Phylogeny and biogeography ofOrobanchaceae

Orobanchaceae, as it is currently defined, includes all levels of parasitic ability ranging from nonparasitic (Lindenbergia) to facultative and obligate hemiparasites to obligate holoparasites. Several genera are of economic importance as crop weeds and have been studied by scientists interested in developing methods of control, but most genera have not been studied in a comparative framework. In this study we have used ITS sequence data to build a phylogenetic framework with which to examine previous systematic hypotheses of relationships among genera, and biogeographic hypotheses of either a Cretaceous, Gondwanan or mid-Tertiary, Laurasian origin of the family. A single-most parsimonious ITS tree was produced from a combined data set of nucleotides and gap characters. Our results support the current classification ofOrobanchaceae and a hypothesis of a mid-Tertiary, Laurasian origin of the family.     

Preliminary study on phylogenetic position and delimitation of the ciliate arthrodontous genera of the moss family Mniaceae

The history of the generic and sectional concepts in the traditional moss family Mniaceae is summarised. The division of the Mniaceae into nine genera has been generally accepted. A phylogenetic analysis, based on 35 Mniaceae samples as ingroup and one Leptostomataceae and three Bryaceae samples as outgroups was completed. A total of 113 new sequences were obtained and 4139 aligned characters were included in the combined dataset. Bayesian inferences based on the combined data set showed five well supported clades, which, as a whole, form the monophyletic family Mniaceae. The number of genera in the traditional Mniaceae is 9 and the number of species is 74. All the genera appear monophyletic except Plagiomnium; accepting Orthomnion at the generic level makes Plagiomnium paraphyletic. The principle that only monophyletic taxa are allowed and may be named necessitates the uniting of Plagiomnium and Orthomnion. The necessary combinations are made. The taxonomy of the genera and sections is discussed. Rhizomnium section Macromnium T.J.Kop. & Y.Sun, sect. nov. is described and the new combination Rhizomnium chlorophyllosum (Kindb.) T.J.Kop. is made. The controversy of paraphyly – monophyly in accepting and naming taxa is discussed and Plagiomnium versus Orthomnion given as an example. All the present genera and species seem to have diverged in the area of the Laurasian supercontinent and the speciation of most genera took place in the temperate forested areas of western and eastern North America, Europe and south-eastern Asia.     

Welcome back New Zealand: regional biogeography and Gondwanan origin of three endemic genera of mite harvestmen (Arachnida, Opiliones, Cyphophthalmi)

Aim Biogeographers have long been intrigued by New Zealand’s biota due to its unique combination of typical ‘continental’ and ‘island’ characteristics. The New Zealand plateau rifted from the former supercontinent Gondwana c. 80 Ma, and has been isolated from other land masses ever since. Therefore, the flora and fauna of New Zealand include lineages that are Gondwanan in origin, but also include a very large number of endemics. In this study, we analyse the evolutionary relationships of three genera of mite harvestmen (Arachnida, Opiliones, Cyphophthalmi) endemic to New Zealand, both to each other and to their temperate Gondwanan relatives found in Australia, Chile, Sri Lanka and South Africa. Location New Zealand (North Island, South Island and Stewart Island). Methods A total of 94 specimens of the family Pettalidae in the suborder Cyphophthalmi were studied, representing 31 species and subspecies belonging to three endemic genera from New Zealand (Aoraki, Neopurcellia and Rakaia) plus six other members of the family from Chile, South Africa, Sri Lanka and Australia. The phylogeny of these taxa was constructed using morphological and molecular data from five nuclear and mitochondrial genes (18S rRNA, 28S rRNA, 16S rRNA, cytochrome c oxidase subunit I and histone H3, totalling c. 5 kb), which were analysed using dynamic as well as static homology under a variety of optimality criteria. Results The results showed that each of the three New Zealand cyphophthalmid genera is monophyletic, and occupies a distinct geographical region within the archipelago, grossly corresponding to palaeogeographical regions. All three genera of New Zealand mite harvestmen fall within the family Pettalidae with a classic temperate Gondwanan distribution, but they do not render any other genera paraphyletic. Main conclusions Our study shows that New Zealand’s three genera of mite harvestmen are unequivocally related to other members of the temperate Gondwanan family Pettalidae. Monophyly of each genus contradicts the idea of recent dispersal to New Zealand. Within New Zealand, striking biogeographical patterns are apparent in this group of short‐range endemics, particularly in the South Island. These patterns are interpreted in the light of New Zealand’s turbulent geological history and present‐day patterns of forest cover.     

A Molecular Phylogenetic Investigation of Bakuella,Anteholosticha, and Caudiholosticha (Protista,Ciliophora, Hypotrichia) Based on Three‐Gene Sequences

Traditionally classifications of the Urostyloida have been mainly based on morphology and morphogenesis. Recent molecular phylogenetic analyses have been largely based on single‐gene data for a limited number of taxa. Consequently, incongruence has arisen between the morphological/morphogenetic and the molecular data. In this study, the three phylogenetic markers (SSU rDNA, ITS1‐5.8S‐ITS2 region, and LSU‐rDNA) of three urostyloid genera represented by four species (Bakuella granulifera, Anteholosticha monilata, Caudiholosticha sylvatica, and C. tetracirra) were sequenced to investigate their phylogeny. The results show that: (1) all three genera should be regarded as the members of the order Urostyloida within the subclass Hypotrichia, as indicated by morphological characters; (2) phylogenetic analyses and sequence similarities both indicate that neither Anteholosticha nor Caudiholosticha are monophyletic and the systematic assignment of both genera awaits further evaluation; and (3) Bakuella has a closer relationship with Urostyla than with bakuellids (e.g. Apobakuella and Metaurostylopsis), suggesting Bakuella may belong to the family Urostylidae rather than the family Bakuellidae.     

Tri-locus sequence data reject a “Gondwanan origin hypothesis” for the African/South Pacific crab genus Hymenosoma

Crabs of the family Hymenosomatidae are common in coastal and shelf regions throughout much of the southern hemisphere. One of the genera in the family, Hymenosoma, is represented in Africa and the South Pacific (Australia and New Zealand). This distribution can be explained either by vicariance (presence of the genus on the Gondwanan supercontinent and divergence following its break-up) or more recent transoceanic dispersal from one region to the other. We tested these hypotheses by reconstructing phylogenetic relationships among the seven presently-accepted species in the genus, as well as examining their placement among other hymenosomatid crabs, using sequence data from two nuclear markers (Adenine Nucleotide Transporter [ANT] exon 2 and 18S rDNA) and three mitochondrial markers (COI, 12S and 16S rDNA). The five southern African representatives of the genus were recovered as a monophyletic lineage, and another southern African species, Neorhynchoplax bovis, was identified as their sister taxon. The two species of Hymenosoma from the South Pacific neither clustered with their African congeners, nor with each other, and should therefore both be placed into different genera. Molecular dating supports a post-Gondwanan origin of the Hymenosomatidae. While long-distance dispersal cannot be ruled out to explain the presence of the family Hymenosomatidae on the former Gondwanan land-masses and beyond, the evolutionary history of the African species of Hymenosoma indicates that a third means of speciation may be important in this group: gradual along-coast dispersal from tropical towards temperate regions, with range expansions into formerly inhospitable habitat during warm climatic phases, followed by adaptation and speciation during subsequent cooler phases.     

Phylogeny and historical biogeography of Gondwanan moss-bugs (Insecta: Hemiptera: Coleorrhyncha: Peloridiidae)

The moss bugs of the Peloridiidae, a small group of cryptic and mostly flightless insects, is the only living family in Coleorrhyncha (Insecta: Hemiptera). Today 37 species in 17 genera are known from eastern Australia, New Zealand, New Caledonia and Patagonia, and the peloridiids are thereby a group with a classical southern Gondwanan distribution. To explicitly test whether the present-day distribution of the Peloridiidae actually results from the sequential breakup of southern Gondwana, we provide the first total-evidence phylogenetic study based on morphological and molecular characters sampled from about 75% of recognized species representing 13 genera. The results largely confirm the established morphological phylogenetic context except that South American Peloridium hammoniorum constitutes the sister group to the remaining peloridiids. A timescale analysis indicates that the Peloridiidae began to diversify in the land mass that is today's Patagonia in the late Jurassic (153 Ma, 95% highest posterior density: 78–231 Ma), and that splitting into the three extant well-supported biogeographical clades (i.e. Australia, Patagonia and New Zealand/New Caledonia) is consistent with the sequential breakup of southern Gondwana in the late Cretaceous, indicating that the current transoceanic disjunct distributions of the Peloridiidae are best explained by a Gondwanan vicariance hypothesis.     

Systematics ofLavatera andMalva (Malvaceae,Malveae)—a new perspective

Lavatera andMalva are circumscribed by epicalyx characters, but the distinction is untenable on this basis. Morphological characters and phylogenetic trees from rDNA ITS sequence data indicate the presence of two well-supported species groups different from the traditional genera. One group includes a mixture of closely related species in both genera and forms a more broadly circumscribedMalva, including most disjunctLavatera species—notably four of western North American islands, one Australian and one Canarian species. The other group forms a more narrowly definedLavatera. Another CanarianLavatera species may be a common ancestor to the two groups.     

Minute moss beetles in the Southern Hemisphere: Molecular phylogeny,historical biogeography and habitat shifts (Coleoptera: Hydraenidae)

Minute moss beetles (Hydraenidae) are one of the most speciose and widespread families of aquatic Coleoptera, with an estimated 4000 extant species, found in the majority of aquatic habitats from coastal rock pools to mountain streams and from the Arctic Circle to the Antarctic islands. Molecular phylogenetic works have improved our understanding of the evolutionary history of the megadiverse Hydraena, Limnebius and Ochthebius in recent years, but most genera in the family have not yet been included in any phylogenetic analyses, particularly most of those which are restricted to the Southern Hemisphere. Using a multimarker molecular matrix, sampling over 40% of described species richness and 75% of currently recognized genera, we infer a comprehensive molecular phylogeny of these predominantly Gondwanan Hydraenidae. Whilst the genera we focus on are morphologically diverse, and currently classified across all four hydraenid subfamilies, our phylogenetic analyses suggest that these Gondwanan genera may instead constitute a single clade. As a result of our findings, the African genus Oomtelecopon Perkins syn.n. is shown to nest within Coelometopon Janssens, the New Zealand Homalaena Ordish syn.n. and Podaena Ordish syn.n. are synonymised with Orchymontia Broun, and the South African Pterosthetops Perkins syn.n. is synonymised with Prosthetops Waterhouse, resulting in Pterosthetopini Perkins syn.n. being synonymised with Prosthetopini Perkins. Mesoceratops Bilton & Jäch gen.n. is erected to accommodate six former members of Mesoceration Janssens, which is shown to be polyphyletic. We propose the replacement name Orchymontia ordishi Jäch & Bilton nom.n. for Homalaena dilatata Ordish, 1984 (now a junior homonym); altogether 39 new combinations are proposed. Our Bayesian divergence times infer an origin for this ‘Gondwana group’ of genera in Africa plus Madagascar in the mid-Cretaceous and suggest that both vicariant and dispersal processes, together with extinctions, have shaped the biogeographic history of these beetles in the Southern Hemisphere during the Cretaceous, resulting in geographically conserved extant lineages. Finally, we reconstruct ancestral habitat shifts across our phylogeny, revealing numerous changes in habitat occupancy in these genera, including multiple origins of fully terrestrial, humicolous taxa in different regions.     

Emergence of a superradiation: pselaphine rove beetles in mid‐Cretaceous amber from Myanmar and their evolutionary implications

Pselaphinae is an exceptionally species‐rich, globally distributed subfamily of minute rove beetles (Staphylinidae), many of which are inquilines of social insects. Deducing the factors that drove pselaphine diversification and their evolutionary predisposition to inquilinism requires a reliable timescale of pselaphine cladogenesis. Pselaphinae is split into a small and highly plesiomorphic supertribe, Faronitae, and its sister group, the ‘higher Pselaphinae’ – a vast multi‐tribe clade with a more derived morphological ground plan, and which includes all known instances of inquilinism. The higher Pselaphinae is dominated by tribes with a Gondwanan taxonomic bias. However, a minority of tribes are limited to the Nearctic and Palearctic ecozones, implying a potentially older, Pangaean origin of the higher Pselaphinae as a whole. Here, I describe fossils from mid‐Cretaceous (～99 million years old) Burmese amber that confirm the existence of crown‐group higher pselaphines on the Eurasian supercontinent prior to contact with Gondwanan landmasses. Protrichonyx rafifrons gen. et sp.n. is placed incertae sedis within the higher Pselaphinae. Boreotethys gen.n. , erected for B. grimaldii sp.n . and B. arctopteryx sp.n. , represents an extinct sister taxon and putative stem group of Bythinini, a Recent tribe with a primarily Holarctic distribution. The Laurasian palaeolocality of the newly described taxa implies that higher pselaphines are indeed probably of Jurassic, Pangaean extraction and that the Laurasian‐Gondwanan tribal dichotomy of this clade may have developed vicariantly following Pangaean rifting. Higher pselaphines probably predate the earliest ants. Their physically protective morphological ground plan may have been a preadaptation for myrmecophily when ants became diverse and ecologically ubiquitous, much later in the Cenozoic. This published work has been registered in ZooBank, http://zoobank.org/urn:lsid:zoobank.org:pub:36E3FE2A-B947-422D-89CA-0EF43B99C382 .     

On the phylogenetic position and systematics of extant and fossil Aclopinae (Coleoptera: Scarabaeidae)

The Aclopinae is a small subfamily within the family Scarabaeidae. It currently comprises five extant genera with 28 species, and eight fossil genera with 25 species. The systematic position of Aclopinae within the family Scarabaeidae is uncertain, particularly because representative species of Aclopinae have been absent in previous phylogenetic studies. Here we performed phylogenetic analyses using morphological and molecular data to investigate the phylogenetic position of fossil and extant Aclopinae. For this objective, we expanded and revised a former morphological data matrix (composed of 68 characters) including all extant genera of Aclopinae. We complemented our morphological investigations with a molecular phylogenetic analysis based on four genes of several extant taxa of Aclopinae and a wide sample of diverse Scarabaeoidea. Our phylogenetic analyses show that all the type species of the fossil genera formerly included within Aclopinae do not belong within the extant Aclopinae clade and support both the exclusion of those fossil taxa and the monophyly of the extant genera of Aclopinae: Aclopus Erichson, Desertaclopus Ocampo & Mondaca, Gracilaclopus Ocampo & Mondaca, Neophanaeognatha Allsopp and Phanaeognatha Hope. Our results also show that the fossil taxa Prophaenognatha robusta Bai et al. and Ceafornotensis archratiras Woolley are closely related to Ochodaeidae, while the remaining type species of fossils formerly included in Aclopinae (Cretaclopus longipes (Ponomarenko), Holcorobeus vittatus Nikritin, Juraclopus rodhendorfi Nikolajev, Mesaclopus mongolicus (Nikolajev), and Mongolrobeus zherikhini Nikolajev) belong to a distinct lineage closely related to Diphyllostomatidae. Based on these results, the subfamily Aclopinae appears monophyletic and sister to the ‘pleurostict’ lineage. Consequently, we propose the following changes to the current classification of the fossil taxa: Holcorobeus monreali (Gómez‐Pallerola) belongs to Carabidae (incertae sedis) as proposed by the original author, and we place Ceafornotensis Woolley, Cretaclopus Nikolajev, Holcorobeus Nikritin, Juraclopus Nikolajev, Mesaclopus Nikolajev, Mongolrobeus Nikolajev and Prophaenognatha Bai et al. in Scarabaeoidea (incertae sedis). Furthermore, we provide an identification key to, and diagnoses of, the genera, illustrations of diagnostic characters and checklists of their included species. The evolutionary perspective presented provides new insights into the evolution of the pleurostict condition in Scarabaeoidea and the biogeography of this group, which is now regarded as Gondwanan, probably evolving during the Cretaceous and not from the upper Jurassic as previously assumed.     

Grazing insects reduce algal biomass in a neotropical stream

The Darwinulidae are the only surviving post-Palaeozoic darwinulocopine family of an extensive radiation that reached its maximum in the Permian. Whereas at least some Palaeozoic darwinulids are known from sexual populations, the surviving lineages after the end-Permian mass extinction have abandoned sex since 200 million years ago. This makes the extant family Darwinulidae one of the few putative ancient asexual groups. Only about 30 species in 5 genera are presently known. The phylogeny of these taxa is here analysed using both morphological characters and molecular data. Twelve characters on valve morphology and 17 characters pertaining to appendages are used to construct the most parsimonious (unrooted) cladogram of 12 species in 5 genera. DNA sequences of one nuclear (ITS1) and a mitochondrial (COI) gene of 6 species in 5 genera are used to construct rooted maximum parsimony trees. Both molecular and morphological trees show a high degree of congruence, indicating that Alicenula and Vestalenula mostly cluster closely together, while Penthesilenula and Microdarwinula constitute a robust group. The position of the monospecific genus Darwinulais more variable, but is mostly closer to the two former genera. Congeneric species always cluster together in the morphological cladograms, and these results thus confirm that the five genera recognised by Rossetti & Martens (1998) are good phyletic units. An approximate molecular clock (calibrated with fossil data) indicates that the extant darwinulids share a common ancestor, which lived at least 100 million years ago.     

On the phylogenetic relationships of Vincelestes neuquenianus

This short review paper compares the lower jaw and lower dentition of the small Mesozoic mammal Vincelestes neuquenianus with some other Laurasian and Gondwanan taxa. On this basis a set of 90 characters recognised by recent authors was assembled and used to construct a cladogram. The topology suggests that the early Cretaceous mammal from Patagonia, Vincelestes, is nested within a clade comprising ‘other Gondwanan mammals’, separated from Laurasian taxa. In general, because there is a lack of Mesozoic mammal skulls from Gondwana, meaning that the skull of Vincelestes can only be compared with cranial material from Laurasia, an incomplete understanding of relationships has resulted in earlier studies. The prototribosphenic condition of Vincelestes is supported by the cladistic analysis presented here and permits a number of interesting speculations because it is of later age than Jurassic tribosphenic mammals from Gondwana. It is proposed that the tribosphenic condition may have developed first amongst taxa on Pangea, before the separation of Laurasia and Gondwana.     

A morphometrics‐based phylogeny of the temperate Gondwanan mite harvestmen (Opiliones,Cyphophthalmi, Pettalidae)

A phylogenetic estimation of the temperate Gondwanan mite harvestman family Pettalidae (Arachnida, Opiliones, Cyphophthalmi) was conducted using 143 morphological variables (59 raw and 84 scaled measurements) from 37 ingroup and 15 outgroup terminals. We used custom algorithms to do pairwise comparisons between characters and identify sets of dependent characters, which were collapsed using principal components analysis. We analysed the resulting data without discretization under the parsimony criterion. Monophyly or paraphyly of most groups suspected from previous molecular and morphological phylogenetic studies were recovered. Trees were optimized for monophyly of 20 different focus clades by varying character phylogenetic independence. This yielded a final tree with monophyly of 15 out of 20 focus clades, including the South African pettalids, which contains the troglomorphic species Speleosiro argasiformis Lawrence, 1931. Two of the remaining five clades were found paraphyletic, with the genera Aoraki, Rakaia, and Siro always being found polyphyeletic.     

Chromosomal diversification in the flightless Western Mediterranean bushcricket genus Odontura (Orthoptera: Tettigoniidae: Phaneropterinae) inferred from molecular data

We used molecular characters to infer the phylogenetic position of the Western Mediterranean bushcricket genus Odontura and to trace its high karyotype diversity. Analysis of 1391 base pairs of two mitochondrial genes (COI and ND1) and one nuclear sequence (ITS2) was conducted. Phylogenetic topologies were estimated using maximum parsimony, maximum likelihood and likelihood‐based Bayesian inference. The genus Odontura is a phylogenetic outlier in respect of all other European Phaneropterinae genera and has been proposed to have originated from a hitherto unknown ancestor. Our results support the monophyly of the genus Odontura and the recognition of two subgenera: Odontura and Odonturella. We found that both Sicilian taxa of the subgenus Odontura have a completely identical morphology and song patterns. Combining these results, we proposed that both should be treated as subspecies: O. (Odontura) stenoxypha stenoxypha and O. (O.) st. arcuata. Bioacoustic data also proved to support independent markers, with song characteristics reflecting the molecular topology. Mapping the karyotypic characters onto the phylogenetic tree allows a reconstruction of the directions and transitional stages of chromosome differentiation. The number of autosomes within the genus Odontura ranges from 26 to 30. In addition to the ancestral X0 sex determination mechanism, neo‐XY and neo‐X₁X₂Y sex chromosomes have evolved independently.     

Ribosomal ITS Sequences Allow Resolution of Freshwater Sponge Phylogeny with Alignments Guided by Secondary Structure Prediction

Freshwater sponges include six extant families which belong to the suborder Spongillina (Porifera). The taxonomy of freshwater sponges is problematic and their phylogeny and evolution are not well understood. Sequences of the ribosomal internal transcribed spacers (ITS1 and ITS2) of 11 species from the family Lubomirskiidae, 13 species from the family Spongillidae, and 1 species from the family Potamolepidae were obtained to study the phylogenetic relationships between endemic and cosmopolitan freshwater sponges and the evolution of sponges in Lake Baikal. The present study is the first one where ITS1 sequences were successfully aligned using verified secondary structure models and, in combination with ITS2, used to infer relationships between the freshwater sponges. Phylogenetic trees inferred using maximum likelihood, neighbor-joining, and parsimony methods and Bayesian inference revealed that the endemic family Lubomirskiidae was monophyletic. Our results do not support the monophyly of Spongillidae because Lubomirskiidae formed a robust clade with E. muelleri, and Trochospongilla latouchiana formed a robust clade with the outgroup Echinospongilla brichardi (Potamolepidae). Within the cosmopolitan family Spongillidae the genera Radiospongilla and Eunapius were found to be monophyletic, while Ephydatia muelleri was basal to the family Lubomirskiidae. The genetic distances between Lubomirskiidae species being much lower than those between Spongillidae species are indicative of their relatively recent radiation from a common ancestor. These results indicated that rDNA spacers sequences can be useful in the study of phylogenetic relationships of and the identification of species of freshwater sponges.     

Biogeographical origins and diversification of the exoneurine allodapine bees of Australia (Hymenoptera,Apidae)

Aim Early diversification of allodapine bees occurred in Africa c. 50 Ma. They are most abundant in sub‐Saharan Africa and Australia, and one of the oldest phylogenetic divergences in the tribe involves a split between an African + Malagasy clade and an Australian clade. The historical biogeographical scenario for this has been highly problematic, entailing an Eocene dispersal from Africa to Australia, followed by an unresolved, and apparently rapid, set of bifurcations leading to the Australian ‘exoneurine’ genera. Here we use an expanded taxon set of Australian species to explore the timing and historical biogeography of the exoneurine radiation. Location Australia, Africa, Madagascar. Methods One nuclear gene (F2 copy of elongation factor 1α) and two mitochondrial genes (cytochrome c oxidase subunit I and cytochrome b) were sequenced for 33 Australian exoneurine species from all five genera found on the continent, as well as for an additional 37 species from all non‐parasitic genera in the remainder of the tribe. We used Bayesian inference analyses to study phylogenetic topology and penalized likelihood analyses to infer key dates of divergence within the tribe. We also used lineage‐through‐time (LTT) analyses and Bayesian analyses to explore the tempo of radiations and biogeographical history of the exoneurines. Results Results from the phylogenetic analyses were congruent with previous studies, indicating a single colonization event c. 34 Ma, too late for Gondwanan vicariance models, and too early for a Laurasian dispersal route. In contrast to earlier studies, we show that this colonization event did not result in an ancient rapid radiation. However, LTT patterns indicated a rapid radiation of the temperate‐adapted genera Exoneura and Brevineura, but not of the xeric‐adapted genus Exoneurella, from 10 to 6 Ma. Main conclusions Our results indicate a trans‐oceanic dispersal event from Africa to Australia, most likely via Antarctica, with an accelerated diversification of temperate‐adapted lineages during the major Late Miocene event referred to as the ‘Hill Gap’. This is the first study to link radiations in Australian bee faunal elements to changing climate, and differs from many other plant and insect phylogenetic studies by showing increased radiation of temperate clades, rather than xeric clades, with increasing aridification of Australia.     

Phylogeny and biogeography of tetralophodont rodents of the tribe Oryzomyini (Cricetidae: Sigmodontinae)

Oryzomyini is the richest tribe among the Sigmodontine rodents, encompassing 32 living and extinct genera and including an increasing number of recently described species and genera. Some Oryzomyini are tetralophodont showing a reduction in the number of molar folds to four, while most taxa in this tribe retain the plesiomorphic pentalophodont state. We applied phylogenetic methods, molecular dating techniques and ancestral area analyses to members of an oryzomyini clade informally named ‘D’ in former studies and included related fossil tetralophodont forms. Based on 98 morphological characters and sequences of five gene fragments, we found that the tetralophodont condition is paraphyletic. Among living taxa, Pseudoryzomys is sister to Holochilus, and Lundomys is derived from a basal divergence. A clade formed by living Holochilus and the fossils Noronhomys and Carletonomys is sister to Holochilus primigenus, making Holochilus paraphyletic. Therefore, we describe a new genus that accommodates the fossil H. primigenus. Because trans‐Andean taxa currently share a common ancestor with taxa of cis‐Adean distribution, the northern Andes uplift may have worked as a postdispersal barrier. The tetralophodont lineages diverged during the Pliocene from a cis‐Andean ancestor, and the Great Plains in South America may have favoured the diversification of tetralophodont forms adapted to open habitats during the Pliocene.     

Phylogeny and morphological evolution of the amblystegiaceae (Bryopsida)

To circumscribe the moss family Amblystegiaceae, we performed a broad-scale analysis of trnL-trnF spacer sequence data for 168 species of the Hypnales and 11 species of the Hookeriales and additional analyses of trnL-trnF and atpB-rbcL (chloroplast DNA), one nuclear region, the internal transcribed spacers of 18S-26S rDNA, and 68 morphological characters for a reduced data set of 54 species of Hypnales. The traditionally circumscribed Amblystegiaceae are polyphyletic and include the Amblystegiaceae s. str. and the Calliergonaceae fam. nov., plus several taxa closely related to other Hypnalean families. Generic relationships within the redefined Amblystegiaceae were investigated by analyzing data from the three DNA regions and morphology as used in the broader analysis. Reconstruction of morphological evolution was evaluated using maximum-parsimony and maximum-likelihood. Numerous independent character-state transitions implied by the phylogeny suggest that morphological characters that have traditionally been used to delineate the Amblystegiaceae are homoplastic. Sporophytic traits, which are generally given primacy over gametophytic traits in moss classification, are more labile than previously thought, and many characters that are related to sporophyte specializations are strongly correlated with habitat conditions. The evolution of several gametophyte features previously thought to be reliable for delineating the family are also strongly correlated with habitat. These observations help to explain the instability of the Amblystegiaceae in previous taxonomic and phylogenetic analyses based on morphology.     

Phylogenetic classification of the Drosophilidae Rondani (Diptera): the role of morphology in the postgenomic era

Molecular sequences now overwhelm morphology in phylogenetic inference. Nonetheless, most molecular studies are conducted on a limited number of taxa, as DNA rarely can be analysed from old museum types or fossils. During the last 20 years, more than 150 molecular studies have challenged the current phylogenetic classification of the family Drosophilidae Rondani based on morphological characters. Most studies concerned a single genus, Drosophila Fallén, and included only few representative species from 17 out of the 78 genera of the family. Therefore, these molecular studies were unable to provide an alternative classification scheme. A supermatrix analysis of seven nuclear and one mitochondrial genes (8248 bp) for 33 genera was conducted using outgroups from one calyptrate and four ephydroid families. The Bayesian phylogeny was consistent with previous molecular studies including whole genome sequences and divided the Drosophilidae into four monophyletic clades. Morphological characters, mostly male genitalia, then were compared thoroughly between the four clades and homologous character states were identified. These states were then checked for 70 genera and a revised phylogenetic, family‐group classification for the Drosophilidae is proposed. Two genera –Cladochaeta Coquillett and Diathoneura Duda – of the tribe Cladochaetini Grimaldi are transferred to the family Ephydridae. The Drosophilidae is divided into two subfamilies: Steganinae Hendel (30 genera) and Drosophilinae Rondani (43 genera). A further two genera, Apacrochaeta Duda and Sphyrnoceps de Meijere, are incertae sedis, and Palmophila Grimaldi, is synonymized with Drosophila syn.n. The Drosophilinae is subdivided into two tribes: the re‐elevated Colocasiomyini Okada (nine genera) and Drosophilini Okada. The paraphyly of the genus Drosophila was not resolved to avoid affecting the binomina of important laboratory model species; however, its subgeneric classification was revised in light of molecular and morphological data. Three subgenera, namely Chusqueophila Brncic, Phloridosa Sturtevant and Psilodorha Okada, were synonymized with the subgenus Drosophila (Drosophila) Fallén syns.n. Among the 45 species groups and 5 species complexes of Drosophila (Drosophila), 22 groups and 1 complex were transferred to the subgenus Drosophila (Siphlodora) Patterson & Mainland and 6 groups, 2 species subgroups and 3 complexes are considered incertae sedis within the genus Drosophila. Different morphological characters provide different signals at different phylogenetic scales: thoracic characters (wing venation and presternal shape) discriminate families; grasping and erection‐related characters discriminate subfamilies to tribes; whereas phallic paraphyses, i.e. auxiliary intromittent organs, discriminate genera and Drosophila subgenera. The study shows the necessity of analysing morphological characters within a molecular phylogenetic framework to translate molecular phylogenies into taxonomically‐comprehensive classifications.     

Molecular and morphological characterization of a poorly known marine ciliate, Myoschiston duplicatum precht 1935: implications for phylogenetic relationships between three morphologically similar genera -- Zoothamnium, Myoschiston, and Zoothamnopsis (Ciliophora, Peritrichia, Zoothamniidae)

We studied the morphology and molecular phylogeny of Myoschiston duplicatum, a peritrich ciliate that has been recorded as an epibiont of crustaceans, but which we also identified on marine algae from Korea. The important morphological characteristics revealed by silver staining of Myoschiston species have not been described because they are rarely collected. Using morphological methods, we redescribed the type species of the genus, Myoschiston duplicatum, and provided an improved diagnosis of Myoschiston. In addition, the coding regions for nuclear small subunit (SSU) rRNA and internal transcribed spacer 1‐5.8S‐internal transcribed spacer 2 sequences were sequenced. Phylogenetic analyses that included available SSU rDNA sequences of peritrichs from GenBank strongly supported a position of M. duplicatum within the family Zoothamniidae. In addition, phylogenetic analyses were performed with single datasets (ITS1‐5.8S‐ITS2) and combined datasets (SSU rDNA + ITS1‐5.8S‐ITS2) to explore further the phylogenetic relationship in the family Zoothamniidae between the three morphologically similar genera—Zoothamnium, Myoschiston, and Zoothamnopsis.