suggest, moreover, that stifftails are polyphyletic. Mitochondrial cytochrome b gene sequences of eight stifftail species traditionally supposed to form a clade were compared with each other and with sequences from 50 other anseriform and galliform species. Stifftail ducks are not the sister group of sea ducks but lie outside the typical ducks (Anatinae). Of the four traditional stifftail genera, monophyly of Oxyura and its sister group relationship with Nomonyx are strongly supported. Heteronetta probably is the sister group of that clade, but support is weak. Biziura is not a true stifftail. Within Oxyura, Old World species (O. australis, O. leucocephala, O. maccoa) appear to form a clade, with New World species (O. jamaicensis, O. vittata) branching basally. Incongruence between molecules and morphology is interpreted to be the result of adaptive specialization and functional convergence in the hind limbs of Biziura and true stifftails. When morphological characters are divided into classes, only hind-limb characters are significantly in conflict with the molecular tree. Likewise, null models of synonymous and nonsynonymous substitution based on patterns of codon-degeneracy and chemical dissimilarity indicate that the nucleotide and amino acid changes postulated by the molecular tree are more plausible than those postulated by the morphological tree. These findings teach general lessons about the utility of highly adaptive characters (in particular those related to foraging ecology) and underscore the problems that convergence can pose for attempts to recover phylogeny. They also demonstrate how the concept of natural data partitions and simple models of evolution (e.g., parsimony, likelihood, neutrality) can be used to test the accuracy of independent phylogenetic estimates and provide arguments in favor of one tree topology over another.     

Leave it to the leaves: a molecular phylogenetic study of Malaxideae (Epidendroideae, Orchidaceae)

Nuclear ITS and plastid matK sequences were collected for 71 taxa of Malaxideae (Orchidaceae). Resulting cladograms are highly resolved and well supported by jackknife analyses. These indicate that the traditional classification system of the tribe using characters primarily related to floral morphology does not reflect the evolutionary history of these taxa. Rather, the tribe is split into two major clades: one of terrestrial species and another of epiphytes. Within the epiphytic clade, taxa with laterally compressed leaves (Oberonia) are monophyletic, whereas the remaining taxa (Liparis pro parte) have elongate conduplicate leaves and form a paraphyletic grade of at least two additional monophyletic lineages. Within the terrestrial clade, taxa with plicate leaves (Liparis p.p. and Malaxis p.p.) clearly separate from taxa with conduplicate leaves (Liparis p.p. and Malaxis p.p.). Although further taxon sampling should take place before nomenclature is changed, it seems evident that Malaxideae will need to be divided into at least seven genera. Furthermore, the transition from epiphytic to terrestrial habit is documented to have occurred only once in Malaxideae, and the value of vegetative over reproductive features in classifying some groups of orchids is again demonstrated.     

Soft anatomy, diffuse homoplasy, and the relationships of lizards and snakes

Most previous phylogenetic analyses of squamates (‘lizards’ and snakes) employing large character sets have focused on osteology. Soft anatomical traits bearing on this problem have usually been considered in small subsets. Here, a comprehensive phylogenetic analysis of squamate soft anatomy is attempted. 126 informative characters are assessed for 23 squamate lineages, representing snakes, amphisbaenians, dibamids, and all the traditionally recognized ‘families’ of lizards. The traditionally recognized groupings Iguania, Scleroglossa, Gekkota, Scincomorpha, Anguimorpha and Varanoidea are corroborated in this analysis. More controversial taxa are resolved as follows. Xantusiids, amphisbaenians and dibamids cluster with gekkotans, and snakes are strongly allied with anguimorphs in general, and varanids in particular. Nearly all these clades are congruent with those found in a recent comprehensive osteological analysis; the strong support for snake‐varanid relationships found in both studies is particularly notable. This congruence is surprising given that previous studies of soft anatomy tended to give differing and often heterodox results. These previous results can be attributed to overrepresentation of misleading characters in small isolated data sets. Such misleading signals are minimized when data sets are combined. For instance, the snake‐varanid clade is contradicted by many characters, and analyses of particular organ systems therefore give differing results. However, characters that are incongruent with the snake‐varanid clade also disagree with each other (diffuse homoplasy), rather than forming coherent support for some particular alternative clade (concerted homoplasy). In a combined analysis these incongruent but diffuse characters cancel each other out to leave a very strong (and orthodox) phylogenetic signal. These results underscore the view that the raw amount of homoplasy — as revealed by consistency and retention indices — is not the only determinant of phylogenetic signal; the distribution of that homoplasy is also important. Thus, questioning a phylogenetic hypothesis (e.g. the snake‐varanid clade) by identifying numerous conflicting characters is insufficient — the structure of the conflicting characters should be assessed in a rigorous phylogenetic analysis.     

Genealogical concordance between the mating type locus and seven other nuclear genes supports formal recognition of nine phylogenetically distinct species within the Fusarium graminearum clade

Species limits were investigated within the Fusarium graminearum clade (Fg clade) through phylogenetic analyses of DNA sequences from portions of 11 nuclear genes including the mating-type (MAT) locus. Nine phylogenetically distinct species were resolved within the Fg clade, and they all possess contiguous MAT1-1 and MAT1-2 idiomorphs consistent with a homothallic reproductive mode. In contrast, only one of the two MAT idiomorphs was found in five other species, four of which were putatively asexual, and the other was heterothallic. Molecular evolutionary analyses indicate the MAT genes are under strong purifying selection and that they are functionally constrained, even in species for which a sexual state is unknown. The phylogeny supports a monophyletic and apomorphic origin of homothallism within this clade. Morphological analyses demonstrate that a combination of conidial characters could be used to differentiate three species and three species pairs. Species rank is formally proposed for the eight unnamed species within the Fg clade using fixed nucleotide characters.