Towards a monophyletic genus Albinaria (Gastropoda, Pulmonata): the first molecular study into the phylogenetic position of eastern Albinaria species

Recent molecular phylogenetic studies of the terrestrial snail genus Albinaria have caused a radical reassessment of its taxonomy. These studies, however, were limited to western species. This paper examines mitochondrial 12S sequences and nuclear ITS1 & 2 sequences of both eastern and western species, and demonstrates that Albinaria, in its most recent definition, is not monophyletic. Both molecular datasets place ' Albinaria ' hedenborgi from Lebanon in a well-supported clade with species of the genus Cristataria , distributed south-east of the vicariant range of Albinaria . The remaining species from Cyprus, Turkey and Greece constitute a well-supported monophyletic group. These two clades form geographical clusters, whereas Albinaria in the current definition (including ' A. '  hedenborgi ) has a disjunct distribution. ' A.' hedenborgi should therefore be classified with Cristataria , together with the morphologically similar and geographically close ' A. '  nadimi .  © 2005 The Linnean Society of London, Zoological Journal of the Linnean Society , 2005, 143 , 531−542.     

Evidence for ecological speciation in the sister species Candidula unifasciata (Poiret, 1801) and C. rugosiuscula (Michaud, 1831) (Helicellinae, Gastropoda)

This paper studies the speciation of two land snail species in south-east France. By using two mitochondrial and one nuclear gene, the species are shown to be sister species within the larger clade of western European Candidula species. The species never occurred syntopically, but a narrow contact zone population was identified. Recent range expansions inferred from phylogeographical methods indicated that the present day distributions are not limited by the colonization capacity of the species. Analysis of environmental variables suggested distribution along an ecotone. The gastropod community is also correlated to this gradient. Morphometric shell analysis showed that the divergence between the sister species is a result of desiccation-resistant shell characters. We therefore conclude that the cause for the ecological speciation is most probably the establishment of the Mediterranean climate ≈ 3.2 mya. A model of ecological speciation with a moving ecotone is put forward.  © 2003 The Linnean Society of London, Biological Journal of the Linnean Society , 2003, 79, 611–628.     

Mitochondrial phylogeny of Arvicolinae using comprehensive taxonomic sampling yields new insights

Comprehensive taxonomic sampling can vastly improve the accuracy of phylogenetic reconstruction. Here, we present the most inclusive phylogenetic analysis of Arvicolinae (Mammalia, Rodentia) to date, combining all published cytochrome  b gene sequences of greater than 1097 bp and new sequences from two monotypic genera. Overall, the phylogenetic relationships between 69 species of voles and lemmings, representing 18 genera and 10 tribes, were studied. By applying powerful modern approaches to phylogenetic reconstruction, such as maximum likelihood and Bayesian analysis, we provide new information on the early pulse of evolution within the Arvicolinae. While the position of two highly divergent lineages, Phenacomys and Ondatra , could not be resolved, the tribe Lemmini, appeared as the most basal group of voles. The collared lemmings (Dicrostonychini) grouped together with all of the remaining tribes. The two previously unstudied monotypic genera Dinaromys and Prometheomys form a moderately well-supported monophyletic clade, possibly a sister group to Ellobius (Ellobiusini). Furthermore, with one exception, all tribes ( sensu Musser & Carleton, 2005) proved to be monophyletic and can thus be regarded as meaningful evolutionary entities. Only the tribe Arvicolini emerged as paraphyletic in both analyses because of the unresolved phylogenetic position of Arvicola terrestris . Steppe voles of the genus Lagurus were solidly supported as a sister group to the Microtus and allies clade.  © 2008 The Linnean Society of London, Biological Journal of the Linnean Society , 2008, 94 , 825–835.     

Phylogenetic relationships and evolution of Orbiniidae (Annelida, Polychaeta) based on molecular data

The phylogenetic relationships of orbiniid taxa were reconstructed based on sequence data of the mitochondrial 16S rRNA and nuclear 18S rRNA genes. Both genes were analysed separately and in combination using maximum likelihood, Bayesian inference and maximum parsimony. Regardless of the method used, a clade consisting of the investigated Orbiniidae, Methanoaricia dendrobranchiata and Questa was strongly supported by the 18S dataset. The analysis of the combined dataset suggests inclusion of M. dendrobranchiata within the Orbiniidae with close relationships to species of Orbinia and Phylo, rather than as a sister taxon to all other orbiniids. Evidence is given for the paraphyletic status of Leitoscoloplos , Naineris , Orbinia , Phylo and Scoloplos , which represent the most species-rich genera of the Orbiniidae. It is thus reasoned that the morphological characters presently used for genus diagnosis are not informative for cladistic analysis. No support is found for the hypothesis that taxa of the Protoariciinae represent juveniles of Orbiniinae. Instead, in the case of Protoaricia oerstedi , strong support for a progenetic origin is found.  © 2005 The Linnean Society of London, Zoological Journal of the Linnean Society , 2005, 144 , 59−73.     

Phylogenetic analysis of Nymphaeales using fast-evolving and noncoding chloroplast markers

The Nymphaeales (water-lilies and relatives) represent one of the earliest branching lineages of angiosperms and comprise about 70 aquatic species. Here, we present a comprehensive study of phylogenetic relationships within the Nymphaeales from a dataset containing 24 representatives of the order, including all currently recognized genera and all subgenera of the genus Nymphaea , plus 5 outgroup taxa. Nine different regions of the chloroplast genome − comprising spacers, group II introns, a group I intron, and a protein coding gene − were analysed. This resulted in a character matrix of 6597 positions and an additional 369 characters obtained from coded length mutations. Maximum parsimony and Bayesian analyses of the complete dataset yielded congruent, fully resolved and well-supported trees. Our data confirm the monophyly of the Cabombaceae but do not provide convincing support for the monophyly of Nymphaeaceae with respect to Nuphar . Moreover, the genus Nymphaea is inferred to be paraphyletic with respect to Ondinea , Victoria and Euryale . In fact, the Australian endemic Ondinea forms a highly supported clade with members of the Australian Nymphaea subgenus Anecphya . In addition, Victoria and Euryale are inferred to be closely related to a clade comprising all night-blooming water-lilies ( Nymphaea subgenera Hydrocallis and Lotos ). An experimental approach showed taxon sampling to be of influence on the nodes reconstructed in core Nymphaeaceae. The results underscore that more diverse genera, if not clearly known to be monophyletic, should be represented by all major lineages.  © 2007 The Linnean Society of London, Botanical Journal of the Linnean Society , 2007, 154 , 141–163.     

Phylogeny and classification of the Scopulini moths (Lepidoptera: Geometridae, Sterrhinae)

The phylogenetic relationships of the genera in the geometrid tribe Scopulini (Lepidoptera: Sterrhinae) were examined using 141 characters of adult morphology and ecology. The study material included 92 species, representing all previously recognized genera and covering the morphological variation and full geographical range of the tribe. The cladistic analysis resulted in 20 equally parsimonious trees and a strict consensus cladogram based on these was well resolved. A majority of the recovered synapomorphic characters have been used previously in the taxonomy of the tribe. However, many novel characters were found in the sclerotized structures of the thorax. Many previously recognized genera were found to be nonmonophyletic and based on the present revised, synapomorphy-based classification, the number of recovered genera is reduced considerably. Twenty new generic synonyms and 90 new or revived species combinations are proposed. Seven genera are considered valid, with the large genus Scopula Schrank including over 85% of all species in the tribe. The taxonomic history of the tribe is reviewed and the problems of earlier classifications are discussed. A key to the genera is presented, although an informal diagnosis is preferred. All recognized genera are illustrated and a revised world checklist of the Scopulini is presented.  © 2005 The Linnean Society of London, Zoological Journal of the Linnean Society , 2005, 143 , 473−530.     

A phylogenetic analysis of the genera of Lejeuneaceae (Hepaticae)

The Lejeuneaceae are the largest family of the liverworts (Hepaticae), with almost a thousand species in 91 currently accepted genera. We analysed phylogenetic relationships of 69 genera, representing all major subfamilies and tribes recognized in the family, by using 49 informative morphological characters (31 gametophytic, 18 sporophytic), one chemical character, and applying equal and successive weighting of characters and parsimony analysis. In all trees recovered, the Lejeuneaceae were monophyletic with Nipponolejeunea (subfam. Nipponolejeuneoideae) forming the basalmost lineage. The remaining genera clustered in two major groups, the monophyletic Lejeuneoideae (52 genera) and the paraphyletic Ptychanthoideae (16 genera). Within each, several multigeneric lineages corresponding in part to previously described taxa were recovered: the Acrolejeuneinae and Ptychanthinae clades in the Ptychanthoideae, and the Brachiolejeuneinae, Lejeuneeae and Tuyamaella–Cololejeunea clades in the Lejeuneoideae. Bryopteris , a genus sometimes treated as a separate family, was nested in the Ptychanthinae clade. The Tuyamaella–Cololejeunea lineage corresponded with three previously recognized subfamilies (Cololejeuneoideae, Myriocoleoideae and Tuyamaelloideae) and contained genera with neotenic features, in two subclades. These features seemed to have originated by multiple heterochronic events: single origins were detected for 'protonemal neoteny' and 'primary neoteny', whereas 'secondary neoteny' probably evolved twice. Relationships within the large Lejeuneeae clade (43 genera) remained largely unresolved, although several putative lineages were detected in majority rule trees. Additional characters such as DNA sequences may provide better phylogenetic resolution in this group.  © 2003 The Linnean Society of London, Botanical Journal of the Linnean Society , 2003, 143 , 391–410.     

Geographical diversification of the genus Cicer (Leguminosae: Papilionoideae) inferred from molecular phylogenetic analyses of chloroplast and nuclear DNA sequences

Cicer L. (Leguminosae: Papilionoideae) consists of 42 species of herbaceous or semi-shrubby annuals and perennials distributed throughout the temperate zones of the Northern Hemisphere. The origin and geographical relationships of the genus are poorly understood. We studied the geographical diversification and phylogenetic relationships of Cicer using DNA sequence data sampled from two plastid regions, trnK / matK and trnS - trnG , and two nuclear regions, the internal transcribed spacer (ITS) and external transcribed spacer (ETS) regions of nuclear ribosomal DNA, from 30 species. The results from the phylogenetic analyses of combined nuclear and chloroplast sequence data revealed four well-supported geographical groups: a Middle Eastern group, a West-Central Asian group, an Aegean–Mediterranean group, and an African group. Age estimates for Cicer based on methods that do not assume a molecular clock (for example, penalized likelihood) demonstrate that the genus has a Mediterranean origin with considerable diversification in the Miocene/Pliocene epochs. Geological events, such as mountain orogenesis and environmental changes, are major factors for the dispersal of Cicer species. The early divergence of African species and their geographically distinct region in the genus suggest a broader distribution pattern of the genus in the past than at present.  © 2007 The Linnean Society of London, Botanical Journal of the Linnean Society, 2007, 154 , 175–186.     

Phylogeny of Labidodemas and the Holothuriidae (Holothuroidea: Aspidochirotida) as inferred from morphology

The Holothuriidae is one of the three established families within the large holothuroid order Aspidochirotida. The approximately 185 recognized species of this family are commonly classified in five nominal genera: Actinopyga , Bohadschia , Holothuria , Pearsonothuria and Labidodemas. Maximum parsimony analyses on morphological characters, as inferred from type and nontype material of the five genera, revealed that Labidodemas comprises highly derived species that arose from within the genus Holothuria . The paraphyletic status of the latter, large (148 assumed valid species) and morphologically diverse genus has recently been recognized and is here confirmed and discussed. Nevertheless, we adopt a Darwinian or eclectic classification for Labidodemas , which we retain at generic level within the Holothuriidae. We compare our phylogeny of the Holothuriidae with previous classifications of its genera and subgenera, and make suggestions concerning possible systematic changes.  © 2005 The Linnean Society of London, Zoological Journal of the Linnean Society , 2005, 144 , 103−120.     

The evolutionary history of the Chydoridae (Crustacea: Cladocera)

Although much is known about the evolutionary history of the pelagic 'cladocerans', there is little information on benthic families such as the Chydoridae. In this study, we examine the phylogenetic history of 37 chydorid species using sequence variation in two mitochondrial genes, COI and 16S rDNA, and one nuclear gene, 18S rDNA. The four recognized subfamilies of chydorids (Eurycercinae, Saycinae, Aloninae and Chydorinae) were well supported, being separated by large sequence divergences of 14.3–16.4%. By contrast, the existing taxonomic system appears to be less clear at a generic level, since many genera (e.g. Alona , Chydorus , Pleuroxus ) consist of an amalgam of distantly related species. However, among those genera which are monophyletic, levels of divergence are very high, suggesting that they originated somewhere in the mid-Palaeozoic. The factors involved in promoting diversification in this group are discussed.  © 2003 The Linnean Society of London, Biological Journal of the Linnean Society , 2003, 79, 629–643.     

Genetic cohesion of Eresus walckenaeri (Araneae, Eresidae) in the eastern Mediterranean

The eresid spider genus Eresus is morphologically and ecologically conservative. At least three species occur in Europe. However, deep genetic divergence among geographical samples within two species, E. cinnaberinus and E. sandaliatus , may suggest more cryptic species. In the present study we investigate the genetic cohesion of the third species, Eresus walckenaeri , throughout its eastern Mediterranean distribution range, relative to the E. cinnaberinus–E. sandaliatus species complex. Eresus walckenaeri specimens were monophyletic. Genetic discreteness of E. walckenaeri in a region of sympatry with its sister species in Greece provides evidence for species integrity of E. walckenaeri within the European Eresus species complex. Eresus walckenaeri exhibited high concordance between geographical location and mtDNA genealogy. Two major phylogeographical clades were found in the Greek–Turkish and Syrian–Israel parts of the investigated area, respectively (∼6.5% sequence divergence). Concordance between geography and genetic divergence was further observed between Aegean island samples and their corresponding Greek and Turkish mainland samples, suggesting regional subdivision with gradual but potentially high dispersal propensity. Monophyly and limited regional distribution indicate Mediterranean endemic origin.  © 2005 The Linnean Society of London, Biological Journal of the Linnean Society , 2005, 86 , 1–9.     

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.     

Molecular evolution of southern North American Cyprinidae (Actinopterygii), with the description of the new genus Tampichthys from central Mexico

Most of the recognized species of the genus Dionda inhabit drainages of the Gulf of Mexico from central Mexico to central Texas, USA, and have been considered a monophyletic group based on morphological, osteological, and allozyme investigations. Phylogenetic relationships of 15 species of Dionda and 34 species from closely related genera were inferred from one mitochondrial (cytb) and three nuclear gene sequences (S7, Rhodopsin, Rag1) totaling 4487 nucleotides. Separate analyses of all four genes yield congruent phylogenies; however the 15 putative species of Dionda evaluated were never recovered as a monophyletic group when species from nine related genera were included in the analyses. Among the ingroup taxa, one well-supported and highly divergent clade is consistently recognized and consists of six recognized and three undescribed northern species currently recognized in the genus Dionda. These nine species inhabit present or past tributaries of the Rio Grande basin of northern Mexico and southern USA, and were recovered as a basal clade in all analyses. Another large, also strongly supported clade, consisting of seven genera, include five southern recognized species currently in the genus Dionda, forming the sister group to the Codoma clade. These five species comprise the "Southern Dionda clade" and inhabit headwaters of the Pánuco-Tamesí drainage and some adjacent coastal rivers in the Tampico Embayment. The consistent and repeated identification of eight different clades recovered in most of the separate gene analyses strongly supports a division of the non-natural genus Dionda. A new genus, Tampichthys, is proposed for the clade of species endemic to east-central Mexico and formerly in Dionda. Tampichthys and the putative monotypic genus Codoma are more related to Mexican species of the genera Cyprinella and Notropis than to other species referred to Dionda sensu stricto.     

Systematics and biogeography of the widespread Neotropical gekkonid genus Thecadactylus (Squamata), with the description of a new cryptic species

The systematics of the widespread neotropical gekkonid genus Thecadactylus is investigated using a combination of morphological, morphometric and mtDNA (cytochrome b ) sequence data, forming a total evidence dataset. The analysis tackles the common yet complex problem of a widespread taxon consisting of one or more cryptic species that are difficult to diagnose using morphology alone. The data are analysed using both maximum parsimony and Bayesian inference. Virtually all analyses resolve a well-supported south-western Amazonian clade distinct from the remainder of the recognized T. rapicauda . The south-western Amazonian clade is not only robustly supported, but also exclusive, geographically coherent and sufficiently distinct to warrant specific recognition. The new species is diagnosable on the basis of molecular sequences that are 23.0–26.9% divergent from those of T. rapicauda , and morphological evidence. Bayesian inference analysis robustly resolves meaningful and repeatable patterns of relationship. The biogeography of Thecadactylus is interpreted in the context of its two constituent species, and difficulties of resolving systematic and biogeographical patterns in widespread, cosmopolitan taxa are discussed. © 2007 The Linnean Society of London, Zoological Journal of the Linnean Society , 2007, 149 , 339–370.     

A revision and phylogenetic analysis of Stapeliopsis (Apocynaceae)

A survey of morphological characters is carried out for Stapeliopsis . The information obtained from this is combined with molecular data from the plastid trn L-F DNA region and ITS1 of the nuclear encoded 18S−26S rRNA cistron, to obtain a hypothesis of the evolutionary relationships among the species. It is shown that Stapeliopsis is monophyletic in a combined molecular and morphological analysis. Stapeliopsis is sister to a clade containing Huernia , Orbea and Tromotriche . The species of Stapeliopsis group into two clades. One contains S. khamiesbergensis , S. neronis and S. urniflora , and this is highly supported. The remaining species fall into an unsupported clade in which S. exasperata is sister to the others. The genera Hermanschwartzia Plowes and Neopectinaria Plowes are rejected. It is shown that a synapomorphy for Stapeliopsis is the laterally flattened inner corona-lobes, which touch the anthers only at their bases. Eight species of Stapeliopsis are recognized, with no subgeneric divisions.  © 2005 The Linnean Society of London, Botanical Journal of the Linnean Society , 2005, 148 , 125–155.     

Relationships, classification and evolution of Scleranthus (Caryophyllaceae) as inferred from analysis of morphological characters

Study of floral anatomy, micromorphology, palynology and onotogeny has revealed new characters for phylogenetic analysis in the genus Scleranthus . Cladistic analysis of these characters, along with those previously available, suggests that the genus consists of Eurasian/Mediterranean and Australasian sister clades. Gynoecial morphology and development are closely similar in all species, suggesting the genus is monophyletic despite its disjunct northern and southern hemisphere distribution. Variation in pollen:ovule ratios and their implications for the evolution of Scleranthus species are also discussed and it is concluded that a range of breeding strategies intermediate between autogamy and xenogamy exists in the genus. Single-stamened species of Scleranthus are likely to be obligate autogams, despite their comparatively high pollen:ovule ratios in relation to autogamic species of other genera.  © 2002 The Linnean Society of London, Botanical Journal of the Linnean Society , 2002, 140 , 15–29.     

Python phylogenetics: inference from morphology and mitochondrial DNA

We used nucleotide sequences from four mitochondrial genes and structural features of the mitochondrial control region, combined with a revised, previously published, morphological data set to infer phylogenetic relationships among the pythons. We aimed to determine which of two competing hypotheses of relationships of the genera Aspidites and Python best explains the evolutionary and bioegeographical history of the family. All analyses of the combined data recover a set of relationships in which (1) the genus Python is paraphyletic with the two east Asian species, P. reticulatus and P. timoriensis , as the sister lineage to the seven Australo-Papuan python genera. We support recognition of a distinct genus for the P. reticulatus  +  P. timoriensis clade; (2) the remaining species of the genus Python form a clade which is the sister lineage to the remainder of the family; (3) the genus Aspidites is embedded among the Australo-Papuan genera. The seemingly primitive characteristics of Aspidites may be better interpreted as reversals or specializations that have accompanied a switch to burrowing in this genus. Resolution of the relationships among the Australo-Papuan lineages is weak, possibly because of rapid diversification early in the history of the radiation. We assessed the tempo of the Indo-Australian python radiation using a maximum likelihood framework based on the birth–death process. We find strong support for elevated speciation rates during the period when Australia collided with the proto-Indonesian archipelago. The data support an origin for pythons outside Australia, followed by a radiation into Australia during the mid-Tertiary.  © 2008 The Linnean Society of London, Biological Journal of the Linnean Society , 2008, 93 , 603–619.