Outline of phylogeny and character evolution in Rhizocarpon (Rhizocarpaceae, lichenized Ascomycota) based on nuclear ITS and mitochondrial SSU ribosomal DNA sequences

The phylogeny of the lichen genus Rhizocarpon (Rhizocarpaceae, lichenized Ascomycota) was investigated using nucleotide sequences from the ITS region of the nuclear ribosomal DNA and the SSU region of the mitochondrial ribosomal DNA from 13 species of Rhizocarpon , Catolechia wahlenbergii and Poeltinula cerebrina . Phylogenetic estimations were performed using maximum parsimony and Bayesian MCMC tree sampling. Twelve phylogenetic null hypotheses were tested using MCMC tree sampling. The evolution of five morphological characters was assessed by mapping them onto MCMC tree samples. The results indicate that Rhizocarpon in its current sense is polyphyletic and can only be made monophyletic if R. hochstetteri is excluded or Poeltinula , and possibly also Catolechia , are included. The root placement in the Rhizocarpaceae is ambiguous, either Catolechia or Poeltinula + R. hochstetteri being the sistergroup to the rest of the family. Previously suggested infrageneric arrangements based on presence or absence of the yellow substance rhizocarpic acid in the thallus or the septation of the ascospores are unnatural. Some species with grey or brown thallus may have evolved from a yellow ancestor. Spore septation and colour, amyloidity of the thalline medulla, and the presence of stictic acid complex and rhizocarpic acid are shown to have changed multiple times during the course of evolution.  © 2002 The Linnean Society of London, Biological Journal of the Linnean Society , 2002, 77 , 535–546.     

Character divergences and convergences in canopy-dwelling Loranthaceae

The Loranthaceae is the largest plant family with aerial branch parasites termed mistletoes. Three genera of Loranthaceae are terrestrial root parasites and the remaining 72 genera are aerial parasites. Several characters, including habit, haustorial type, germination pattern, pollen morphology, chromosome number, inflorescence morphology and flower merosity, fusion, symmetry and size, are considered to reflect evolutionary relationships within the family. Convergence is a common evolutionary pattern and can confound interpretations of evolution. We investigated character evolution by mapping character states onto a phylogenetic tree based on the nuclear ITS and chloroplast trnL–trnF regions. Convergences in form were found in several characters, including habit, haustorial type, flower symmetry and merosity. These convergences typically correspond to ecological parameters such as pollination syndrome or stresses associated with the canopy habit. Other characters such as chromosome number and germination pattern illustrate divergent evolution among clades.  © 2006 The Linnean Society of London, Botanical Journal of the Linnean Society , 2006, 150 , 101–113.     

Morphological character evolution and molecular trees in sepiids (Mollusca: Cephalopoda): is the cuttlebone a robust phylogenetic marker?

The sepiids are characterized by their cuttlebone or sepion, an internal shell resulting from secondary mineralization of a chitinous 'gladius'. The various species are identified using a combination of shell criteria and 'soft-part' characters. Using mitochondrial genes, we established phylogenetic relationships of sepiids including the three accepted genera ( Sepia , Sepiella , Metasepia ) and a species complex of uncertain status ( Doratosepion ). We showed the Sepia genus to be paraphyletic and found no direct correlation between geographical distribution and systematics. We mapped, on the molecular tree, shell characteristics commonly used as reliable diagnostic criteria for taxonomy. Due to the plasticity of the shell, these characters did not appear phylogenetically informative. In an attempt to define systematic categories related to phylogenetic relationships, new clear synapomorphies need to be established for each genus, necessitating a revision of the genus Sepia .  © 2006 The Linnean Society of London, Biological Journal of the Linnean Society , 2006, 89 , 139–150.     

The use of colour characters in phylogenetic reconstruction

The use of coloration as a source of characters in phylogenetic reconstruction is investigated using 54 published data sets. Studies were divided into two categories based on a priori postulated roles of the coloration: (1) aposematic and mimetic coloration and (2) nonaposematic, nonmimetic coloration plus dual signals. Colour characters superficially appear to provide similar phylogenetic signal to morphological ones in the case of aposematic and mimetic coloration but significantly less in other situations. However, the data indicated that the apparent signal in the aposematic/mimetic studies tends to be in greater conflict with the morphological signal. It is proposed that this reflects constraints in the evolution of colour characters that are part of aposematic/mimetic patterns and not that they are necessarily good indicators of phylogeny.  © 2006 The Linnean Society of London, Biological Journal of the Linnean Society , 2006, 88 , 193–202.     

The systematic relationships of glucosinolate-producing plants and related families: a cladistic investigation based on morphological and molecular characters

A cladistic analysis is performed using 94 morphological and biochemical characters for 42 genera to compare a phylogeny based on morphological data with those obtained using different genes ( rbc L, atp B, 18S RNA, mat K) or their combination with morphological data, and to understand the floral evolution within the expanded Brassicales (Capparales) relative to Sapindales and Malvales. The tree produced with morphological data is congruent with those obtained from macromolecular studies in obtaining a well-supported glucosinolate-producing clade and an expanded Sapindales. The combined analysis of the morphological and molecular characters is generally well resolved with support for many of the relationships. The inclusion of the fossil taxon Dressiantha demonstrates the value of inserting fossil evidence in phylogenetic analyses. However, the fossil appears to be related to the Anacardiaceae and not to the Brassicales. The core Brassicales are well supported by a number of synapomorphies, although the internal position of Tovariaceae and Pentadiplandraceae is not well resolved. Emblingiaceae appears to be related to Bataceae and Salvadoraceae. Several significant morphological characters are mapped on the combined trees and their evolutionary significance is discussed. Within Brassicales and Sapindales several well supported clades can be recognized which merit ordinal or subordinal status, putting the present orders at a higher level; these include: Tropaeolales, Setchellanthales, Batidales, Brassicales (Brassiciflorae), Burserales, Sapindales and Rutales (Sapindiflorae). The present scheme of affinities within the Brassicales corresponds well with a gradual morphological evolution in the order.  © 2006 The Linnean Society of London, Botanical Journal of the Linnean Society , 2006, 151 , 453–494.     

Mitochondrial DNA phylogeny of the woodpecker genus Veniliornis (Picidae, Picinae) and related genera implies convergent evolution of plumage patterns

The woodpecker genus Veniliornis comprises 12 species, all restricted to the New World tropics. The seemingly distantly related genus Picoides is broadly distributed in Eurasia and North America with two putative species, P. lignarius and P. mixtus , occurring in South America. The two genera are clearly distinct with respect to general plumage colouration and patterning as well as habitat utilization and thus traditionally have been placed in different tribes. Phylogenetic analyses of mtDNA sequences from the COI and cyt b genes indicated that both genera are reciprocally paraphyletic. The two South American species of Picoides belong to a clade comprising most species of Veniliornis , but V. fumigatus of Central and north-western South America belongs to a clade comprising species of Picoides . The mtDNA tree also indicated that Veniliornis is not closely related to the genus Piculus, as is implicit in current classifications. Misclassifications involving Veniliornis at both the generic and tribal levels appear to result from convergent evolution of plumage traits in specific forest types. We infer that the common ancestor of Veniliornis entered South America approximately at the time the Isthmus of Panama was formed, and diversification within South America was rapid.  © 2006 The Linnean Society of London, Biological Journal of the Linnean Society , 2006, 87 , 611–624.     

Exploring the genomic mysteries of polyploidy in cotton

For several years allopolyploid cottons have been the subject of evolutionary investigations into the genomic mysteries of polyploidy. An array of genomic interactions have been documented, including interlocus concerted evolution, differential rates of genomic evolution and intergenomic sequence transfer. Substantial alterations in gene expression have occurred in response to allopolyploidization, including gene silencing and expression changes that vary by organ. Some of the molecular phenomena occurring in polyploids appear to be non-Mendelian. Many of the genomic and expression alterations have occurred on an evolutionary timescale, whereas others reflect more immediate consequences of genomic merger.  © 2004 The Linnean Society of London, Biological Journal of the Linnean Society, 2004, 82 , 573–581.     

Phylogenetics of Echinodorus (Alismataceae) based on morphological data

Echinodorus (Alismataceae) is a genus of aquatic and semi-aquatic herbs naturally distributed from Argentina to the USA but commonly used as ornamentals in aquaria worldwide. The phylogeny of the genus was studied on the basis of 96 morphological characters. The analysis resulted in a single most-parsimonious tree supporting a polyphyletic origin of the genus. However, subgenus Echinodorus together with Echinodorus nymphaeifolius formed a clade. Two large clades can be recognized in Echinodorus s.s. , but previous subdivisions of the genus are not supported and some earlier proposed subspecific combinations were shown to be non-monophyletic. Addition of continuous characters coded as value ranges enhanced both the resolution and the support values of the tree. Hence, inclusion of continuous overlapping data is encouraged in phylogenetic studies.  © 2006 The Linnean Society of London, Botanical Journal of the Linnean Society , 2006, 150 , 291–305.     

The utility of morphological characters in gastropod phylogenetics: an example from the Calyptraeidae

Organismal taxonomy is often based on a single or a small number of morphological characters. When they are morphologically simple or known to be plastic, we may not have great confidence in the taxonomic conclusions of analyses based on these characters. For example, calyptraeid gastropod shells are well known for their simplicity and plasticity, and appear to be subject to frequent evolutionary convergences, but are nevertheless the basis for calyptraeid taxonomy. In a case like this, knowing how the pattern of relationships inferred from morphological features used in traditional taxonomy compares to the patterns of relationships inferred from other morphological characters or DNA sequence data would be useful. In this paper, I examine the relative utility of traditional taxonomic characters (shell characters), anatomical characters and molecular characters for reconstructing the phylogeny of calyptraeid gastropods. The results of an ILD test and comparisons of the recovered tree topologies suggest that there is conflict between the DNA sequence data and the morphological data. Very few of the nodes recovered by the morphological data were recovered by any other dataset. Despite this conflict, the inclusion of morphological data increased the resolution and support of nodes in the topology recovered from a combined dataset. The RIs and CIs of the morphological data on the best estimate topology were not any worse than these indices for the other datasets. This analysis demonstrates that although analyses can be misled by these convergences if morphological characters are used alone, these characters contribute significantly to the combined dataset.  © 2003 The Linnean Society of London . Biological Journal of the Linnean Society , 2003, 78 , 541–593.     

Evolution of epiphytes in Davalliaceae and related ferns

The evolution of epiphytes in Davalliaceae was investigated by field observations and molecular phylogenetic analyses. Field studies revealed that in Davalliaceae and related ferns, epiphytes in a broad sense are classified into climber, secondary hemi-epiphyte, and obligate epiphyte, based on combinations of the places (ground vs. tree) of inferred spore germination and sporophyte growth. Some species of Davalliaceae have multiple life forms, i.e. secondary hemi-epiphyte and obligate epiphyte, whereas others are obligate epiphytes. Phylogenetic trees obtained from rbcL and accD gene sequences supported that secondary hemi-epiphytic Oleandra is sister to the epiphytic Davalliaceae and polygrammoid ferns. Analyses of life form evolution based on the phylogenetic relationships suggested that obligate epiphytes of the Davalliaceae and polygrammoid ferns evolved from secondary hemi-epiphytes, or less likely from climbers. We hypothesized a scenario for the evolution of life forms in Davalliaceae and related groups that involves successive changes in rhizome habit, root function, and germination place. Rhizome dorsiventrality and scale morphology, shared by climbers, secondary hemi-epiphytes, and obligate epiphytes examined, may be other innovations for the ferns to have evolved into epiphytes.  © 2006 The Linnean Society of London, Botanical Journal of the Linnean Society , 2006, 151 , 495–510.     

Lucinidae (Bivalvia) – the most diverse group of chemosymbiotic molluscs

Recent molecular analyses have demonstrated that the traditional Lucinoidea, comprising the extant families Lucinidae, Thyasiridae, Ungulinidae, Fimbriidae, and Cyrenoididae, is not monophyletic. Thyasiridae and Ungulinidae are unrelated to Lucinidae, a result corroborated by clear morphological differences between the groups. Chemosymbiosis in Thyasiridae and Lucinidae has been independently derived. Within the family Lucinidae, previous ideas of relationship and subfamilial divisions based on shell characters have little support from molecular results. Anatomical characters of the ctenidia, mantle gills, and posterior apertures have potential in phylogenetic analysis but rigorous analysis of shell characters is also needed. Although there is a good fossil record of Lucinidae throughout the Cenozoic and Mesozoic, in the Palaeozoic fossils are less frequent and most need reappraisal. The Silurian Ilionia prisca is probably the earliest fossil with convincing lucinid features, followed in the Devonian by Phenacocyclas and some Paracyclas species.  © 2006 The Linnean Society of London, Zoological Journal of the Linnean Society , 2006, 148 , 421–438.     

Taxonomic relevance of the gametophytic generation in a strictly rupicolous fern group: Asplenium seelosii s.l.

The systematics of the Asplenium seelosii complex has been debated for a long time. This complex includes strictly rupicolous plants that live on limestone cliffs mainly in the mountains of south-west Europe: the Alps, the Pyrenees, and several mountain ranges of the eastern Iberian Peninsula. The disjunct distribution of its populations and several morphological characters, i.e. leaf indumentum and the structure of the perispore, have been used to distinguish two species and up to four subspecies. The goal of this study was to determine whether the characters of the gametophytic generation and young sporophytes can contribute to the recognition of the proposed taxa. The analysis of all of these characters together differentiated two groups that correspond to the established species, A. seelosii and A. celtibericum , but not enough differences were found to separate the subspecies in each of them.  © 2006 The Linnean Society of London, Botanical Journal of the Linnean Society , 2006, 151 , 375–386.     

A new dwarf Coffea (Rubiaceae) from southern Cameroon

A distinctive new species of dwarf monocaulous Coffea (Rubiaceae) from Cameroon is described and illustrated. Coffea mapiana is the second dwarf monocaulous known from Cameroon. Its diagnostic characters are elucidated and its taxonomic affinities are discussed; a conservation assessment is provided.  © 2006 The Linnean Society of London, Botanical Journal of the Linnean Society , 2006, 151 , 425–430.     

Evolutionary relationships among the Pulmonate land snails and slugs (Pulmonata, Stylommatophora)

We have incorporated an additional 56 species of land snails and slugs in our ribosomal (r) RNA molecular phylogeny. The new taxa include representatives of several important groups. The molecular tree now includes 160 species of stylommatophoran land snails and slugs in 144 genera in 61 families. In the rDNA tree, the Stylommatophora are principally divided into an 'achatinoid' and a 'non-achatinoid' clade. Within these clades, several major land snail groups, including the Orthurethra, Elasmognatha, Limacoidea, and Helicoidea, are supported. Overall, the rDNA molecular phylogeny has remained stable following the incorporation of the additional taxa, with these additions having little impact on the major evolutionary patterns in the tree. Taxonomic coverage of the Orthurethra, Orthalicidae, Camaenidae, and Bradybaenidae is increased significantly. The camaenids and bradybaenids form a complex, and both appear to be paraphyletic. Several families of uncertain affinity, such as the Sagdidae and Thyrophorellidae, are included for the first time. The Sagdidae are shown to belong to the Helicoidea, and the Thyrophorellidae to the Achatinoidea.  © 2006 The Linnean Society of London, Biological Journal of the Linnean Society , 2006, 87 , 593–610.     

Are protochordates chordates?

This paper challenges the widely accepted view that protochordates (lancelets and tunicates) should be included together with vertebrates within the monophyletic assemblage of the chordates since they share a few distinguishing characters, such as a dorsally located notochord and central nervous system (CNS). The homology of these axial structures is not supported convincingly by morphology and molecular biology. Besides, for notochord and CNS to be dorsal, the embryos of protochordates, unlike those of vertebrates, should be orientated with the blastopore coincident with the dorsal side. This embryonic orientation is never reported in other bilaterians and is inconsistent with the genetic control of the body axes. Alternatively, protochordates could be orientated just as the vertebrates according to the regulation of axial patterning. In this case, the notochord and CNS appear to be located on the ventral side. As suggested by molecular and structural data, they may correspond to the stomodaeal/ventral midline cells and CNS of gastroneuralians. This conclusion may have far-reaching implications concerning the origin of the vertebrates and the evolution of nervous systems and neural crest/placodes.  © 2006 The Linnean Society of London, Biological Journal of the Linnean Society , 2006, 87 , 261–284.     

Correlated evolution of aquatic prey-capture strategies in European and American natricine snakes

The evolution of aquatic prey-capture strategies in snakes has been suggested as a model system for the study of convergence. However, hypotheses of correlated evolution of prey-capture strategy with different aspects of foraging niche have never been tested quantitatively. Whereas a considerable amount of data is available for North American species, data for European species are scarce. In this study we combine original data on prey-capture strategies and strike velocities for European natricines with data for North American Natricinae obtained from the literature. We did not find any evidence for correlated evolution between prey-capture strategy and strike velocity with diet, but there was a significant correlation with prey density. Thus, our study suggests that prey density, rather than diet, played an important role in the evolution of the different prey-capture strategies and strike velocities of natricine snakes.  © 2006 The Linnean Society of London, Biological Journal of the Linnean Society , 2006, 88 , 73–83.     

On the sex-specific mechanisms of butterfly flight: flight performance relative to flight morphology, wing kinematics, and sex in Pararge aegeria

Many evolutionary ecological studies have documented sexual dimorphism in morphology or behaviour. However, to what extent a sex-specific morphology is used differently to realize a certain level of behavioural performance is only rarely tested. We experimentally quantified flight performance and wing kinematics (wing beat frequency and wing stroke amplitude) and flight morphology (thorax mass, body mass, forewing aspect ratio, and distance to centre of forewing area) in the butterfly Pararge aegeria (L.) using a tethered tarsal reflex induced flight set-up under laboratory conditions. On average, females showed higher flight performance than males, but frequency and amplitude did not differ. In both sexes, higher flight performance was partly determined by wing beat frequency but not by wing stroke amplitude. Dry body mass, thorax mass, and distance to centre of forewing area were negatively related to wing beat frequency. The relationship between aspect ratio and wing stroke amplitude was sex-specific: females with narrower wings produced higher amplitude whereas males show the opposite pattern. The results are discussed in relation to sexual differences in flight behaviour.  © 2006 The Linnean Society of London, Biological Journal of the Linnean Society , 2006, 89 , 675–687.     

Chromosomal variability in the genus Primula (Primulaceae)

Chromosome numbers and measurements were recorded in 47 individuals of ten taxa of Primula , representing eight species and two subspecies from ten populations. The basic numbers of chromosomes were x  = 8, 9 or 11, and they were mostly metacentric, medium-long to medium-small, ranging in length from c . 3.6 µm to 1.6 µm. Diploid chromosome numbers of 2 n  = 2 x  = 24 and 22 were scored for the first time in P. loeseneri Kitag. and P. prenantha Balf. & Sm., respectively. A new ploidy level of 2 n  = 4 x  = 44 was found in P. burmanica Balf. & King. The recorded diploid numbers of the remaining species confirmed earlier reports. Interspecific variability in chromosome numbers was correlated with heterogeneity in their mean length. Comparison of the data with those in the literature revealed that the observed variability of chromosomal characters was compatible with the other taxonomic criteria and supports the current taxonomic delimitation. Chromosomal variation at the diploid level is the predominant feature in Primula evolution, and allopatric speciation has played a major role in its specific diversity. Subgen. Aleuritia could represent the main clade from which the other subgenera have evolved. The origin of the chromosome numbers, geographical distribution and evolution of the species were assessed, and the parallel polyphyletic mode of evolution in the genus was confirmed.  © 2006 The Linnean Society of London, Botanical Journal of the Linnean Society , 2006, 150 , 211–219.     

Phylogenetic relationships based on morphology among the Diospyros (Ebenaceae) species endemic to the Mascarene Islands

The Diospyros (Ebenaceae) species which colonized the Mascarene Islands, namely Mauritius, Reunion and Rodrigues, have been decimated over the years by human settlements. Of the 14 endemic species that have been described and collected for herbaria, Diospyros angulata is now believed to be extinct in Mauritius. The phylogenetic relationships of the 14 Diospyros species were determined using maximum parsimony analysis of 35 morphological characters. This analysis separated the Mascarene Diospyros into two major clades, with D. revaughanii , D. egrettarum and D. leucomelas grouped in the same strongly supported most basal clade while the rest of the species formed the other major clade. High bootstrap values were obtained for the sister species D. angulata and D. boutonania , and the clade clustering the upland species D. neraudii , D. nodosa and D. pterocalyx . There was also relatively strong support for the clade comprising D. hemiteles and D. melanida , which are located in mid altitude regions. These results indicate that Diospyros species most probably colonized the coastal areas of Mauritius and then moved to mid altitude habitats before finally reaching the upland regions. There are also strong indications that D. borbonica and D. diversifolia , endemic to Reunion and Rodrigues, respectively, resulted from migrations from Mauritius.  © 2006 The Linnean Society of London, Botanical Journal of the Linnean Society , 2006, 150 , 307–313.