Simultaneous analysis of basal Hymenoptera (Insecta): introducing robust-choice sensitivity analysis

Molecular characters are analysed on their own and in combination with morphological data to examine the phylogenetic relationships of the basal lineages of Hymenoptera ('Symphyta'). This study covers 47 sawfly genera and nine apocritan families and includes molecular sequences from five genes − 12S, 16S, 18S and 28S ribosomal genes and cytochrome oxidase 1 − as well as 343 morphological characters. A robust-choice sensitivity analysis is performed with the data. First, the simultaneous analysis is repeated three times, each time employing a different step matrix for weighting the transformations of the molecular characters. Then, the results of all three simultaneous analyses are summarized in a strict consensus in order to avoid basing the conclusions on a narrow set of assumptions. This methodology is discussed in the paper. The relationships among superfamilies largely confirm previous hypotheses, being (Xyeloidea (Tenthredinoidea s.l. (Pamphilioidea (Cephoidea (Siricoidea (Xiphydrioidea (Orussoidea Apocrita))))))), where Siricoidea is understood as Siricidae+Anaxyelidae. However, the relationships within Tenthredinoidea s.s. proposed here are novel: ({Argidae Pergidae}[ Athalia {(Diprionidae Cimbicidae) Tenthredinidae minus Athalia }]).  © 2003 The Linnean Society of London . Biological Journal of the Linnean Society , 2003, 79, 245–275.     

The evolution of CAM in the subfamily Pitcairnioideae (Bromeliaceae)

A molecular phylogeny for the subfamily Pitcairnioideae was inferred to examine the distribution of crassulacean acid metabolism in the subfamily. For this purpose, a neighbour-joining tree with p-distances was built using a MatK chloroplast gene data set. The phylogenetic results of our analysis confirmed the monophyletic condition of most genera examined: Brocchinia , Dyckia , Encholirium , Fosterella , Hechtia and Puya . A paraphyletic basal sequence showed Hechtia branching off from the basal node, followed by Brocchinia , Cottendorfia  +  Navia phelpsiae, and Puya . The remaining taxa were divided into two groups: (a) Deuterocohnia meziana , Dyckia , Encholirium ; Fosterella ; Deuterocohnia spp. +  Pitcairnia heterophyla ; (b) Pepinia , Pitcairnia spp. and Navia igneosicola . The basal placement of the CAM genera Hecthia indicates that CAM may be a 'primitive condition' in Pitcairnioideae and that C₃ species may have lost the ability to induce CAM. In this molecular tree, CAM metabolism appeared scattered throughout the tree. Current knowledge, however, does not exclude the possibility that CAM arose only once and it has been switching on and off in various lineages. Further detailed studies on photosynthetic metabolisms and the phylogenetic distribution of characters will provide a better basis on which to evaluate photosynthetic origins.  © 2003 The Linnean Society of London, Biological Journal of the Linnean Society , 2003, 80 , 261–268.     

New data on the Cainotheriidae (Mammalia, Artiodactyla) from the early Oligocene of south-western France

The Cainotheriidae are small artiodactyls that suddenly appeared in the late Eocene of western Europe. A revision of early Oligocene cainotheriid lineages is proposed on the basis of newly dated material from the Quercy Phosphorites (south-western France). A significant diversification of the group occurred at the end of the Eocene. Few species seem to have persisted through the Eocene/Oligocene boundary, but the Cainotheriidae subsequently diversified rapidly during the early Oligocene.  © 2005 The Linnean Society of London, Zoological Journal of the Linnean Society , 2005, 144 , 145−166.     

The phylogeny and taxonomy of Hippopotamidae (Mammalia: Artiodactyla): a review based on morphology and cladistic analysis

The phylogeny and taxonomy of the whole family Hippopotamidae is in need of reconsideration, the present confusion obstructing palaeoecology and palaeobiogeography studies of these Neogene mammals. The revision of the Hippopotamidae initiated here deals with the last 8 Myr of African and Asian species. The first thorough cladistic analysis of the family is presented here. The outcome of this analysis, including 37 morphological characters coded for 15 extant and fossil taxa, as well as non-coded features of mandibular morphology, was used to reconstruct broad outlines of hippo phylogeny. Distinct lineages within the paraphyletic genus Hexaprotodon are recognized and characterized. In order to harmonize taxonomy and phylogeny, two new genera are created. The genus name Choeropsis is re-validated for the extant Liberian hippo. The nomen Hexaprotodon is restricted to the fossil lineage mostly known in Asia, but also including at least one African species. The genus Hippopotamus is confirmed. These changes represent substantial advances for understanding the evolutionary history of the Hippopotamidae, and provide a new framework for future studies.  © 2005 The Linnean Society of London, Zoological Journal of the Linnean Society , 2005, 143 , 1–26.     

Molecular phylogeny and diversification history of Prosopis (Fabaceae: Mimosoideae)

The genus Prosopis is an important member of arid and semiarid environments around the world. To study Prosopis diversification and evolution, a combined approach including molecular phylogeny, molecular dating, and character optimization analysis was applied. Phylogenetic relationships were inferred from five different molecular markers ( mat K- trn K, trn L- trn F, trn S- psb C, G3pdh, NIA). Taxon sampling involved a total of 30 Prosopis species that represented all Sections and Series and the complete geographical range of the genus. The results suggest that Prosopis is not a natural group. Molecular dating analysis indicates that the divergence between Section Strombocarpa and Section Algarobia plus Section Monilicarpa occurred in the Oligocene, contrasting with a much recent diversification (Late Miocene) within each of these groups. The diversification of the group formed by species of Series Chilenses, Pallidae, and Ruscifoliae is inferred to have started in the Pliocene, showing a high diversification rate. The moment of diversification within the major lineages of American species of Prosopis is coincident with the spreading of arid areas in the Americas, suggesting a climatic control for diversification of the group. Optimization of habitat parameters suggests an ancient occupation of arid environments by Prosopis species.  © 2008 The Linnean Society of London, Biological Journal of the Linnean Society , 2008, 93 , 621–640.     

Similarity

Recent debates concerning conflicting hypotheses of higher-level phylogeny such as the sister-group relationships of tetrapods, turtles, birds and snakes, serve as examples in the analysis of the nature of morphological evidence as it is currently used in phylogeny reconstruction. We note a recent shift of emphasis towards ever-larger data matrices, which may come at the cost of detailed character analysis and argumentation. Because the assessment of morphological characters necessarily entails a conceptual element of abstraction, there is also a threat that preconceived notions of phylogeny influence character analysis. Because the test of congruence does not address character analysis in itself, we argue that character hypotheses, i.e. primary conjectures of homology, need to be testable, and potentially refutable, in their own right. We demonstrate the use of classical criteria of homology (topological relations and/or connectivity, in conjunction with the subsidiary criteria of special similarity and intermediate forms) in the test, and refutation, of morphological characters. Rejection of the classical criteria of homology in the test of morphological character hypotheses requires the formulation of alternative methods of test and potential falsification of morphological characters that have so far not been proposed. © 2002 The Linnean Society of London, Biological Journal of the Linnean Society , 2002, 75 , 59–82.     

The evolution of venom-delivery systems in snakes

The Colubroidea represents approximately 2300 of the 2700 species of living snakes and includes all venomous taxa. Although many morphological studies of colubroid snakes have been carried over the last hundred years, the phylogenetic relationships within this group are poorly known. In this study, components of the venom-delivery system (VDS) were examined within the context of two conflicting phylogenetic hypotheses proposed in 1988 by Cadle and in 1998 by Kraus & Braun. The results suggest that several major morphological changes occurred early in colubroid evolution: a Duvernoy's gland evolved, the posterior maxillary teeth became specialized relative to the anterior maxillary teeth, and the attachment of the pterygoideus muscle moved forward to a position associated with the posterior maxillary teeth. These innovations may have allowed the great radiation of colubroid snakes that led to the Colubroidea representing such a large percentage of living snakes. More recently, three separate lineages of colubroids have independently evolved highly specialized front-fanged VDSs with large and complex venom glands, venom gland compressor muscles, and tubular fangs.  © 2003 The Linnean Society of London, Zoological Journal of the Linnean Society, 2003, 137 , 337−354.     

Weintrauboa, a new genus of pimoid spiders from Japan and adjacent islands, with comments on the monophyly and diagnosis of the family Pimoidae and the genus Pimoa (Araneoidea, Araneae)

The spider genus Weintrauboa new genus (Araneae, Pimoidae) is described to place two species of pimoids from Japan and adjacent islands that were formerly classified in the linyphiid genus Labulla . Weintrauboa contortipes (Karsch) new comb., the type species, and W. chikunii (Oi) new comb. are redescribed. Parsimony analysis of morphological characters provides robust support for the monophyly of the genus Weintrauboa and corroborates the monophyly of Pimoa , Pimoidae, and the clade Linyphiidae plus Pimoidae. New diagnoses for Pimoa and Pimoidae are provided.  © 2003 The Linnean Society of London, Zoological Journal of the Linnean Society , 2003, 139 , 261–281     

Patterns of diversification on old volcanic islands as revealed by the woodlouse-hunter spider genus Dysdera (Araneae, Dysderidae) in the eastern Canary Islands

Long-term erosion and subsidence cause dramatic alterations in the physical and ecological features of oceanic islands. Although oceanic islands have been extensively used as models for the study of speciation, little attention has been given to investigating evolutionary patterns in old volcanic islands that have suffered severe climatic degradation. The spider genus Dysdera has diversified across the Canary Islands and has evolved endemisms in the low-elevation, xeric eastern islands, which sharply contrast with the younger, higher, and more humid western islands. A combined phylogenetic analysis of seven mitochondrial and nuclear genes reveals that the eastern Canaries were colonized twice, although only one lineage underwent in situ diversification. Origins of the speciose lineage remain obscure, but probably preceded diversification of present-day Iberian and North African species. A second colonization of the eastern Canaries from North Africa has occurred in more recent times. Molecular analyses reveal several instances of geographically coherent cryptic lineages further supported by morphometric evidence. Analyses of diversification rates suggest deceleration of diversification over the course of time, and this is compatible with increasing extinction rates due to drastic yet continuous ecological changes. Extinction may also explain incongruent patterns of morphological differentiation and species coexistence. Despite a general trend towards community impoverishment, there is also evidence for recent speciation events linked to ecological shifts, which may illustrate the origins of nonspeciose relic lineages on islands.  © 2008 The Linnean Society of London, Biological Journal of the Linnean Society , 2008, 94 , 589–615.     

A new species of the genus Lightiella: the first record of Cephalocarida (Crustacea) in Europe

A new species of Cephalocarida belonging to the genus Lightiella is described. Like all known species of Lightiella , the new species is characterized by reduction of trunk segment 8, which also lacks both pleura and thoracopods. The diagnostic characters of the species are: (1) one seta on the inner distal corner of the penultimate endopodal segment of second maxilla and thoracopods 1–5; (2) only one claw on the distal segment of the endopod of thoracopod 6. A cladistic analysis of 27 morphological characters was used to estimate the phylogeny of all species of Lightiella , with all other cephalocarid species used as outgroups. The discovery of this species in the Mediterranean fills a gap in the distribution of the genus and of the entire class.  © 2006 The Linnean Society of London, Zoological Journal of the Linnean Society , 2006, 148 , 209–220.     

Heritable genetic variation and potential for adaptive evolution in asexual aphids (Aphidoidea)

Aphid life cycles can encompass cyclical parthenogenesis, obligate parthenogenesis, obligate parthenogenesis with male production and an intermediate 'bet-hedging' strategy where an aphid genotype will over-winter by continuing to reproduce by parthenogenesis and by investment in sexually produced eggs. In this paper, we focus on aphid lineages that reproduce entirely parthenogenetically (asexual aphids), in contrast to those that have any sexual forms in the annual cycle. Using modern molecular techniques, aphid biologists have made many empirical observations showing that asexual lineages are widespread both geographically and temporally. Indeed, we are collectively beginning to gather data on the evolution and persistence of these lineages through time. Here we review aphid karyology and parthenogenesis, both essential for interpretation of the molecular and ecological evolution of aphid asexual lineages. We describe the growing list of studies that have identified aphid genotypes that are both temporally and geographically widespread. We then collate examples of molecular and chromosomal evolution in asexual aphids and review the literature pertaining to phenotypic evolution and ecological diversification of asexual aphid lineages. In addition, we briefly discuss the potential of bacterial endosymbionts and epigenetic effects to influence the evolution of asexual aphid lineages. Lastly we provide a list of aphid taxa believed to be obligately asexual. This will be a useful resource for those seeking parthenogenetic animals as study systems. In conclusion, we present guidelines for the use of the term clone in aphid biology and stress the need for well-designed and well-executed studies examining the potential of asexual aphid lineages for adaptive evolution.  © 2003 The Linnean Society of London. Biological Journal of the Linnean Society , 2003, 79 , 115–135.     

Ecological diversity and adaptive tendencies in the tropical fern Trichomanes L. (Hymenophyllaceae) with special reference to climbing and epiphytic habits

Among the basal fern families, the Hymenophyllaceae, with more than 600 species, display a high diversity in terms of their morphology and the habitats that they occupy. We have chosen to focus on Trichomanes L., a clearly defined genus for which a phylogeny is presently being developed, to investigate the appearance of the climbing and epiphytic habits, as well as the related supposed adaptive characters. In this study we present the first review of the different ecological types within the genus: terrestrial, climbing (divided into hemi-epiphytic forms and true lianas), and epiphytic types. The study of several features concerning stem morphology and leaf size allows a proposal on relationships between ecology and plant morphology. Terrestrial species display a thick monocaulous rhizome with robust roots and short internodes. Climbing species are characterized by a branched, thick, creeping rhizome with long internodes. Epiphytic species also exhibit long, creeping and branching stems with long internodes but the rhizome is fine to filiform. Under these circumstances, there is a reduction of root system and frond size leading to dwarfism in numerous instances. This may be related to an extreme hygrophilous epiphytic strategy. Finally, hypotheses on the evolution of these habits and hence on the evolutionary relationships between ecology and characters are presented and discussed.  © 2003 The Linnean Society of London, Botanical Journal of the Linnean Society , 2003, 142 , 41–63.     

Phylogenetic relationships among gekkotan lizards inferred from C-mos nuclear DNA sequences and a new classification of the Gekkota

A phylogeny of gekkotan lizards was derived from C- mos nuclear DNA sequence data. Forty-one currently recognized genera, representing all major gekkotan lineages, were included in the study. A total of 378 bp of partial C- mos gene sequences was obtained and aligned. Maximum parsimony (MP) and maximum likelihood (ML) trees were generated based on unweighted analysis using P AUP *; similar tree topologies were recovered by both methods. The Eublepharidae were monophyletic and its relationship to other major clades was poorly resolved. The Pygopodidae of Kluge (1987) was monophyletic, but relationships within this group differed from those retrieved by previous analyses. The Diplodactylini + padded carphodactylines were the sister group of pygopods + padless carphodactylines. The Gekkonidae were monophyletic, but we found no evidence in support of the Teratoscincinae, as Teratoscincus was embedded well within the gekkonids. Both MP and ML analyses supported the basal position of Sphaerodactylus within the gekkonids, in contrast to morphologically based hypotheses. We propose a new higher order classification of the Gekkota that reflect these results. Five gekkotan families: Eublepharidae, Gekkonidae, Pygopodidae, Diplodactylidae, and Carphodactylidae are recognized. The higher order status of the sphaerodactyls will require more intensive sampling of this group. Our results support the hypothesis that the early cladogenesis of the Gekkota was associated with the split of Eastern Gondwanaland from Western Gondwanaland. Divergences among living genera in the Eublepharidae and the Eastern Gondwanan lineages (Diplodactylidae, Pygopodidae and Carphodactylidae) may be older than those in the Gekkonidae.  © 2004 The Linnean Society of London, Biological Journal of the Linnean Society , 2004, 83 , 353–368.     

Systematics and phylogeny of the tribe Paragini (Diptera: Syrphidae) based on molecular and morphological characters

We studied the phylogeny and systematics of the tribe Paragini (Diptera: Syrphidae) using morphological and molecular data. The paper presents separate parsimony analyses of both adult morphological characters and partial DNA sequence data from mitochondrial cytochrome c oxidase I and nuclear ribosomal 28S rRNA gene, as well as a combined analysis of all the data. The data set of morphological characters included some features of the male terminalia (i.e. shape of the ejaculatory apodeme; relative position of elements of the aedeagal complex; shape of surstylar apodeme; shape of the aedeagal apodeme) not previously used in the systematics of the Paragini. The trees obtained from separate parsimony analyses of molecular and morphological data produced almost identical topologies. Four lineages are supported by the combined data set, and we establish two new subgenera, i.e. Serratoparagus Vujić et Radenković subgen. nov., and Afroparagus Vujić et Radenković subgen. nov., and redefine Pandasyopthalmus Stuckenberg, 1954 stat. rev. and Paragus Latreille, 1804, stat. rev. The monophyly of the Pandasyopthalmus clade, including the species fitting neither of the current species groups ( jozanus -group) of Paragini, is established. Diagnoses of all known species groups are presented, including a new arrangement of almost all valid species of Paragini.  © 2008 The Linnean Society of London, Zoological Journal of the Linnean Society , 2008, 152 , 507–536.     

A new species of Viola L. (Violaceae) from South Anatolia

A new species of Viola L., Viola yildirimlii M. Dinç & Y. Bağcı sp. nov. from South Anatolia is described and illustrated. It is found on the rocky slopes of Aladağ National Park, in the county of Adana, south Turkey, at an elevation of 1800 m. It belongs to Viola , subsect. Viola , and is similar to the Turkish endemics Viola isaurica Contandr. & Quézel and V. kizildaghensis M. Dinç & Ş. Yıldırımlı. Diagnostic morphologic characters for a detailed discrimination from two similar taxa and other Turkish Eflagellatae species are discussed.  © 2003 The Linnean Society of London, Botanical Journal of the Linnean Society , 2003, 141 , 477–482.     

A phylogenetic analysis of the arachnid orders based on morphological characters

Morphological evidence for resolving relationships among arachnid orders was surveyed and assembled in a matrix comprising 59 euchelicerate genera (41 extant, 18 fossil) and 202 binary and unordered multistate characters. Parsimony analysis of extant genera recovered a monophyletic Arachnida with the topology (Palpigradi (Acaromorpha (Tetrapulmonata (Haplocnemata, Stomothecata nom. nov. )))), with Acaromorpha containing Ricinulei and Acari, Tetrapulmonata containing Araneae and Pedipalpi (Amblypygi, Uropygi), Haplocnemata (Pseudoscorpiones, Solifugae) and Stomothecata (Scorpiones, Opiliones). However, nodal support and results from exploratory implied weights analysis indicated that relationships among the five clades were effectively unresolved. Analysis of extant and fossil genera recovered a clade, Pantetrapulmonata nom nov. , with the topology (Trigonotarbida (Araneae (Haptopoda (Pedipalpi)))). Arachnida was recovered as monophyletic with the internal relationships (Stomothecata (Palpigradi, Acaromorpha (Haplocnemata, Pantetrapulmonata))). Nodal support and exploratory implied weights indicated that relationships among these five clades were effectively unresolved. Thus, some interordinal relationships were strongly and/or consistently supported by morphology, but arachnid phylogeny is unresolved at its deepest levels. Alternative hypotheses proposed in the recent literature were evaluated by constraining analyses to recover hypothesized clades, an exercise that often resulted in the collapse of otherwise well-supported clades. These results suggest that attempts to resolve specific nodes based on individual characters, lists of similarities, evolutionary scenarios, etc., are problematic, as they ignore broader impacts on homoplasy and analytical effects on non-target nodes.  © 2007 The Linnean Society of London, Zoological Journal of the Linnean Society , 2007, 150 , 221–265.     

A molecular study of phylogenetic relationships and evolution of antipredator strategies in Australian Diplodactylus geckos, subgenus Strophurus

We present phylogenetic analyses of the lizard genus Diplodactylus subgenus Strophurus using 1646 aligned positions of mitochondrial DNA sequences containing 893 parsimony-informative characters for samples of 12 species of Strophurus and 19 additional Australian gecko species. Sequences from three protein-coding genes (ND1, ND2 and COI) and eight intervening transfer RNA genes were examined using parsimony, maximum-likelihood and Bayesian analyses. Species of Strophurus appeared to form a monophyletic group with the possible exception of S. taenicauda . Strophurus has evolved two distinct defence/display characteristics: caudal glands, which expel an unpalatable substance, and striking mouth colours. Caudal glands appeared to have arisen once in a common ancestor of Strophurus , with dermal augmentation of caudal glands characterizing a subclade within the subgenus. Evolution of yellow and dark-blue mouth colours in Strophurus occurred in the context of diurnal activity and may be interpreted as an augmentation of defensive behavioural displays. Molecular divergence suggests that arboreality evolved in a common ancestor of Oedura and Strophurus approximately 29 Mya and that the caudal glands of Strophurus arose approximately 25 Mya.  © 2004 The Linnean Society of London, Biological Journal of the Linnean Society , 2004, 82 , 123–138.     

The adaptive significance of coloration in lagomorphs

Lagomorph pelage coloration was matched to habitat type, geographical region, altitude and behaviour to explore the adaptive significance of coloration patterns in this little-studied order of mammals. Analyses were conducted with and without taking phylogeny into account. The former analyses were based on a weighted, phylogenetic supertree for all extant species of lagomorphs that we constructed using morphological and molecular data from 146 papers in the literature. Although our analyses represent an initial, somewhat crude investigation, several clear trends are evident. First, overall body coloration across lagomorphs tends to match the background as shown for pale and red coloration and perhaps seasonal pelage change. The case for countershading being a method of concealment is far less strong. Second, ear tips appear to have a communicative role since they are conspicuous in many different habitats. Third, hypotheses for tail tips having a communicative role, for extremities being dark for physiological reasons, and for Gloger's rule received only partial support.  © 2003 The Linnean Society of London, Biological Journal of the Linnean Society , 2003, 79, 309–328.     

Combining molecular, morphological and ecological data to infer species boundaries in a cryptic tropical pitviper

Few operational methods exist for delimiting species boundaries, and these usually require sampling strategies that are unrealistic for widespread organisms that occur at low densities. Here we apply molecular, morphological and ecological species delimitation criteria to a wide-ranging, fragmented group of Asian green pitvipers, the Popeia popeiorum complex. A mitochondrial DNA phylogeny for the group indicates two well-differentiated clades, corresponding mainly to northern and southern parts of its range. Strong phylogeographical structure within each clade suggests isolation in forest refugia during the Pliocene and a southward colonization of the Sunda islands during the Pleistocene. Multivariate analysis of morphological characters reveals a generally conserved pattern of geographical variation, incongruent with the recovered phylogenetic history. We compare groups delineated by mtDNA variation to morphological and ecological divisions in the complex, and discuss the implications of these for the taxonomy of the group. Discordance between species boundaries inferred from different criteria suggests that combining independent sources of data provides the most reliable estimation of species boundaries in organisms that are difficult to sample in large numbers.  © 2006 The Linnean Society of London, Biological Journal of the Linnean Society , 2006, 87 , 343–364.