A molecular phylogeny and a revised classification of tribe Lepisoreae (Polypodiaceae) based on an analysis of four plastid DNA regions

Phylogenetic relationships within the palaeotropical tribe Lepisoroideae (Polypodiaceae) were investigated by studying sequence variation of four plastid DNA regions: rbcL, rps4 plus rps4‐trnS IGS, trnL intron plus trnL‐F IGS, rbcL‐atpB IGS plus part of atpB. In total, over 4000 nucleotides were sequenced for 39 species. Seven well‐supported clades were found in the analyses of the combined data set. We provide a new classification of Lepisoroideae by integrating phylogenetic results and known variation of morphological characters. The two small genera Neocheiropteris and Tricholepidium are supported as monophyletic, the genus Paragramma is resurrected and the genera Lepisorus, Neolepisorus, Lemmaphyllum and Lepidomicrosorium are re‐circumscribed. We proposed 14 new combinations, among which Caobangia is treated as a synonym of Lemmaphyllum. A key for identifying the recognized genera is presented. © 2010 The Linnean Society of London, Botanical Journal of the Linnean Society, 2010, 162 , 28–38.     

A new Oligocene Ctenodactylinae (Rodentia: Mammalia) from Ulantatal (nei Mongol): new insight on the phylogenetic origins of the modern Ctenodactylidae

The four living genera of Ctenodactylidae (Rodentia) are the only survivors of a flourishing Tertiary group. In this paper, we describe a new Oligocene species from Ulantatal (Chinese Mongolia) that highlights the origins of crown ctenodactylids. This species, Helanshania deserta gen. et sp. nov. , is lophodont and displays semi‐hypsodont teeth, a dental pattern that is somewhat transitional between that of primitive Oligocene ctenodactylids and the later hypsodont genera. We perform here a cladistic assessment of the dental evidence for species produced by the successive radiations of the group. In order to get new data, to decipher homologies for the dental pattern of modern ctenodactylids, and to specify their dental replacement, we describe additional dental material of Ctenodactylus, Massoutiera, and Felovia. The phylogenetic analysis (using PAUP) considered 45 characters (mainly dental) and 31 species. The performed heuristic searches yielded 596 equally most parsimonious trees. Protataromys and Karakoromys are stem ctenodactylids and appear as the earliest offshoots of the Ctenodactylidae clade, which represents a well‐supported family rank. Within this family, the Tataromyinae appear paraphyletic, whereas the Ctenodactylinae sensu lato are a clade including the new taxon Helanshania. As such, a revision of the Tataromyinae is envisaged and a new subfamily is erected (Yindirtemyinae). Amongst the Ctenodactylinae, a tribe Ctenodactylini encompassing the crown ctenodactylines is proposed. © 2010 The Linnean Society of London, Zoological Journal of the Linnean Society, 2010, 160 , 531–550.     

Calibrated chronograms,fossils, outgroup relationships,and root priors: re‐examining the historical biogeography of Geraniales

We re‐examined the recent study by Palazzesi et al., (2012) published in the Biological Journal of the Linnean Society (107: 67–85), that presented the historical diversification of Geraniales using BEAST analysis of the plastid spacer trnL–F and of the non‐coding nuclear ribosomal internal transcribed spacers (ITS). Their study presented a set of new fossils within the order, generated a chronogram for Geraniales and other rosid orders using fossil‐based priors on five nodes, demonstrated an Eocene radiation of Geraniales (and other rosid orders), and argued for more recent (Pliocene–Pleistocene) and climate‐linked diversification of genera in the five recognized families relative to previous studies. As a result of very young ages for the crown of Geraniales and other rosid orders, unusual relationships of Geraniales to other rosids, and apparent nucleotide substitution saturation of the two gene regions, we conducted a broad series of BEAST analyses that incorporated additional rosid fossil priors, used more accepted rosid ordinal topologies, or altered the placement of one fossil Geraniales prior. Our results indicate that their ages are 20–50% too young owing to a combination of (1) strong nucleotide saturation of the DNA regions starting at 65 Mya, (2) lack of a root (rosid stem) or other rosid ordinal stem fossil‐based priors, (3) the inability of the two DNA regions (with alignment issues) to obtain a monophyletic Geraniales as well as reasonable relationships of Geraniales to other rosid orders, and (4) apparent issues with the nodal placement of a Pelargonium fossil. The Geraniales crown is much older (Campanian of the Cretaceous; 86 Mya), the posterior age distribution on all but two fossil nodes are well older than the priors, the placement of a Pelargonium‐like fossil is more likely at the crown rather than the stem, but their models of diversification within several clades linked to climatic and orogeny appear supported. We discuss a number of the inherent issues of relaxed‐clock dating and outline some ‘best practice’ approaches for such studies. © 2014 The Linnean Society of London, Biological Journal of the Linnean Society, 2014, 113 , 29–49.     

Eocene handfishes from Monte Bolca,with description of a new genus and species,and a phylogeny of the family Brachionichthyidae (Teleostei: Lophiiformes)

The family Brachionichthyidae, commonly known as the handfishes, is a small group of lophiiform fishes, the living species of which are restricted in distribution mostly to shallow temperate and subtropical waters of Tasmania and southern and eastern Australia. Despite their narrow present‐day distribution, and the extreme rarity of lophiiforms in the fossil record, handfishes are well represented in the Eocene of Monte Bolca, Italy. A revision of the known fossil material shows the presence of two fossil species in two monotypic genera, ?Histionotophorus and ? Orrichthys gen. nov. Diagnoses of the family Brachionichthyidae, the two fossil genera, as well as two recognized extant genera Brachionichthys and Sympterichthys are provided. An osteological analysis of ?Histionotophorus bassani revealed many new features as well as reinterpretations of some previously described skeletal parts. A phylogenetic analysis of brachionichthyid genera and representatives of the antennarioid families Antennariidae, Tetrabrachiidae, and Lophichthyidae, using 36 morphological characters, strongly supported monophyly of brachionichthyids and antennarioids, the former taxon representing the sister group of the other families of the latter. Within the Brachionichthyidae, the two extant genera Brachionichthys and Sympterichthys form a species pair, as do the extinct genera ?Histionotophorus and ? Orrichthys gen. nov. Biogeographical considerations suggest that the present geographical range of handfishes can be considered a residual distribution of a temporally and spatially dynamic range shift. © 2010 The Linnean Society of London, Zoological Journal of the Linnean Society, 2010, 160 , 621–647.     

Discordant mitochondrial and nuclear gene phylogenies in emydid turtles: implications for speciation and conservation

Do phylogenies and branch lengths based on mitochondrial DNA (mtDNA) provide a reasonable approximation to those based on multiple nuclear loci? In the present study, we show widespread discordance between phylogenies based on mtDNA (two genes) and nuclear DNA (nucDNA; six loci) in a phylogenetic analysis of the turtle family Emydidae. We also find an unusual type of discordance involving the unexpected homogeneity of mtDNA sequences across species within genera. Of the 36 clades in the combined nucDNA phylogeny, 24 are contradicted by the mtDNA phylogeny, and six are strongly contested by each data set. Two genera (Graptemys, Pseudemys) show remarkably low mtDNA divergence among species, whereas the combined nuclear data show deep divergences and (for Pseudemys) strongly supported clades. These latter results suggest that the mitochondrial data alone are highly misleading about the rate of speciation in these genera and also about the species status of endangered Graptemys and Pseudemys species. In addition, despite a strongly supported phylogeny from the combined nuclear genes, we find extensive discordance between this tree and individual nuclear gene trees. Overall, the results obtained illustrate the potential dangers of making inferences about phylogeny, speciation, divergence times, and conservation from mtDNA data alone (or even from single nuclear genes), and suggest the benefits of using large numbers of unlinked nuclear loci. © 2010 The Linnean Society of London, Biological Journal of the Linnean Society, 2010, 99 , 445–461.     

铬黄圆痕叶蝉属的订正及圆痕叶蝉族巴西二新属二新种描记（半翅目：叶蝉科）

基于比较形态学对曾归入圆痕叶蝉亚科铬黄圆痕叶蝉属Chromagallia的8个有效种（C. saucia (St?l), C. flavofasciata (St?l), C. longistilata (Coelho & Dutra), C. carvalhoi Gon?alves et al., C. lamasi Gon?alves et al., C. lanceolata Gon?alves et al., C. paraguayensis Gon?alves et al.和C. zanolae Gon?alves et al.）进行了订正,明确了该属的范围仅限于具有黄斑的3个种（C. flavofasciata (St?l), C. longistilata (Coelho & Dutra) 和C. rodriguesoi sp. nov.）,对该属进行了重新描述,并修订了鉴别特征。此外,对模式种C. flavofasciata 进行了重新描记,首次提供了C. longistilata的雌性生殖器图,并作了描记。把曾归入铬黄圆痕叶蝉属Chromagallia具有红斑的6个种移出并新建了2个新属：Rubragallia 和Neorubragallia,其中Rubragallia 包括R. saucia (St?l) n. comb.和R. paraguayensis (Gon?alves et al.) n. comb., Neorubragallia包括N. lamasi (Gon?alves et al.) n. comb., N. lanceolata (Gon?alves et al.) n. comb., N. zanolae (Gon?alves et al.) n. comb., N. carvalhoi (Gon?alves et al.) n. comb. 和N. mervini sp. nov.。文中提供了3个属的分种检索表,并对不同种的分类地位及3个属的划分进行了讨论。     

Towards a phylogeny of the flesh flies (Diptera: Sarcophagidae): morphology and phylogenetic implications of the acrophallus in the subfamily Sarcophaginae

The morphology of the acrophallus, the distal portion of the male phallus carrying the phallotreme, was studied in 72 exemplar species representing 56 genera and subgenera of the flesh fly subfamily Sarcophaginae. For 42 of those species, scanning electron microscopy was used to clarify the phallic morphology. Terms used to describe the male genitalia were updated based on new interpretations of homology. Male genitalic characters, combined with other morphological characters of adult males and females and of larvae, were used to construct a phylogeny. The monophyly of the subfamily was supported, and some generic‐level sister‐group relationships proposed in the literature, but without previous cladistic analyses, were also supported. The genus Blaesoxipha Loew, as currently recognized, was not monophyletic in our analysis. The genus Helicobia Coquillett is synonymized with Sarcophaga Meigen syn. nov. and treated as a subgenus of the latter. The Sarcophaga subgenera Neobellieria Blanchard and Mehria Enderlein were not monophyletic. Many of the clades in the analysis were supported primarily or exclusively by male genitalic character states, highlighting the importance of the male genitalia as a source of morphological characters for sarcophagine phylogeny. © 2010 The Linnean Society of London, Zoological Journal of the Linnean Society, 2010, 158 , 740–778.     

Does host plant richness explain diversity of ectomycorrhizal fungi? Re‐evaluation of Gao et al. (2013) data sets reveals sampling effects

The generally positive relationship between biodiversity of groups of directly or indirectly interacting organisms is one of the most important ecological concepts (Gaston, 2000 Nature, 405 , 220–227; Scherber C, Eisenhauer N, Weisser WW et al., 2010 Nature, 468 , 553–556). In a recent issue of Molecular Ecology, Gao C, Shi N‐N, Liu Y‐X et al. (2013: 22 , 3403–3414) reported that the richness of plants and ectomycorrhizal fungi is positively correlated both at local and at global scales. Here, we challenge these findings by re‐analysis of data and ascribe the reported results to sampling effect and poor data compilation.     

Genetically and geographically isolated lineages of a tropical bat (Chiroptera: Molossidae) show demographic stability over the late Pleistocene

The newly described molossid bat, Chaerephon atsinanana Goodman et al., 2010, endemic to eastern Madagascar, shows notably high levels of phylogeographic and genetic structure compared with allopatric Chaerephon leucogaster Grandidier, 1869 from western Madagascar. Such highly significant structuring of haplotypes among altitudinally and latitudinally stratified population groups is contrary to the expected panmixia in strong flying bats. The null model of concordance in historical demographic patterns across these two Chaerephon species was not supported. Mismatch and Bayesian skyline analyses indicated ancient stable C. atsinanana populations of constant size during the last two major Pleistocene glacial periods, making retreat into and expansion from glacial refugia an unlikely explanation for such high levels of structure, in accordance with expectations for tropical bats. Analyses were consistent with post‐refugial population expansion in the less diverse and structured C. leucogaster during the end of the last Pleistocene glacial period. We hypothesise that the pronounced genetic structuring in C. atsinanana may result from female philopatry. Furthermore, differing demographic histories of the two species may have been shaped by differing climate or habitat preferences, consistent with evidence from MaxEnt ecological niche modelling, which shows differences in variables influencing the current predicted distributions. Fossil Quaternary pollen deposits further indicate greater stability in past climatic patterns in eastern versus western Madagascar. © 2012 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, 106 , 18–40.     

Phylogenetic study of the Characinae (Teleostei: Characiformes: Characidae)

The Characinae is a subunit of the Characidae of special significance in including Charax, the type genus of the family and the order Characiformes. Twelve genera and 79 species have been traditionally assigned to the Characinae, but the subfamily still lacks a phylogenetic diagnosis. Herein, a data matrix including 150 morphological characters and 64 taxa (35 species representing all genera of the Characinae and 29 included in other lineages within the Characiformes) was submitted to two cladistic analyses that differ in the inclusion/exclusion of Priocharax due to the difficulty of coding most of the character states in the miniature species of this genus. Both analyses resulted in a non‐monophyletic Characinae and this subfamily is herein restricted to only seven of the original 12 genera forming the clade (Phenacogaster((Charax Roeboides)(Acanthocharax(Cynopotamus(Acestrocephalus Galeocharax))))), which is supported by ten non‐ambiguous synapomorphies and is more closely related to other genera of the Characidae than those traditionally placed in the subfamily. A second clade includes the members of the tribe Heterocharacini (Lonchogenys(Heterocharax Hoplocharax)) as the sister‐group of Gnathocharax, supported by seven non‐ambiguous synapomorphies. This clade is more closely related to a taxon formed by Roestes and Gilbertolus based on seven non‐ambiguous synapomorphies. Results do not corroborate a close relationship between Roestes–Gilbertolus and the Cynodontinae. Inclusion of the genus Priocharax suggests that it is related more closely to the Heterocharacini, but the profound modifications in its anatomy possibly related to ontogenetic truncations obscure a better understanding of its relationships. A new classification of the Characinae and the Heterocharacinae is proposed. © 2012 The Linnean Society of London, Zoological Journal of the Linnean Society, 2012, 165 , 809–915.     

Reconsideration of anopheline mosquito phylogeny (Diptera: Culicidae: Anophelinae) based on morphological data

The phylogeny of anopheline mosquitoes (Culicidae: Anophelinae) is re‐examined using morphological data derived from adults, fourth‐instar larvae and pupae. Based on the data set of Sallum et al. (2000), we add some previously missing data and simplify and recode characters to eliminate ambiguities and more accurately reflect homologies, with special emphasis on characters of the male genitalia that provide the main criteria for the subgeneric classification of genus Anopheles. The principal aim of the study is to assess objectively the phylogenetic relationships and classification of two taxa not included by Sallum et al. (2000): Anopheles corethroides, a representative of the Australasian Stigmaticus Group, and An. kyondawensis, an unusual Oriental species whose adult and pupal stages were only recently discovered. The revised data set consists of 167 characters for 66 species representing the three traditionally recognised genera of Anophelinae, the six traditionally accepted subgenera of genus Anopheles and all informal series and most species groups of subgenera Anopheles, Cellia and Nyssorhynchus. The data are analysed using equal weighting (EW) and implied weighting (IW). Analysis under EW generates a strict consensus tree with principal lineages consistent with those reported by Sallum et al. (2000). Analysis under IW supports the monophyly of Anophelinae, the basal position of Chagasia, the monophyly of subgenera Cellia, Kerteszia and Nyssorhynchus, and the sister relationship of Kerteszia + Nyssorhynchus, but otherwise yields relationships that differ significantly in one respect or another from those obtained in all previous analyses of both morphological and molecular data. Subgenus Anopheles is arrayed as a polyphyletic lineage basal to a monophyletic clade comprising the Neotropical Kerteszia + Nyssorhynchus and the Old World Cellia in a sister‐group relationship. Bironella, Lophopodomyia and Stethomyia are firmly nested within subgenus Anopheles, which would nevertheless still be paraphyletic if these taxa were subsumed within it. Anopheles kyondawensis is well supported as the sister group of Bironella + all other Anopheles. Bironella, Stethomyia, An. corethroides and several other Anopheles clades are each strongly supported in a pectinate series of relationships, terminating in the clade comprising subgenera Cellia, Kerteszia and Nyssorhynchus. These relationships and other aspects of the phylogeny are discussed in relation to the formal and informal classification of genus Anopheles.     

Bacteriophage exclusion,a new defense system

The ability to withstand viral predation is critical for survival of most microbes. Accordingly, a plethora of phage resistance systems has been identified in bacterial genomes (Labrie et al, 2010 ), including restriction‐modification systems (R‐M) (Tock & Dryden, 2005 ), abortive infection (Abi) (Chopin et al, 2005 ), Argonaute‐based interference (Swarts et al, 2014 ), as well as clustered regularly interspaced short palindromic repeats (CRISPR) and associated protein (Cas) adaptive immune system (CRISPR‐Cas) (Barrangou & Marraffini, 2014 ; Van der Oost et al, 2014 ). Predictably, the dark matter of bacterial genomes contains a wealth of genetic gold. A study published in this issue of The EMBO Journal by Goldfarb et al ( 2015 ) unveils bacteriophage exclusion (BREX) as a novel, widespread bacteriophage resistance system that provides innate immunity against virulent and temperate phage in bacteria.     

Karyomorphology of three species in Dipentodon (Dipentodontaceae), Perrottetia (Celastraceae), and Tapiscia (Tapisciaceae) of the order Huerteales and their phylogenetic implications

Abstract The karyomorphology of three species in Dipentodon (Dipentodontaceae), Perrottetia (Celastraceae), and Tapiscia (Tapisciaceae), namely Dipentodon sinicus, Perrottetia racemosa, and Tapiscia sinensis, was investigated in the present study. Recent molecular research has discovered close relationships among these three genera, which has led to the establishment of the order Huerteales with Perrottetia being placed in Dipentodontaceae. Herein we report the chromosome numbers of D. sinicus and P. racemosa for the first time, and present their karyotype formulas as 2n= 34 = 22 sm + 12 st (D. sinicus), 2n= 20 = 11 m + 9 sm (P. racemosa), and 2n= 30 = 22 m(2SAT) + 8sm (T. sinensis). Asymmetry of their karyotypes is categorized to be Type 3B in D. sinicus, Type 2A in P. racemosa, and Type 2A in T. sinensis. Each of the species shows special cytological features. Compared with Perrottetia, Dipentodon has a different basic chromosome number, a higher karyotype asymmetry, and different karyomorphology of its interphase nuclei, mitotic prophase, and metaphase. Thus, on the basis of these results, we have reservations regarding the suggestion of placing Dipentodon and Perrottetia together in the family Dipentodontaceae.     

Resolving the unresolved tribe: a molecular phylogenetic framework for the Merremieae (Convolvulaceae)

Tribe Merremieae, as currently circumscribed, comprise c. 120 species classified in seven genera, the largest of which (Merremia) is morphologically heterogeneous. Previous studies, with limited sampling, have suggested that neither Merremieae nor Merremia are monophyletic. In the present study, the monophyly of Merremia and its allied genera was re‐assessed, sampling 57 species of Merremieae for the plastid matK, trnL–trnF and rps16 regions and the nuclear internal transcribed spacer (ITS) region. All genera of Merremieae and all major morphotypes in Merremia were represented. Phylogenetic analyses resolve Merremieae in a clade with Ipomoeae, Convolvuleae and Daustinia montana. Merremia is confirmed as polyphyletic and a number of well‐supported and morphologically distinct clades in Merremieae are recognized which accommodate most of the species in the tribe. These provide a framework for a generic revision of the assemblage. © 2015 The Linnean Society of London, Botanical Journal of the Linnean Society, 2015.     

Early evolution of Cupedidae revealed by a mid‐Cretaceous reticulated beetle from Myanmar (Coleoptera: Archostemata)

Cupedidae, the most species‐rich family of the archaic suborder Archostemata, were abundant, diverse and widespread in the Mesozoic, yet little is known about the early evolution and biogeography. This stems, in part, from a lack of exceptionally preserved fossils from the Mesozoic and of formal phylogenetic study of both extant and extinct taxa. Here we describe and illustrate a new fossil from mid‐Cretaceous Burmese amber, and provide a phylogeny combining both fossils and all known extant genera of Archostemata. A dataset of 43 ingroup taxa and four outgroup taxa based on 110 morphological characters was analysed under parsimony. The results indicate that Priacma LeConte and Paracupes Kolbe, as well as the Cretaceous genera Barbaticupes Jarzembowski et al. and Mallecupes Jarzembowski et al., together form a sister clade to the rest of Cupedidae. Priacma megapuncta sp.n. is attributed to the relict North American Priacma by the presence of distinct subtruncate elytral apices, lateral elytral margins with two rows of sharp teeth, and peculiar fixing epipleural folds near the elytral apices. Our discovery of the first fossil species of Priacma in Burmese amber reveals the antiquity and wider distribution of the genus in the late Mesozoic. This published work has been registered in ZooBank, http://zoobank.org/urn:lsid:zoobank.org:pub:313565C2‐4F42‐48BD‐8720‐F379DE202868 .