Molecular phylogeny and zoogeography of the freshwater crayfish genus Cherax Erichson (Decapoda: Parastacidae) in Australia

The evolutionary history and biogeography of freshwater-dependent taxa in Australia is of intrinsic interest given the present-day aridity of this continent. Cherax is the most widespread and one of the most species-rich of Australia's nine freshwater crayfish genera. The phylogenetic relationships amongst 19 of the 23 Australian Cherax were established from mitochondrial DNA sequences representing the 12S rRNA and 16S rRNA gene regions. The relationships among species support an initial east–west separation, followed by a north–south divergence in eastern Australia. Molecular clock estimations suggest that these divergences date back to the Miocene. The phylogenetic relationships support endemic speciation within geographical regions and indicate that long-distance dispersal has not led to recent speciation as previously hypothesized. This new evolutionary scenario is consistent with the climatic history of Australia and the evolutionary history of other similarly distributed freshwater-dependent organisms in Australia.  © 2004 The Linnean Society of London, Biological Journal of the Linnean Society , 2004, 81 , 553–563.     

Phylogenetic relationships among Rhacophorinae (Rhacophoridae, Anura, Amphibia), with an emphasis on the Chinese species

The partial nucleotide sequence of mitochondrial 12S and 16S rRNA genes was determined for 23 Chinese species of Rhacophoridae (Amphibia: Anura), representing four of the eight recognized genera. Using Buergeriinae as the outgroup, phylogenetic analyses (maximum parsimony, maximum likelihood, and Bayesian inference) were performed in combination with already published mitochondrial 12S and 16S sequences of Rhacophorinae frogs. In all cases, Philautus romeri Smith, 1953 is recovered as the sister taxon to all other Rhacophorinae, although the support values are weak. Chirixalus doriae Boulenger, 1893 is closer to Chiromantis [ Chiromantis rufescens (Günther, 1868) and Chiromantis xerampelina Peters, 1854] than to Chirixalus vittatus (Boulenger, 1887). The clade { Philautus odontotarsus Ye & Fei, 1993, [ Philautus idiootocus (Kuramoto & Wang, 1987), Kurixalus eiffingeri (Boettger, 1895)]} is recovered with strong support. The monophyly of Theloderma and Rhacophorus rhodopus Liu & Hu, 1959 is not supported. It is suggested that Philautus albopunctatus Liu & Hu, 1962 should be placed into the synonymy of Theloderma asperum (Boulenger, 1886), and that Philautus rhododiscus Liu & Hu, 1962 should be assigned to Theloderma , so as to correct the paraphyly. Additionally, the monophyly of ' Aquixalus ' is not supported, and this requires further examination. Results also indicate that the Rhacophorus leucomystax (Gravenhorst, 1829)/ Rhacophorus megacephalus (Hallowell, 1861) complex needs further revision. Studies employing broader sampling and more molecular markers will be needed to resolve the deep relationships within the subfamily Rhacophorinae.  © 2008 The Linnean Society of London, Zoological Journal of the Linnean Society, 2008, 153 , 733–749.     

Evolutionary systematics of the Indian mouse Mus famulus Bonhote, 1898: molecular (DNA/DNA hybridization and 12S rRNA sequences) and morphological evidence

The genus Mus encompasses 38 species of mice divided into four subgenera: Mus , Pyromys , Nannomys and Coelomys . Each of these four taxa is characterized by discrete morphological as well as biochemical traits. We used two different molecular approaches to determine the relationships between these subgenera: DNA/DNA hybridization and 12S rRNA mitochondrial sequences. We compared the resulting phylogenies from each method and with phylogenies derived from morphological data. The degree of resolution of each molecular approach is discussed. The two molecular studies indicate that Mus , Pyromys , Nannomys and Coelomys are clearly distinct monophyletic groups, as previously indicated by morphological data and other biochemical and molecular approaches. There is one divergence between previous morphological and the molecular and morphological studies presented here: the position of the Indian species Mus famulus . This taxon, which was formerly included in the subgenus Coelomys , is demonstrated here to belong to the subgenus Mus. We also propose the following relationships within Mus sensu lato : Mus and Pyromys are the closest relatives, followed by Nannomys and Coelomys , whose relationships are still unclear. This arrangement is more robustly supported by DNA/DNA hybridization than by 12S rRNA data. A molecular time scale for the evolution within Mus sensu lato is proposed, using as a reference the Mus/Rattus divergence estimated by the fossil record at around 12 mya.  © 2003 The Linnean Society of London, Zoological Journal of the Linnean Society , 2003, 137 , 385–401.     

Systematics of African lowland rainforest Praomys (Rodentia, Muridae) based on molecular and craniometrical data

Representatives of the genus Praomys occur throughout the African intertropical zone. It is unclear how many species this genus contains, nor do we know the exact distribution ranges and phylogenetic relationships of these taxa. Using molecular (16S rRNA gene sequencing) and morphological (multivariate craniometry) analyses we clarify the taxonomy and phylogenetic relationships among the Praomys occurring in Africa's lowland tropical rainforests. We studied most species known from this area, based on specimens collected in seven countries (Guinea, Ivory Coast, Cameroon, Central African Republic, Gabon, Congo Republic and Democratic Republic of Congo). In our study, Praomys appears to be monophyletic. Our results identify two species complexes: the jacksoni complex includes at least two species ( P. jacksoni and P. mutoni ) and the tullbergi complex contains at least four species ( P. tullbergi , P. rostratus , P. misonnei , P. petteri ). Although the 16S rRNA gene appears insufficient to resolve the phylogenetic relationships among all the members of the tullbergi species complex, it is suitable for the identification of most of the studied species, and its use has allowed us to redefine the geographical limits of several species.  © 2005 The Linnean Society of London, Zoological Journal of the Linnean Society , 2005, 145 , 539–553.     

A molecular approach to the phylogenetic relationships of the western palaearctic Helicoidea (Gastropoda: Stylommatophora)

Molecular phylogenetic relationships among 45 members of the Helicoidea (Gastropoda: Stylommatophora) were examined using partial mitochondrial 16S rRNA sequences. Phylogenetic relationships were inferred using maximum parsimony, maximum likelihood and Bayesian methods. The reconstructed phylogenies showed a good degree of support for more recent branches, but gave little support to deeper nodes. Mitochondrial rDNA data further confirmed monophyletic status of helicids, recognized monachine hygromiid and bradybaenid clades and resolved a number of relationships in the helicelline hygromiids. With the respect to the latter assemblage, most of the anatomically based groups are confirmed, corroborating the diagnostic value of the dart-sac complex and a close affinity between Ichnusomunda sacchii and species of the genus Cernuella . Nevertheless, some well resolved branches challenge previous systematic arrangements, grouping species previously placed in different arrangements. In particular, support was not found for the monophyly of helicelline hygromiids with pedal penial innervation. Possible explanations for these incongruencies are suggested. 16S sequence data are appropriate for studies of relationships within the different species groups and less so for recovery of more ancient radiations in the Helicoidea. It will be valuable to combine the 16S data with other gene sequences to estimate basal relationships.  © 2005 The Linnean Society of London, Biological Journal of the Linnean Society , 2005, 85 , 501–512.     

Molecular systematics of the suborder Trogiomorpha (Insecta: Psocodea: 'Psocoptera')

Phylogenetic relationships among extant families in the suborder Trogiomorpha (Insecta: Psocodea: 'Psocoptera') were inferred from partial sequences of the nuclear 18S rDNA and Histone 3 and mitochondrial 16S rDNA genes. Analyses of these data produced trees that largely supported the traditional classification; however, monophyly of the infraorder Psocathropetae (= Psyllipsocidae + Prionoglarididae) was not recovered. Instead, the family Psyllipsocidae was recovered as the sister taxon to the infraorder Atropetae (= Lepidopsocidae + Trogiidae + Psoquillidae), and the Prionoglarididae was recovered as sister to all other families in the suborder. Character states previously used to diagnose Psocathropetae are shown to be plesiomorphic. The sister group relationship between Psyllipsocidae and Atropetae was supported by two morphological apomorphies: the presence of a paraproctal anal spine and an anteriorly opened phallosome. Based on these sequence data and morphological observations, we propose a new classification scheme for the Trogiomorpha as follows: infraorder Prionoglaridetae (Prionoglarididae), infraorder Psyllipsocetae (Psyllipsocidae), infraorder Atropetae (Lepidopsocidae, Trogiidae, Psoquillidae).  © 2006 The Linnean Society of London, Zoological Journal of the Linnean Society , 2006, 146 , 287–299.     

Mitochondrial differentiation, introgression and phylogeny of species in the Tegenaria atrica group (Araneae: Agelenidae)

The relationships between the three members of the Tegenaria atrica group ( T. atrica , T. saeva and T. gigantea ) were examined with DNA sequence data from mitochondrial CO1, 16S rRNA, tRNA^leu(CUN) and ND1 genes. Members of this group of large house spiders have overlapping distributions in western Europe and hybridize with each other to a variable degree. The close relatedness of all three species was supported by all analyses. T. saeva and T. gigantea are more closely affiliated than either is to T. atrica . Haplotypes clearly assignable to T. gigantea were also present in many specimens of T. saeva , suggesting asymmetrical introgression of mtDNA from T. gigantea into T. saeva . Molecular clock calibrations (CO1) suggest that deeper divisions within the genus Tegenaria may be in excess of 10 million years old, and that the evolutionary history of the T. atrica group has been moulded by Quaternary glacial–interglacial cycles.  © 2004 The Linnean Society of London, Biological Journal of the Linnean Society , 2004, 81 , 79–89.     

Evolution of St Helena arborescent Astereae (Asteraceae): relationships of the genera Commidendrum and Melanodendron

The cladistic relationships of endemic Commidendrum (four species) and Melanodendron (one species) from St Helena were inferred from sequences of ITS1 and ITS2 of nuclear ribosomal DNA. Despite showing a range of morphological and ecological variation, the four species of Commidendrum , C. spurium , C. robustum , C. rotundifolium , and C. rugosum , form a closely related monophyletic group with percentage sequence divergence between 0.2 and 0.9%. Melanodendron integrifolium is sister to Commidendrum indicating that the two genera may have evolved from a common ancestor that arrived in St Helena via a single dispersal event. The closest relatives of Commidendrum and Melanodendron appear to be South African, in the predominantly shrubby genus Felicia , although further sampling of South African Astereae is required. We discuss the evolution and adaptive radiation of these rare and threatened species with particular reference to the possible role of heterochrony.  © 2004 The Linnean Society of London, Botanical Journal of the Linnean Society , 2004, 144 , 69–83.     

Phylogenetic relationships of the north-eastern Atlantic and Mediterranean blenniids

The phylogenetic relationships of 27 north-eastern Atlantic and Mediterranean blennioids are analysed based on a total of 1001 bp from a combined fragment of the 12S and 16S mitochondrial rDNA. The most relevant results with implications in current blenniid taxonomy are: (1) Lipophrys pholis and Lipophrys (=  Paralipophrys ) trigloides are included in a well-supported clade that by the rule of precedence must be named Lipophrys ; (2) the sister species of this clade are not the remaining species of the genus Lipophrys but instead a monotypic genus comprising Coryphoblennius galerita ; (3) the smaller species of Lipophrys were recovered in another well-supported and independent clade, which we propose to be recognized as Microlipophrys ; (4) although some authors included the genera Salaria and Lipophrys in a single group we have never recovered such a relationship. Instead, Salaria is more closely related to the genera Scartella and Parablennius ; (5) the genus Parablennius , which was never recovered as a monophyletic clade, is very diverse and may include several distinct lineages; (6) the relative position of Aidablennius sphynx casts some doubts on the currently recognized relationships between the different blenniid tribes. Meristic, morphological, behavioural and ecological characters support our results and are also discussed. The possible roles of the tropical West African coast and the Mediterranean in the diversification of blenniids are discussed.  © 2005 The Linnean Society of London, Biological Journal of the Linnean Society , 2005, 86 , 283–295.     

Congruence between molecular phylogeny and cuticular design in Echiniscoidea (Tardigrada,Heterotardigrada)

Although morphological characters distinguishing echiniscid genera and species are well understood, the phylogenetic relationships of these taxa are not well established. We thus investigated the phylogeny of Echiniscidae, assessed the monophyly of Echiniscus, and explored the value of cuticular ornamentation as a phylogenetic character within Echiniscus. To do this, DNA was extracted from single individuals for multiple Echiniscus species, and 18S and 28S rRNA gene fragments were sequenced. Each specimen was photographed, and published in an open database prior to DNA extraction, to make morphological evidence available for future inquiries. An updated phylogeny of the class Heterotardigrada is provided, and conflict between the obtained molecular trees and the distribution of dorsal plates among echiniscid genera is highlighted. The monophyly of Echiniscus was corroborated by the data, with the recent genus Diploechiniscus inferred as its sister group, and Testechiniscus as the sister group of this assemblage. Three groups that closely correspond to specific types of cuticular design in Echiniscus have been found with a parsimony network constructed with 18S rRNA data. © 2013 The Linnean Society of London     

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.     

Gut-associated yeast in bark beetles of the genus Dendroctonus Erichson (Coleoptera: Curculionidae: Scolytinae)

Scolytine bark beetles are the most destructive pests of conifers; they sometimes aggregate in such large numbers that they actually kill their hosts. They maintain close relationships with yeasts and fungi, in particular those that are assumed to aid in digestive, detoxification processes and pheromone production. In this study, 403 yeast strains were isolated from the guts, ovaries, eggs and frass of nine bark beetle species in the genus Dendroctonus Erichson. The beetles were collected from 10 conifer species at 34 locations in Mexico, Guatemala and the USA. Yeast identification was based on partial DNA sequences from 18S rDNA, 26S rDNA and internal transcribed spacer (ITS1), as well as morphological and physiological characteristics. A combined phylogenetic analysis delimited 11 clades with sequences similar to Candida arabinofermentans , C. ernobii , C. membranifaciens (including C. lessepsii , Pichia mexicana and P. scolyti ), C. oregonensis , C. piceae , Kuraishia capsulata (including K. capsulata and K. cf. molischiana ), Pichia americana , P. canadensis , P. glucozyma , P. guilliermondii and an undescribed species of Candida . Nucleotide divergences between the major clades were at least 5% while, with the exception of 30 isolates, yeasts within clades differed from named reference species at fewer than 1% of the nucleotide sites. There do not appear to be obligate relationships between particular yeasts and specific anatomical partitions, nor between particular yeasts and bark beetle species. Some yeasts do appear to be preferentially associated with bark beetles feeding on different conifer genera and therefore host plant defences may limit yeast community diversity in Dendroctonus .  © 2009 The Linnean Society of London, Biological Journal of the Linnean Society , 2009, 98 , 325–342.     

An integrative approach to species delimitation in Benthomangelia (Mollusca: Conoidea)

DNA sequences are currently used to propose primary hypotheses of species delimitation, especially when morphological variability is difficult to assess. In an integrative taxonomy framework, these hypotheses are then compared with other characters, such as morphology or geography, to produce robust species delimitations. For this purpose, the cytochrome oxidase subunit I (COI) gene has been sequenced for almost 50 specimens of the genus Benthomangelia , a deep-sea marine gastropod genus, collected in the South-West Pacific. Five genetic groups, displaying low and high genetic distances respectively within and between groups, were defined. COI hypotheses were compared with both the results obtained with the independent nuclear 28S gene and with an elliptic Fourier analysis of the shape of the last whorl of the shell. 28S gene analysis confirmed the same well-supported groups as COI, and elliptic Fourier analysis identified several morphological characters that vary similarly to genetic variability.  © 2009 The Linnean Society of London, Biological Journal of the Linnean Society , 2009, 96 , 696–708.     

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.     

Canarian land snail diversity: conflict between anatomical and molecular data on the phylogenetic placement of five new species of Napaeus (Gastropoda, Pulmonata, Enidae)

Five new species of land snail (family Enidae) are described from La Gomera (Canary Islands) of which the majority, on the basis of anatomy alone, could be incorporated within a new supraspecific taxon. In addition to the morphological study of these new species, a region of the 16S mitochondrial gene is sequenced from three of the new species and a range of species of Napaeus from within its two subgenera ( Napaeinus and Napaeus ) . There is a disparity between the morphological and preliminary molecular phylogenetic data. Possible explanations for this conflict are discussed, as well as the evolutionary relationships among these different taxa, and it is suggested that this group may be an excellent model for further studies of adaptation and diversification.  © 2006 The Linnean Society of London, Biological Journal of the Linnean Society , 2006, 89 , 169–187.     

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.     

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.     

Phylogeography and conservation genetics of endangered European Margaritiferidae (Bivalvia: Unionoidea)

Margaritifera margaritifera and M. auricularia are among the most endangered freshwater mussels in the world, and the only species of the genus found in Europe. Our genetic study explores allozymic variability (27 loci) and differentiation at the mitochondrial sequence level (partial COI and 16S rRNA gene sequences). The Spanish M. auricularia population showed genetic parameters of variation that were of the same order as those of other freshwater molluscs (though at the lower end of the range), probably permitting its potential recovery. The difference between this species and M. margaritifera was clearly established (ten diagnostic allozymic loci, Nei = 0.462, and mean nucleotide divergence around 9.4%). The M. margaritifera populations analysed showed a certain degree of population genetic structure (according to allozyme data) that was not, however, related to a geographical cline. Nevertheless, two mitochondrial lineages (albeit very closely related) were identified: a northern lineage extending from Ireland to the Kola Peninsula including the western Atlantic coast, and a second cluster distributed from Ireland to the Iberian Peninsula. The phylogenetic relationships between these two species and other related taxa were established. The putative M. m. durrovensis could be considered an 'ecophenotype'. Palaeobiogeographical scenarios are presented and indicate unexpected 'recent' gene flow between M. margaritifera populations that were theoretically isolated in the early Tertiary.  © 2003 The Linnean Society of London, Biological Journal of the Linnean Society 2003, 78, 235–252.     

Mitochondrial DNA phylogeny and morphological diversity in the genus Mastus (Beck, 1837): a study in a recent (Holocene) island group (Koufonisi, south-east Crete)

Three endemic Cretan land snail species of the genus Mastus (Beck, 1837) from the island group of Koufonisi (south-east Crete) and the eastern part of Crete, were studied by multivariate analysis of shell morphology and analysis of mtDNA sequences. The phylogeny of the populations studied and the processes effecting the genetic and morphological diversity of the species were investigated. Extremely high mtDNA sequence divergence was observed both within and between populations. The Cretan populations could not be distinguished morphologically, while the populations of the islets were more distinct. We argue that the active geological past of the area (including sea level changes) and the long-term presence of humans has produced a mixing up of Mastus populations leading to the accumulation of high divergence of mtDNA sequences on a small spatial scale. The limited morphological diversity and the distinct shell 'identity' of the islets' populations can be attributed to the selective pressures of the island group.  © 2003 The Linnean Society of London, Biological Journal of the Linnean Society , 2003, 78, 383–399.     

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.