PHYLOGENY OF THE BASAL LINEAGES OF STREPTOPHYTA BASED ON RBCL AND ATPB GENE SEQUENCE DATA

The streptophytes comprise the Charophyceae sensu Mattox and Stewart (a morphologically diverse group of fresh‐water green algae) and the embryophytes (land plants). Several charophycean groups are currently recognized. These include the Charales, Coleochaetales, Chlorokybales, Klebsormidiales and Zygnemophyceae (Desmidiales and Zygnematales). Recently, SSU rRNA gene sequence data allied Mesostigma viride (Prasinophyceae) with the Streptophyta. Complete chloroplast sequence data, however, placed Mesostigma sister to all green algae, not with the streptophytes. Several morphological, ultrastructural and biochemical features unite these lineages into a monophyletic group including embryophytes, but evolutionary relationships among the basal streptophytes remain ambiguous. To date, numerous studies using SSU rRNA gene sequences have yielded differing phylogenies with varying degrees of support dependent upon taxon sampling and choice of phylogenetic method. Like SSU data, chloroplast DNA sequence data have been used to examine relationships within the Charales, Coleochaetales, Zygnemophyceae and embryophytes. Representatives of all basal streptophyte lineages have not been examined using chloroplast data in a single analysis. Phylogenetic analyses were performed using DNA sequences of rbcL (the genes encoding the large subunit of rubisco) and atpB (the beta‐subunit of ATPase) to examine relationships of basal streptophyte lineages. Preliminary analyses placed the branch leading to Mesostigma as the basal lineage in the Streptophyta with Chlorokybus, the sole representative of the Chlorokybales, branching next. Klebsormidiales and the enigmatic genus Entransia were sister taxa. Sister to these, the Charales, Coleochaetales, embryophytes and Zygnemophyceae formed a monophyletic group with Charales and Coleochaetales sister to each other and this clade sister to the embryophytes.     

Phylogenetic relationships within the South American fish family Anostomidae (Teleostei,Ostariophysi, Characiformes)

Analysis of a morphological dataset containing 152 parsimony‐informative characters yielded the first phylogenetic reconstruction spanning the South American characiform family Anostomidae. The reconstruction included 46 ingroup species representing all anostomid genera and subgenera. Outgroup comparisons included members of the sister group to the Anostomidae (the Chilodontidae) as well as members of the families Curimatidae, Characidae, Citharinidae, Distichodontidae, Hemiodontidae, Parodontidae and Prochilodontidae. The results supported a clade containing Anostomus, Gnathodolus, Pseudanos, Sartor and Synaptolaemus (the subfamily Anostominae sensu Winterbottom) albeit with a somewhat different set of relationships among the species within these genera. Anostomus as previously recognized was found to be paraphyletic and is split herein into two monophyletic components, a restricted Anostomus and the new genus Petulanos gen. nov. , described herein. Laemolyta appeared as sister to the clade containing Anostomus, Gnathodolus, Petulanos, Pseudanos, Sartor and Synaptolaemus. Rhytiodus and Schizodon together formed a well‐supported clade that was, in turn, sister to the clade containing Anostomus, Gnathodolus, Laemolyta, Petulanos, Pseudanos, Sartor and Synaptolaemus. Anostomoides was sister to the clade formed by these nine genera. Leporinus as currently defined was not found to be monophyletic, although certain clades within that genus were supported, including the species with subterminal mouths in the former subgenus Hypomasticus which we recognize herein as a genus. Abramites nested in Leporinus, and Leporellus was found to be the most basal anostomid genus. The presence of cis‐ and trans‐Andean species in Abramites, Leporellus, Leporinus and Schizodon, all relatively basal genera, suggests that much of the diversification of anostomid species pre‐dates the uplift of the Andean Cordilleras circa 11.8 million years ago. Several important morphological shifts in anostomid evolution are illustrated and discussed, including instances of convergence and reversal. © 2008 The Linnean Society of London, Zoological Journal of the Linnean Society, 2008, 154 , 70–210.     

Evolutionary history of the burnet moth genus Zygaena Fabricius, 1775 (Lepidoptera: Zygaenidae) inferred from nuclear and mitochondrial sequence data: phylogeny, host–plant association, wing pattern evolution and historical biogeography

Burnet moths of the genus Zygaena are a striking group of primarily diurnal Lepidoptera displaying an exceptional phenotypic plasticity. Previous attempts to elucidate the phylogenetic history of the group had been confounded by a perplexing pattern of characters or insufficient taxon sampling. In the present study, we infer a phylogeny of the genus Zygaena by analysing 5.4 kb of their nuclear and mitochondrial DNA. Eighty‐four of the 98 currently recognized species in this genus are considered, including representatives of all described species groups. RNA coding sequences are aligned with reference to zygaenoid moth specific secondary structure models of corresponding molecules. We conduct phylogenetic analyses within a Bayesian framework applying partition specific substitution parameters; covariation of paired sites in RNA gene sequences is accommodated by using doublet substitution models. The molecular data reveal that a considerable number of currently recognized species groups in Zygaena are not monophyletic. The traditional subgeneric classification proves to be artificial as well; Agrumenia and Zygaena (sensu stricto) are polyphyletic. Only the subgenus Mesembrynus can be confirmed as a monophyletic species cluster. Optimization of larval host–plant associations and forewing patterns on sampled trees of the Bayesian analyses suggest convergent evolution of similar wing pattern types in distantly related species clusters and a shift from cyanogenic to acyanogenic host‐plants. The phylogenetic results challenge the classic assumption that early species diversification in Zygaena took place in the Irano–Turkestanian region. Rather, the molecular data point to the western Mediterranean area as the geographical origin of the group and imply a subsequent colonization of the Middle East and Central Asia. We discuss the apparently convergent evolution of similar wing patterns in context with the chemical defence system of burnet moths and suggest a species group concept for the genus Zygaena that accounts for the recent findings. © 2007 The Linnean Society of London, Biological Journal of the Linnean Society, 2007, 92 , 501–520.     

Life on the fly: phylogenetics and evolution of the helicopter damselflies (Odonata,Pseudostigmatidae)

Ingley, S.J., Bybee, S.M., Tennessen, K.J., Whiting, M.F. & Branham, M.A. (2012). Life on the fly: phylogenetics and evolution of the helicopter damselflies (Odonata, Pseudostigmatidae). —Zoologica Scripta, 41, 637–650. Helicopter damselflies (Odonata: Pseudostigmatidae) form a relatively small, yet highly specialized group of odonates, including the largest extant odonate (wingspan of ～190 mm). Pseudostigmatids are found throughout Central and South America, with the exception of one species that is found exclusively in East Africa. Pseudostigmatids oviposit exclusively in phytotelmata and forage on orb‐weaver spiders, which they pluck from webs. Pseudostigmatids also exhibit unique forms of both broad and narrow wings. Although the ecology of these behaviours and morphological features have been studied, their phylogenetic origins and evolutionary history are unknown. Here, we examine the origins of pseudostigmatid wing forms, oviposition in phytotelmata and spider feeding within a modern phylogenetic context, testing for single origins of each character. Phylogenetic analyses are based on 59 morphological characters and ～5 kb of sequence data. Our findings include a well‐supported monophyletic Pseudostigmatidae and Coryphagrion grandis as sister to the Neotropical genera. The genus Mecistogaster is paraphyletic, with Pseudostigma nested within the clade. The genus Microstigma is supported as monophyletic and forms a sister group relationship to the clade of Megaloprepus and Anomisma. The sister group relationship to Pseudostigmatidae is less clear. On the basis of this phylogenetic analysis, we propose three new tribes (Coryphagrionini, Microstigmatini and Mecistogastrini). As Pseudostigmatidae is monophyletic, the behaviour of gleaning spiders from webs appears to derive from a single origin. There are two origins of broad wings within Pseudostigmatidae. Oviposition in phytotelmata most certainly evolved multiple times within Coenagrionoidea. These findings provide new insights into pseudostigmatid evolution that can be used to generate hypotheses regarding behaviour and morphological adaptation in this unique and threatened group of damselflies.     

Molecular phylogeny of sea snakes reveals a rapidly diverged adaptive radiation

Evolutionary relationships within and between the marine hydrophiine sea snake groups have been inferred primarily using morphological characters, and two major groups traditionally are recognized. The Aipysurus group comprises nine species in two genera, and the taxonomically chaotic Hydrophis group comprises as many as 40 species, of which 27 are generally allocated to the genus Hydrophis and 13 to ten additional genera. In addition to these two major groups are three putatively ‘primitive’ monotypic genera, Hydrelaps darwiniensis, Ephalophis greyi and Parahydrophis mertoni. The present study investigated the evolutionary relationships of 23 representative species of marine hydrophiines, comprising 15 species from the Hydrophis group, six species from the Aipysurus group, and H. darwiniensis and P. mertoni, to address two broad aims. First, the aim was to provide a robust phylogeny for sea snakes to test previous phylogenetic hypotheses based on morphology, and thus provide some taxonomic stability to the group. Second, there was interest in evaluating the hypothesis that the Hydrophis group might represent a rapidly diverged adaptive radiation. A large mitochondrial DNA data set based on the cytochrome b gene (1080 bp, 401 parsimony informative) and the 16S rRNA gene (510 bp, 57 parsimony informative) was assembled and these data were analysed using parsimony, maximum‐likelihood and Bayesian approaches. All analyses yielded virtually the same optimal tree, confirming that hydrophiine sea snakes comprise at least three lineages. The Aipysurus group formed a strongly supported and well‐resolved monophyletic clade. The Hydrophis group also formed a strongly supported clade; however, resolution among the genera and species was very poor. Hydrelaps darwiniensis and P. mertoni formed a sister clade to the Hydrophis lineage. Our phylogeny was used to test the validity of previous taxonomic and phylogenetic hypotheses, and to demonstrate that the genus Hydrophis is not monophyletic. Genetic diversity relative to phenotypic diversity is four to seven times greater in the Hydrophis lineage compared with the Aipysurus lineage. The topology of our phylogenetic hypothesis, combined with the levels of genetic divergence relative to morphological diversity, demonstrate that the Hydrophis lineage represents a rapidly diverged adaptive radiation. The data are consistent with the hypothesis that this adaptive radiation may be due to historical sea level fluctuations that have isolated populations and promoted speciation. © 2006 The Linnean Society of London, Biological Journal of the Linnean Society, 2006, 89 , 523–539.     

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.     

Evolution of skull and body shape in Triturus newts reconstructed from three‐dimensional morphometric data and phylogeny

To explore the relationship between morphological change and species diversification, we reconstructed the evolutionary changes in skull size, skull shape, and body elongation in a monophyletic group of eight species that make up salamander genus Triturus. Their well‐studied phylogenetic relationships and the marked difference in ecological preferences among five species groups makes this genus an excellent model system for the study of morphological evolution. The study involved three‐dimensional imagery of the skull and the number of trunk vertebrae, in material that represents the morphological, spatial, and molecular diversity of the genus. Morphological change largely followed the pattern of descent. The reconstruction of ancestral skull shape indicated that morphological change was mostly confined to two episodes, corresponding to the ancestral lineage that all crested newts have in common and the Triturus dobrogicus lineage. When corrected for common descent, evolution of skull shape was correlated to change in skull size. Also, skull size and shape, as well as body shape, as inferred from the number of trunk vertebrae, were correlated, indicating a marked impact of species' ecological preferences on morphological evolution, accompanied by a series of niche shifts, with the most pronounced one in the T. dobrogicus lineage. The presence of phylogenetic signal and correlated evolutionary changes in skull and body shape suggested complex interplay of niche shifts, natural selection, and constraints by a common developmental system. © 2014 The Linnean Society of London, Biological Journal of the Linnean Society, 2014, 113 , 243–255.     

Phylogenetic patterns in larval host plant and ant association of Indo-Australian Arhopalini butterflies (Lycaenidae: Theclinae)

The Oriental butterfly genus Arhopala is by far the most species‐rich genus within the subfamily Theclinae. We investigated whether biotic interactions with larval host plants or ants are phylogenetically constrained in the evolutionary history of Arhopala, by collating available information on the ecology of Arhopala from the literature as well as from personal observations, and analysing and interpreting these data rigorously in a phylogenetic context. Larvae of all species in the sister‐group of Arhopala and Flos feed on Fabaceae. However, the predominant feeding preference of Arhopala s.l., with the exception of a particular monophyletic and species‐rich group, called ‘Group A’, appears to be centred on Fagaceae, with additional records of Dipterocarpaceae feeding. The preference for Fagaceae has strong phylogenetic inertia, as indicated by T‐PTP tests designed to test for phylogenetic signal. Adding all available life‐history data, using the phylogeny presented before as scaffolding, further increased the phylogenetic signal in host plant data. Feeding on Fabaceae (mainly in the outgroup) and Euphorbiaceae also showed significant phylogenetic signal, but feeding on Dipterocarpaceae did not and was found scattered across the phylogeny. Except for the Dipterocarpaceae, phylogenetic signal in feeding preferences was very clear, even despite uneven taxon sampling and apparent lability in host plant use. Ant association also demonstrated historical constraint, but based on the phylogenetic hypothesis presented here it was not clear whether increased ant association intimacy emerged independently various times in Group A, as well as in several basal groups. Our finding of distinct phylogenetic patterns in the host plant and to a lesser degree in ant association data contradicts the hypothesis that life‐history traits are very labile in the Lycaenidae. © 2005 The Linnean Society of London, Biological Journal of the Linnean Society, 2005, 84 , 225–241.     

Phylogenetic revision of the Hippasterinae (Goniasteridae; Asteroidea): systematics of deep sea corallivores,including one new genus and three new species

The Hippasterinae is a subfamily within the Goniasteridae, consisting of five genera and 26 species, which occur in cold‐water settings ranging from subtidal to abyssal depths. All known genera were included in a cladistic analysis resulting in two most parsimonious trees, supporting the Hippasterinae as monophyletic. Our review supports Sthenaster emmae gen. et sp. nov. as a new genus and species from the tropical Atlantic and two new Evoplosoma species, Evoplosoma claguei sp. nov. and Evoplosoma voratus sp. nov. from seamounts in the North Pacific. Hippasteria caribaea is reassigned to the genus Gilbertaster, which previously contained a single Pacific species. Our analysis supports Evoplosoma as a derived deep water lineage relative to its continental‐shelf, shallow water sister taxa. The genus Hippasteria contains approximately 15 widely distributed, but similar‐looking species, which occur in the northern and southern hemispheres. Except for Gilbertaster, at least one species in each genus has been observed or is inferred to prey on deep‐sea corals, suggesting that this lineage is important to the conservation of deep‐sea coral habitats. The Hippasterinae shares several morphological similarities with Circeaster and Calliaster, suggesting that they may be related. © 2010 The Linnean Society of London, Zoological Journal of the Linnean Society, 2010, 160 , 266–301.     

Diversity and biogeography of Ni‐hyperaccumulators of Alyssum section Odontarrhena (Brassicaceae) in the central western Mediterranean: evidence from karyology,morphology and DNA sequence data

The diversity of Alyssum section Odontarrhena in the central–western Mediterranean region was investigated to elucidate relationships and biogeography of Ni‐hyperaccumulators in the group. Karyological, morphometric and molecular phylogenetic analyses were performed on accessions of Ni‐hyperaccumulators from serpentine outcrops and non‐hyperaccumulators from calcareous–dolomitic soils in the region. Alpine and Apennine populations of A. argenteum, Sardinian A. tavolarae and some Tuscan A. bertolonii had a tetraploid chromosome complement and larger silicles, seeds and seed wings than diploid accessions. DNA sequences from the plastid rpoC1 locus corroborated the monophyly of section Odontarrhena but species relationships were poorly resolved. Bayesian analysis of combined ITS‐rpoC1 sequences retrieved three main lineages including hyperaccumulators and non‐hyperaccumulators of contrasting geographical origin. One lineage was mainly continental and included alpine and northern Apennine populations of A. argenteum, the Balkan complex of A. murale and the Iberian group of A. serpyllifolium, sister to Corsican A. robertianum as suggested by their similar diploid karyotype. In this clade no divergence was found between typical A. serpyllifolium and related Ni‐hyperaccumulator races from the Iberian peninsula, supporting their conspecific status. A second lineage was prevalently Mediterranean and included the sister species A. bertolonii and A. tavolarae, and other endemics from Sicily, the southern Balkans and Turkey from dolomite and serpentine habitats. The present data suggest new model systems consisting of hyperaccumulators and non‐hyperaccumulators of proven phylogenetic affinity for further research on the molecular mechanisms of Ni‐hyperaccumulation and serpentine tolerance at the diploid and tetraploid level. © 2013 The Linnean Society of London, Botanical Journal of the Linnean Society, 2013, 173 , 269–289.     

Phylogenetic relationships of the tribe Operophterini (Lepidoptera, Geometridae): a case study of the evolution of female flightlessness

A molecular phylogenetic analysis was conducted in order to reconstruct the evolution of female flightlessness in the geometrid tribe Operophterini (Lepidoptera, Geometridae, Larentiinae). DNA variation in four nuclear gene regions, segments D1 and D2 of 28S rRNA, elongation factor 1α , and wingless , was examined from 22 species representing seven tribes of Larentiinae and six outgroup species. Direct optimization was used to infer a phylogenetic hypothesis from the combined sequence data set. The results obtained confirmed that Operophterini (including Malacodea ) is a monophyletic group, and Perizomini is its sister group. Within Operophterini, the genus Malacodea is the sister group to the genera Operophtera and Epirrita , which form a monophyletic group. This relationship is also supported by morphological data. The results suggest that female flightlessness has evolved independently twice: first in the lineage of Malacodea and, for the second time, in the lineage of Operophtera after its separation from the lineage of Epirrita . An alternative reconstruction (i.e. recovery of flight ability in an ancestor of Epirrita ) appears unlikely for various reasons. The similarities shared by Epirrita with a basal representative of Perizomini, Perizoma didymatum , allow the proposal of a sequence of evolutionary events that has led to flightlessness. It is likely that the transition to female flightlessness in the two lineages of Operophterini occurred after the colonization of stable forest habitats, followed by the evolution of a specific set of permissive traits, including larval polyphagy, limited importance of adult feeding, and adult flight during the cold months of the season.  © 2007 The Linnean Society of London, Biological Journal of the Linnean Society , 2007, 92 , 241–252.     

The diversification of the genus Monodelphis and the chronology of Didelphidae (Didelphimorphia)

To evaluate the monophyletic status of the genus Monodelphis, and its species complexes, we used a 9.3‐kb multimarker alignment to build a phylogenetic tree based on the largest taxon sampling for this didelphid genus to date. Furthermore, using a Bayesian framework and six calibration points, we inferred the divergence times for the major Monodelphis lineages and their current geographical distribution to perform an ancestral state reconstruction for geographical areas. Our results indicate the monophyletic nature of Monodelphis and suggest ‘kunsi’ as a new species complex that includes Monodelphis kunsi and an undescribed species. Monodelphis is further subdivided into three clades showing a common vicariance pattern, with each major clade consisting of a northern South American lineage joined with an Atlantic Forest lineage. This geographic consistency suggests a vicariant event that might have been related to a warm period at the Oligocene/Miocene border, according to our time results. © 2015 The Linnean Society of London     

A comprehensive molecular phylogeny of tiger beetles (Coleoptera,Carabidae, Cicindelinae)

Tiger beetles are a remarkable group that captivates amateur entomologists, taxonomists and evolutionary biologists alike. This diverse clade of beetles comprises about 2300 currently described species found across the globe. Despite the charisma and scientific interest of this lineage, remarkably few studies have examined its phylogenetic relationships with large taxon sampling. Prior phylogenetic studies have focused on relationships within cicindeline tribes or genera, and none of the studies have included sufficient taxon sampling to conclusively examine broad species patterns across the entire subfamily. Studies that have attempted to reconstruct higher‐level relationships of Cicindelinae have yielded conflicting results. Here, we present the first taxonomically comprehensive molecular phylogeny of Cicindelinae to date, with the goal of creating a framework for future studies focusing on this important insect lineage. We utilized all available published molecular data, generating a final concatenated dataset including 328 cicindeline species, with molecular data sampled from six protein‐coding gene fragments and three ribosomal gene fragments. Our maximum‐likelihood phylogenetic inferences recover Cicindelinae as sister to the wrinkled bark beetles of the subfamily Rhysodinae. This new phylogenetic hypothesis for Cicindelinae contradicts our current understanding of tiger beetle phylogenetic relationships, with several tribes, subtribes and genera being inferred as paraphyletic. Most notably, the tribe Manticorini is recovered nested within Platychilini including the genera Amblycheila Say, Omus Eschscholtz, Picnochile Motschulsky and Platychile Macleay. The tribe Megacephalini is recovered as paraphyletic due to the placement of the monophyletic subtribe Oxycheilina as sister to Cicindelini, whereas the monophyletic Megacephalina is inferred as sister to Oxycheilina, Cicindelini and Collyridini. The tribe Collyridini is paraphyletic with the subtribes Collyridina and Tricondylina in one clade, and Ctenostomina in a second one. The tribe Cicindelini is recovered as monophyletic although several genera are inferred as para‐ or polyphyletic. Our results provide a novel phylogenetic framework to revise the classification of tiger beetles and to encourage the generation of focused molecular datasets that will permit investigation of the evolutionary history of this lineage through space and time.     

Molecules, morphology and fossils: a comprehensive approach to odonate phylogeny and the evolution of the odonate wing

We undertook a comprehensive morphological and molecular phylogenetic analysis of dragonfly phylogeny, examining both extant and fossil lineages in simultaneous analyses. The legitimacy of higher‐level family groups and the phylogenetic relationship between families were tested. Thirteen families were supported as monophyletic (Aeshnidae, Calopterygidae, Chlorocyphidae, Euphaeidae, Gomphidae, Isostictidae, Lestidae, Libellulidae, Petaluridae, Platystictidae, Polythoridae, Pseudostigmatidae and Synthemistidae) and eight as non‐monophyletic (Amphipterygidae, Coenagrionidae, Corduliidae, Megapodagrionidae, Protoneuridae and Synlestidae), although Perilestidae and Platycnemididae were recovered as monophyletic under Bayesian analyses. Nine families were represented by one species, thus monophyly was not tested (Epiophlebiidae, Austropetaliidae, Chlorogomphidae, Cordulegastridae, Macromiidae, Chorismagrionidae, Diphlebiidae, Lestoideidae and Pseudolestidae). Epiprocta and Zygoptera were recovered as monophyletic. Ditaxinerua is supported as the sister lineage to Odonata, Epiophlebiidae and the lestid‐like damselflies are sister to the Epiprocta and Zygoptera, respectively. Austropetaliidae + Aeshnidae is the sister lineage to the remaining Anisoptera. Tarsophlebia's placement as sister to Epiprocta or as sister to Epiprocta + Zygoptera was not resolved. Refinements are made to the current classification. Fossil taxa did not seem to provide signals crucial to recovering a robust phylogeny, but were critical to understanding the evolution of key morphological features associated with flight. Characters associated with wing structure were optimized revealing two wing character complexes: the pterostigma–nodal brace complex and the costal wing base & costal–ScP junction complex. In turn, these two complexes appear to be associated; the pterostigma–nodal brace complex allowing for further modification of the wing characters comprised within the costal wing base & costal–ScP junction complex leading the modern odonate wing. © The Willi Hennig Society 2008.     

Phylogenetic analysis of Chloraeinae (Orchidaceae) based on plastid and nuclear DNA sequences

The phylogenetic relationships of subtribe Chloraeinae, a group of terrestrial orchids endemic to southern South America, have not been satisfactorily investigated. A previous molecular phylogenetic analysis based on plastid DNA supported the monophyly of Chloraeinae and Gavilea, but showed that Chloraea is non‐monophyletic and that the sole species of Bipinnula analysed is sister to Geoblasta. However, that analysis included only 18 of the 73 species belonging to this subtribe. Here, the phylogenetic relationships of Chloraeinae were assessed by analysing aproximately 7500 bp of nucleotide sequences from nuclear ribosomal internal transcribed spacer (ITS) and plastid DNA (rbcL, matK, trnL‐trnF, rpoB‐trnC) for 42 species representing all four currently accepted genera of Chloraeinae and appropriate outgroups. Nuclear and plastid data were analysed separately and in combination using two different methods, namely parsimony and Bayesian inference. Our analyses support the monophyly of Chloraeinae and their inclusion in an expanded concept of Cranichideae, but none of the genera of Chloraeinae that includes more than one species is monophyletic. Gavilea and Bipinnula are paraphyletic, with Chloraea chica nested in Gavilea and Geoblasta penicillata in Bipinnula. As currently delimited, Chloraea is polyphyletic. The taxonomic changes proposed recently are for the most part not justifiable on phylogenetic grounds, except for recognition of the monotypic genus Correorchis. The lack of resolution for the relationships among species of ‘core’Chloraea suggests a relatively recent diversification of this group. The current generic classification is in need or revision, but additional study is advisable before carrying out further taxonomic changes. © 2012 The Linnean Society of London, Botanical Journal of the Linnean Society, 2012, 168 , 258–277.     

New taxa refresh the phylogeny and classification of pleurostomatid ciliates (Ciliophora,Litostomatea)

A high diversity of pleurostomatid ciliates has been discovered in the last decade, and their systematics needs to be improved in the light of new findings concerning their morphology and molecular phylogeny. In this work, a new genus, Protolitonotus gen. n., and two new species, Protolitonotus magnus sp. n. and Protolitonotus longus sp. n., were studied. Furthermore, 19 novel nucleotide sequences of SSU rDNA, LSU rDNA and ITS1‐5.8S‐ITS2 were collected to determine the phylogenetic relationships and systematic positions of the pleurostomatid ciliates in this study. Based on both molecular and morphological data, the results demonstrated that: (i) as disclosed by the sequence analysis of SSU rDNA, LSU rDNA and ITS1‐5.8S‐ITS2, Protolitonotus gen. n. is sister to all other pleurostomatids and thus represents an independent lineage and a separate family, Protolitonotidae fam. n., which is defined by the presence of a semi‐suture formed by the right somatic kineties near the dorsal margin of the body; (ii) the families Litonotidae and Kentrophyllidae are both monophyletic based on both SSU rDNA and LSU rDNA sequences, whereas Amphileptidae are non‐monophyletic in trees inferred from SSU rDNA sequences; and (iii) the genera Loxophyllum and Kentrophyllum are both monophyletic, whereas Litonotus is non‐monophyletic based on SSU rDNA analyses. ITS1‐5.8S‐ITS2 sequence data were used for the phylogenetic analyses of pleurostomatids for the first time; however, species relationships were less well resolved than in the SSU rDNA and LSU rDNA trees. In addition, a major revision to the classification of the order Pleurostomatida is suggested and a key to its families and genera is provided.     

Molecular systematics of peppermint and cleaner shrimps: phylogeny and taxonomy of the genera Lysmata and Exhippolysmata (Crustacea: Caridea: Hippolytidae)

Shrimps from the ecologically diverse genera Lysmata and Exhippolysmata are rare among marine invertebrates because they are protandric simultaneous hermaphrodites: shrimps initially mature and reproduce solely as males, and later in life become functional simultaneous hermaphrodites. Considerable progress on the reproductive ecology of members from these two genera has been achieved during the last decade. However, several outstanding issues of systematic nature remain to be addressed. Here, a molecular phylogeny of these two genera was used to examine the overall evolutionary relationship within and between species and genera, and to answer various questions related to the systematic status of several species. The present phylogenetic analysis, including 53 sequences and 26 species of Lysmata and Exhippolysmata, indicates that semiterrestrial shrimps from the genus Merguia represent the sister group to a second natural clade composed by shrimps from the genera Lysmata and Exhippolysmata. Also, the phylogenetic analysis confirmed that the genus Lysmata is paraphyletic, and includes the genus Exhippolysmata, as noted in a preliminary study. The tree partially supports the separation of species with or without a developed accessory branch into two different genera or subgenera (i.e. Lysmata and Hippolysmata having a well‐developed accessory branch, or not, respectively). The genetic distance between the cleaner shrimps Lysmata amboinensis and Lysmata grabhami was smaller than has been observed between other sister species. On the other hand, the topology of the tree indicates that these two entities are reciprocally monophyletic. Thus, this latter result, together with minor but constant differences in the colour pattern reported for these two entities, indicates that there is no reason to stop treating them as different valid species. This study enabled the long overdue resolution of standing taxonomic questions in shrimps from the genera Lysmata and Exhippolysmata. In the future, this phylogeny will help to reveal the conditions favouring the origins of several behavioural and morphological novelties in these unique shrimps. © 2010 The Linnean Society of London, Zoological Journal of the Linnean Society, 2010, 160 , 254–265.     

Molecular systematics and evolution of the subgenus Mesocarabus Thomson, 1875 (Coleoptera: Carabidae: Carabus), based on mitochondrial and nuclear DNA

The subgenus Mesocarabus Thomson, 1875 is a western Palaearctic group that currently includes five species: four of them inhabiting western Europe (Carabus lusitanicus Fabricius, 1801, Carabus problematicus Herbst, 1786, Carabus dufourii Dejean & Boisduval, 1829, and Carabus macrocephalus Dejean, 1826) and one found in the Rif Mountains in northern Morocco (Carabus riffensis Fairmaire, 1872). Representatives of Mesocarabus have been included in previous molecular phylogenetic studies, but taxon‐ or gene‐sampling limitations yielded inconclusive results regarding its monophyly and sister relationship. Here we perform molecular phylogenetic analyses based on five mitochondrial (3625 nt) and eight nuclear (5970 nt) genes sequenced in many Mesocarabus populations, and in related western Palaearctic Carabus Linnaeus, 1758. We conducted parsimony, maximum‐likelihood, and Bayesian analyses and found a well‐supported sister relationship between a monophyletic Mesocarabus with Iberian species of the subgenus Oreocarabus Géhin, 1876. Within Mesocarabus, the European species form a monophyletic lineage sister to Moroccan C. riffensis. A time‐calibrated phylogeny suggests the split between Mesocarabus and Oreocarabus occurred at 11.8 Mya (95% highest posterior density, HPD, 8.7–15.3 Mya), and the divergence between C. riffensis and European Mesocarabus at 9.5 Mya (95% HPD 7.0–12.5 Mya). The early diversification of Mesocarabus and related subgenera during the Miocene, and alternative hypotheses concerning the origin of Mesocarabus in the Iberian Peninsula and the Betic‐Riffian plate are discussed using calibration data and dispersal–vicariance biogeographic analyses. Finally, we found instances of incongruence between mitochondrial DNA and nuclear‐based phylogenies of Mesocarabus, which are hypothesized to be the result of introgressive hybridization. © 2012 The Linnean Society of London, Zoological Journal of the Linnean Society, 2012, 166 , 787–804.