Systematics of the tribe Podalyrieae (Fabaceae) based on DNA, morphological and chemical data

Phylogenetic relationships among nine genera and 28 species of the southern African tribe Podalyrieae were estimated from sequences of the internal transcribed spacer (ITS) of nuclear ribosomal DNA as well as morphological and chemical data. Morphological and ITS sequence data produced cladograms with similar topologies, both supporting the monophyly of Podalyrieae (excluding Hypocalyptus ). The combined data sets indicate that subtribe Xiphothecinae are monophyletic, but embedded within Podalyriinae. The high degree of congruence between previous taxonomic hypotheses and those based on DNA data provides further evidence for the utility of ITS sequences in studying phylogeny.  © 2002 The Linnean Society of London , Botanical Journal of the Linnean Society , 2002, 139 , 159–170.     

Galápagos' Opuntia (prickly pear) cacti: extensive morphological diversity, low genetic variability

Due to the pronounced morphological variation and geographical distribution of Galápagos' Opuntia cacti, numerous hypotheses have been advanced regarding their radiation, diversification, and classification. The currently accepted classification is based on morphology and recognizes six species and fourteen varieties, but the plasticity of many of the characteristics renders any morphological taxonomy problematic. Our analysis of previously published morphological data agrees only partially with the current classification. We present the first molecular phylogeny of these plants. Multiple DNA sequences indicate little genetic distinction among the currently identified species, despite restricted gene flow and limited long distance dispersal within the archipelago. No clear relationship exists between morphological and genetic differences. These results suggest that both molecular and morphological data should be used in conservation planning.  © 2009 The Linnean Society of London, Biological Journal of the Linnean Society , 2009, 96 , 451–461.     

Molecular phylogeny of the genus Philodendron (Araceae): delimitation and infrageneric classification

The genus Philodendron (Araceae) is a large neotropical group whose classification remains unclear. Previous classifications are based on morphological characters, mainly from the inflorescence, flower and leaf shape. The classification by Krause, with few modifications, is still the most commonly used system. To examine phylogenetic relationships in the genus, two ribosomal DNA nuclear markers, internal transcribed spacer (ITS) and external transcribed spacer (ETS), and the chloroplast intron rpl 16, were sequenced and analysed for more than 80 species of Philodendron and its close relative Homalomena . According to the resulting phylogeny, the genus Homalomena may be paraphyletic to the genus Philodendron . The inclusion of the American Homalomena species within the genus Philodendron might resolve this taxonomic problem. All three subgenera of Philodendron were revealed as monophyletic. Below the subgeneric level, the groups obtained in our phylogeny globally correspond to sections recognized in previous classifications. Among the morphological characters used by previous taxonomists to build their classifications, and which we optimized onto one of the most parsimonious trees, most characters were found to be homoplasious. However, leaf shape, characteristics of the sterile zone on the spadix and venation patterns are useful for delimiting subgenera and sections within the genus.  © 2008 The Linnean Society of London, Botanical Journal of the Linnean Society , 2008, 156 , 13–27.     

Molecular phylogeny of the western Atlantic species of the genus Portunus (Crustacea, Brachyura, Portunidae)

The genus Portunus encompasses a comparatively large number of species distributed worldwide in temperate to tropical waters. Although much has been reported about the biology of selected species, taxonomic identification of several species is problematic on the basis of strictly adult morphology. Relationships among species of the genus are also poorly understood, and systematic review of the group is long overdue. Prior to the present study, there had been no comprehensive attempt to resolve taxonomic questions or determine evolutionary relationships within this genus on the basis of molecular genetics. Phylogenetic relationships among 14 putative species of Portunus from the Gulf of Mexico and other waters of the western Atlantic were examined using 16S sequences of the rRNA gene. The resultant molecularly based phylogeny disagrees in several respects with current morphologically based classification of Portunus from this geographical region. Of the 14 species generally recognized, only 12 appear to be valid. We recommend that P. vossi be hereafter regarded as a junior synonym of P. spinimanus and that P. bahamensis be regarded as a junior synonym of P. depressifrons . Our analysis suggests that western Atlantic members of the genus can be subdivided into at least three well-defined clades. Pending further molecular analyses with a large subset of species, it appears that the genus is not monophyletic and that it warrants further taxonomic revision.  © 2007 The Linnean Society of London, Zoological Journal of the Linnean Society , 2007, 150 , 211–220.     

Phylogenetic relationships and biogeographical history of the genus Rhinoclemmys Fitzinger, 1835 and the monophyly of the turtle family Geoemydidae (Testudines: Testudinoidea)

Rhinoclemmys is an interesting genus of turtles biogeographically and ecologically, being the only genus of the family Geoemydidae that occurs in the New World and inhabiting a wide range of habitats from aquatic to highly terrestrial. Here we present a molecular phylogeny of Rhinoclemmys using both mitochondrial and nuclear genes. Our results strongly support the monophyletic and subfamilial status of Rhinoclemmys within the monophyletic family Geoemydidae. Within Rhinoclemmys , two clades are strongly supported, i.e. R. annulata  +  R. pulcherrima and R. areolata  +  R. punctularia  +  R. diademata  +  R. funerea  +  R. melanosterna , but the positions of R. nasuta and R. rubida are still weakly supported. In terms of the biogeographical history, the results of this study, coupled with palaeontological evidence, corroborate the hypothesis that this group migrated from Asia to the Americas across the Bering Strait during the early Eocene. The radiation of Rhinoclemmys in Central and South America corresponds well with vicariance events, including the emergence of the Sierra Madres of Mexico and the Nuclear Highland, and dispersals across the Panama land bridge. Interestingly, our resulting phylogeny suggests this group invaded South America at least four times and that dispersal of R. nasuta to South America probably took place in the early Miocene before the emergence of the Isthmus of Panama. We finally discuss our phylogenetic results with regard to the monophyly of the family Geoemydidae and in the context of previous morphological analyses. © 2008 The Linnean Society of London, Zoological Journal of the Linnean Society , 2008, 153 , 751–767.     

Morphological differentiation among closely related species with disjunct distributions: a case study of Mediterranean Cyclamen L. subgen. Psilanthum Schwarz (Primulaceae)

In Cyclamen subgenus Psilanthum , previous authors have recognized three species ( C. repandum, C. balearicum and C. creticum ), with C. repandum subdivided into three subspecies (ssp. repandum , ssp. peloponnesiacum and ssp. rhodense ), and two varieties (var. vividum and var. peloponnesiacum ) within C. repandum ssp. peloponnesiacum . To examine the validity of this classification and the degree of morphological differentiation among closely related endemic taxa with disjunct distributions, we undertook analyses of three quantitative and eight qualitative morphological traits of flowers and leaves, most of which have previously been used without statistical comparison in the classification of the different taxa. Cyclamen balearicum showed high levels of morphological differentiation from all other taxa in subgenus Psilanthum consistent with its specific status. In contrast, morphological differentiation between C. creticum and subspecies of C. repandum was similar to that among the three subspecies of C. repandum . When compared with a recent molecular phylogeny of this subgenus, our results suggest that C. creticum may best be described as a geographical subspecies of C. repandum . The two varieties of C. repandum ssp. peloponnesiacum showed few significant differences for individual traits and their overall morphology is very similar to each other. The morphology of plants at three sites on Corsica strongly suggest, consistent with molecular data, the occurrence of hybrid populations between C. balearicum (outside of its previously recognized distribution) and local C. repandum .  © 2002 The Linnean Society of London, Botanical Journal of the Linnean Society , 2002, 139 , 133–144.     

Phylogeography and morphological variability in land snails: the Sicilian Marmorana (Pulmonata, Helicidae)

Land snails have long been recognized as suitable organisms for studying phenotypic differentiation and phylogeny in relation to geographical distribution. Morphological data (shell and anatomy biometry on different geographical scales) and partial sequences from mitochondrial genes (cytochrome oxidase subunit I , 16S rDNA) were used to test whether morphological patterns match phylogeny in a diversified group of Sicilian rock-dwelling land snails belonging to the genus Marmorana . The taxonomic implications of the three character sets (shell and anatomical biometry and molecular data) were also considered. The inferred phylogenetic relationships do not match morphological (shell and genitalia) patterns. This result may significantly modify the current taxonomy. Mitochondrial based reconstructions define several supported clades well correlated with geographic distribution and populations were found to be distributed parapatrically. The progressive decline in mitochondrial DNA sequence similarity over a distance of 250 km is consistent with a model of isolation by distance, a pattern previously recognized for other groups of land snails. For one clade of Marmorana , colonization along Mediterranean trade routes appears to be a possibility.  © 2008 The Linnean Society of London, Biological Journal of the Linnean Society , 2008, 94 , 809–823.     

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.     

Phylogeny and biogeography of the Vitrinidae (Gastropoda: Stylommatophora)

The phylogeny of the Vitrinidae is reconstructed in a cladistic analysis based on characters of the genitalia, the copulation behaviour and the radula. The genera with an atrial stimulator turned out to be the earliest branches of the Vitrinidae, whereas the genera with a glandula amatoria form a monophyletic, taxonomically apomorphic group. The differences between the proposed phylogeny and previous hypotheses are discussed. The ancestral areas of the Vitrinidae and its sister group, the limacoid slugs Boettgerillidae–Limacidae–Agriolimacidae, are estimated using weighted ancestral area analysis. The Vitrinidae and the limacoid slugs might have originated by a vicariance event between Central Europe and the Near East. © 2002 The Linnean Society of London. Zoological Journal of the Linnean Society , 2002, 134 , 347–358.     

What is the subtribe Glossonematinae (Apocynaceae: Asclepiadoideae)? A phylogenetic study based on cpDNA spacer

Evidence from the chloroplast trn T-L spacer, trn L intron and trn L-F spacer shows the subtribe Glossonematinae of the tribe Asclepiadeae, hitherto composed of the Arabian and North African genera Glossonema , Odontanthera and Solenostemma , not to be monophyletic. While the affinities of Solenostemma cannot be determined with certainty at present, molecular, karyological and morphological evidence suggests that Glossonema and Odontanthera are closely allied to Pentarrhinum , an African genus of five species, belonging to the Cynanchinae.  © 2002 The Linnean Society of London, Botanical Journal of the Linnean Society , 2002, 139 , 145–158.     

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.     

Falling apart and merging: diversification of slender salamanders (Plethodontidae: Batrachoseps) in the American West

The plethodontid genus Batrachoseps , the slender salamanders, is the most diverse clade of salamanders in western North America, but it has posed taxonomic difficulties because it contains many morphologically cryptic species. A segment of the mitochondrial DNA gene cytochrome b was studied for 278 individuals densely sampled from throughout the range of all 18 described species and several undescribed species. Phylogenetic analyses of the mtDNA data identify six major clades, one corresponding to the subgenus Plethopsis and five within a monophyletic subgenus Batrachoseps. All major clades and most species within these clades display strong phylogeographic structuring. Comparisons of mtDNA and allozyme data show that several allozymically cohesive groups are not monophyletic with respect to mtDNA. We suggest that this phenomenon results from fragmentation of populations, divergence in allopatry, and then recontact and gradual merging of units caused predominantly by male-mediated gene flow. The mtDNA offers evidence that populations were once more isolated than they are now, while the patterns of allozyme variation reflect recent and current interactions among populations. The complex patterns of morphological, allozymic and mtDNA variation associated with the constantly changing geological landscape give insight into the nature of processes responsible for species formation in Batrachoseps .  © 2002 The Linnean Society of London. Biological Journal of the Linnean Society , 2002, 76 , 361–391.     

Phylogeny of the suborder Psocomorpha: congruence and incongruence between morphology and molecular data (Insecta: Psocodea: ‘Psocoptera’)

The largest suborder of bark lice (Insecta: Psocodea: ‘Psocoptera’) is Psocomorpha, which includes over 3600 described species. We estimated the phylogeny of this major group with family‐level taxon sampling using multiple gene markers, including both nuclear and mitochondrial ribosomal RNA and protein‐coding genes. Monophyly of the suborder was strongly supported, and monophyly of three of four previously recognized infraorders (Caeciliusetae, Epipsocetae, and Psocetae) was also strongly supported. In contrast, monophyly of the infraorder Homilopsocidea was not supported. Based on the phylogeny, we divided Homilopsocidea into three independent infraorders: Archipsocetae, Philotarsetae, and Homilopsocidea. Except for a few cases, previously recognized families were recovered as monophyletic. To establish a classification more congruent with the phylogeny, we synonymized the families Bryopsocidae (with Zelandopsocinae of Pseudocaeciliidae), Calopsocidae (with Pseudocaeciliidae), and Neurostigmatidae (with Epipsocidae). Monophyly of Elipsocidae, Lachesillidae, and Mesopsocidae was not supported, but the monophyly of these families could not be rejected statistically, so they are tentatively maintained as valid families. The molecular tree was compared with a morphological phylogeny estimated previously. Sources of congruence and incongruence exist and the utility of the morphological data for phylogenetic estimation is evaluated. © 2014 The Linnean Society of London     

Phylogenetic relationships within Plantago (Plantaginaceae): evidence from nuclear ribosomal ITS and plastid trnL-F sequence data

A molecular phylogenetic study of Plantago L. (Plantaginaceae) analysed nucleotide variation in the internal transcribed spacers (ITS) of nuclear ribosomal and plastid trnL-F regions. Included are 57 Plantago species, with two Aragoa species as the ingroup and three Veronica species as the outgroup. Phylogenetic analysis using maximum parsimony identified five major clades, corresponding to the taxonomic groups Plantago subgenera Plantago, Coronopus, Psyllium, Littorella and Bougueria . Aragoa is sister to genus Plantago . Plantago subgenus Littorella is sister to the other subgenera of Plantago . The results are in general correlated with a morphological phylogenetic study and iridoid glucoside patterns, but Plantago subgenus Albicans is paraphyletic and should be included in Plantago subgenus Psyllium sensu lato to obtain a monophyletic clade with six sections. Plantago section Hymenopsyllium is more closely related to section Gnaphaloides than to section Albicans . Plantago subgenus Bougueria is sister to subgenus Psyllium s.l. section Coronopus in Plantago subgenus Coronopus is subdivided in two series. Only some of the sections can be resolved into series. DNA variation within genus Plantago is high, a result that would not have been predicted on the basis of morphology, which is relatively stereotyped. If we calibrate a molecular clock based on the divergence of P. stauntoni , endemic to New Amsterdam in the southern Indian Ocean, we calculate the time of the split between Plantago and Aragoa to be 7.1 million years ago, which is congruent with the fossil record.  © 2002 The Linnean Society of London, Botanical Journal of the Linnean Society , 2002, 139 , 323–338.     

Phylogeny and biogeography of cichlid fishes (Teleostei: Perciformes: Cichlidae)

Family level molecular phylogenetic analyses of cichlid fishes have generally suffered from a limited number of characters and/or poor taxonomic sampling across one or more major geographic assemblage, and therefore have not provided a robust test of early intrafamilial diversification. Herein we use both nuclear and mitochondrial nucleotide characters and direct optimization to reconstruct a phylogeny for cichlid fishes. Representatives of major cichlid lineages across all geographic assemblages are included, as well as nearly twice the number of characters as any prior family‐level study. In a strict consensus of 81 equally most‐parsimonious hypotheses, based on the simultaneous analysis of 2222 aligned nucleotide characters from two mitochondrial and two nuclear genes, four major subfamilial lineages are recovered with strong support. Etroplinae, endemic to Madagascar (Paretroplus) and southern Asia (Etroplus), is recovered as the sister taxon to the remainder of Cichlidae. Although the South Asian cichlids are monophyletic, the Malagasy plus South Asian lineages are not. The remaining Malagasy lineage, Ptychochrominae, is monophyletic and is recovered as the sister group to a clade comprising the African and Neotropical cichlids. The African (Pseudocrenilabrinae) and Neotropical (Cichlinae) lineages are each monophyletic in this reconstruction. The use of multiple molecular markers, from both mitochondrial and nuclear genes, results in a phylogeny that in general exhibits strong support, notably for early diversification events within Cichlidae. Results further indicate that Labroidei is not monophyletic, and that the sister group to Cichlidae may comprise a large and diverse assemblage of percomorph lineages. This hypothesis may at least partly explain why morphological studies that have attempted to place Cichlidae within Percomorpha, or that have tested cichlid monophyly using only “labroid” lineages, have met with only limited success. © The Willi Hennig Society 2004.     

Maximizing information in systematic revisions: a combined molecular and morphological analysis of a cryptic green pitviper complex (Trimeresurus stejnegeri)

Although the integration of DNA information in taxonomy has been invaluable, logistical problems relating to sampling can seriously limit its applicability. Here we describe the analysis of a morphologically cryptic species complex, in which we maximize the information present by using both a DNA phylogeny and a multivariate morphometric approach. The green pitviper Trimeresurus stejnegeri s.l. is widespread in Asia, with a number of described subspecies (some of which are considered full species by some workers) and two new species that have recently been described from Thailand. The phylogeny indicates three clades, which can also be discerned in the principal component analyses of morphological variation. Combining molecular and morphological information permits evaluation of the taxonomic position of populations not represented in the phylogeny − in particular, the subspecies T. s. chenbihui and T. s. yunnanensis . We discuss nomenclatural issues raised by this analysis, although these cannot be fully resolved until the holotypes of these subspecies can be examined. Finally, we apply a molecular clock calibrated in New World pitvipers, and discuss some of the palaeoclimatic changes that might have impacted upon diversification in this group.  © 2004 The Linnean Society of London, Biological Journal of the Linnean Society, 2004, 82 , 219–235.