Genealogy and palaeodrainage basins in Yunnan Province: phylogeography of the Yunnan spiny frog,Nanorana yunnanensis (Dicroglossidae)

Historical drainage patterns adjacent to the Qinghai‐Tibetan Plateau differed markedly from those of today. We examined the relationship between drainage history and geographic patterns of genetic variation in the Yunnan spiny frog, Nanorana yunnanensis, using approximately 981 base pairs of mitochondrial DNA partial sequences from protein‐coding genes ND1 and ND2, and intervening areas including complete tRNA^Ile, tRNA^Gln and tRNA^Met. Two null hypotheses were tested: (i) that genetic patterns do not correspond to the development of drainage systems and (ii) that populations had been stable and not experienced population expansion, bottlenecking and selection. Genealogical analyses identified three, major, well‐supported maternal lineages, each of which had two sublineages. These divergent lineages were completely concordant with six geographical regions. Genetic structure and divergence were strongly congruent with historical rather than contemporary drainage patterns. Most lineages and sublineages were formed via population fragmentation during the rearrangement of paleodrainage basins in the Early Pliocene and Early Pleistocene. Sympatric lineages occurred only in localities at the boundaries of major drainages, likely reflecting secondary contact of previously allopatric populations. Extensive population expansion probably occurred early in the Middle Pleistocene accompanying dramatic climatic oscillations.     

Phylogeny of the intertidal aleocharine tribe Liparocephalini (Coleoptera: Staphylinidae)

The tribe Liparocephalini (genera Liparocephalus Mäklin, 1853;Diaulota Casey, 1893 [ = Genoplectes Sawada, 1955];Paramblopusa Ahn & Ashe, Amblopusa Casey, 1893;Salinamexus Moore & Legner, 1977 [ = Biophytosus Moore & Legner, 1977]), all of which are exclusively restricted to the Pacific coasts of the Holarctic Region, is hypothesized to be a monophyletic group based on the following synapomorphies: seta v absent (inferred to be lost) from mentum (reversed one time in the Liparocephalus lineage), setae distributed only on mesal surface of galea and apex with setae, one medial seta present on prementum, and contiguous mesocoxal cavities. Natural history and history of the classification of the Liparocephalini are discussed. Phylogenetic analyses of the species of the Liparocephalini are presented based on larval (21 characters, 57 states), adult (49 characters, 115 states), and a combination of larval and adult characters (70 characters, 172 states). Analysis of the combined larval and adult data sets with successive approximation resulted in a single most parsimonious tree (length = 937, CI = 0.885, RI = 0.930) with the following patterns of generic relationships (outgroup (Salinamexus + Biophytosus (Amblopusa (Paramblopusa (Diaulota + Genoplectes, Liparocephalus))))).     

Phylogeny and circumscription of the near-endemic Brazilian tribe Microlicieae (Melastomataceae)

The members of tribe Microlicieae in the flowering plant family Melastomataceae are nearly all endemic to the cerrado biome of Brazil. Traditional classifications of the Melastomataceae have attributed between 15 and 17 genera to the Microlicieae, but subsequent revisions have circumscribed the tribe more narrowly. The monophyly and intergeneric relationships of the Microlicieae were evaluated through phylogenetic analyses with molecular and morphological data sets. Incorporation of DNA sequences from the intron of the chloroplast gene rpl16 into a previously generated family-wide data set yielded a clade comprising Chaetostoma, Lavoisiera, Microlicia, Rhynchanthera, Stenodon, and Trembleya ("core Microlicieae"), with Rhynchanthera as the first-diverging lineage. The other four genera of Microlicieae sampled are placed in other clades: Eriocnema with Miconieae; Siphanthera with Aciotis, Nepsera, and Acisanthera of Melastomeae; Castratella as sister to Monochaetum of Melastomeae; and Cambessedesia as part of an unresolved polytomy in a large clade that includes most Melastomataceae. Analyses of the chloroplast genes rbcL and ndhF that included three core genera produced similar results, as did the combined analysis of all three data sets. Combined parsimony analyses of DNA sequences from rpl16 and the nuclear ribosomal intercistronic transcribed spacer (ITS) region of 22 species of core Microlicieae yielded generally low internal support values. Lavoisiera, recently redefined on the basis of several morphological characters, was strongly supported as monophyletic. A morphological phylogenetic analysis of the Microlicieae based on 10 parsimony-informative characters recovered a monophyletic core Microlicieae but provided no further resolution among genera. Penalized likelihood analysis with two calibration time windows produced an age estimate of 3.7 million years for the time of initial divergence of strictly Brazilian core Microlicieae. This date is in general agreement with the estimated age of the most active stage of development of cerrado vegetation and implies an adaptive shift from hydric to seasonally dry habitats during the early evolution of this group.     

Molecular phylogenetics of tribe Poranthereae (Phyllanthaceae; Euphorbiaceae sensu lato)

Novel insights into the evolutionary history of a taxonomically complex tropical plant group were gained in this study using DNA sequence data. A molecular phylogenetic analysis of the newly circumscribed and expanded tribe Poranthereae (Phyllanthaceae) is presented. Sampling included 97 accessions for 63 of c. 120 species. Largely congruent results have been obtained from nuclear ribosomal ITS and plastid matK sequences. These analyses support the recognition of Andrachne and Leptopus as distinct genera. The deceptively similar Andrachne section Phyllanthopsis, Andrachne ovalis, and Leptopus decaisnei are separate lineages to be segregated. Zimmermannia and Zimmermanniopsis are embedded in Meineckia; Oreoporanthera is embedded in Poranthera; and Archileptopus is embedded in Leptopus. Andrachne section Pseudophyllanthus is polyphyletic, the two Madagascan endemics emerging as a sister clade to Meineckia. The noncontiguous distributions of Andrachne sensu lato and Leptopus sensu lato were found to be the result of separate evolutionary histories of morphologically similar clades, whereas Andrachne sensu stricto and Meineckia remain geographically disjunct. Actephila and Leptopus are sisters with a sympatric distribution in humid Asia. Presence of petals appears to be plesiomorphic for the tribe. Petals are reduced in Actephila and Oreoporanthera and lost in the Meineckia clade.     

A new species of rain-pool frog (Dicroglossidae: Fejervarya) from western Thailand

We describe a new species,Fejervarya muangkanensis sp.nov.,based on a series of specimens collected from Ban Tha Khanun,Thong Pha Phum District,Kanchanaburi Province,Thailand.The new species is easily distinguished from its congeners by morphological and molecular data,and can be diagnosed by the following characters:(1) small size (adult male snout-vent length (SVL) 33.5 mm;female SVL 40.0-40.9 mm);(2) tympanum small,discernible but unclear;(3) poorly developed toe webbing;(4) no lateral line system in adults;(5)characteristic “Fejervaryan” lines present in females;and (6) femoral glands absent.Molecular phylogenetic analysis of mitochondrial 16S rRNA further supports it as a distinct lineage and distinguishes it from its congeners for which sequences are available.     

广义竹叶青蛇属Trimeresurus (sensu lato)的分类和系统学研究进展

广义的竹叶青蛇属于Trimeresurus(sensu lato)包含有40多个物种,广泛分布在南亚和东南亚国家和地区。目前,该类群已经相继被划分为6个属：Trimeresurus(sensu stricto)、Tropidolaemus、Ovophis Protobothrops,Triceratolepidophis,Zhaoermia本文从形态、细胞以及分了系统学等方面对Trimeresurus(sensu lato)的分类和系统学研究进行综述。     

Phylogeny of the tribe Antirrhineae (Scrophulariaceae) based on morphological andndhF sequence data

Phylogenetic relationships within the tribe Antirrhineae (Scrophulariaceae) are analysed and discussed on the basis of parsimony analyses of morphological andndhF gene sequence data. The results indicate that the tribe Antirrhineae consists of four major groups of genera, theAnarrhinum clade, theGambelia clade, theMaurandya clade, and theAntirrhinum clade. TheAnarrhinum clade, consisting of the Old World bee-pollinated generaAnarrhinum andKickxia, is sister to the rest of the tribe. TheGambelia clade consists of the New World generaGambelia andGalvezia, which are very closely related and pollinated by hummingbirds. TheMaurandya clade consists of one subclade includingMaurandya and a number of related bee- or hummingbird-pollinated New World genera and another subclade with the Old World bee-pollinated generaAsarina andCymbalaria. TheAntirrhinum clade consists mainly of bee-pollinated Old World genera, such asAntirrhinum, Linaria, Chaenorhinum, and their segregates, but also includes the New World generaMohavea andHowelliella, of which the latter is known to be partly pollinated by hummingbirds. It is concluded that hummingbirdpollination has evolved independently within Antirrhineae at least three times from bee-pollinated ancestors.     

Phylogeny of the tribe Colletieae, Rhamnaceae

A cladistic analysis based on 63 morphological characters was carried out on the tribe Colletieae including two presumed closely related genera, Geanothus and Noltea as outgroupS. In addition to a parsimony analysis of the equally weighted characters, analyses investigating the effects of character weighting, removal of a presumed hybrid species as well as the impact of uncertainly scored characters were undertaken. In all analyses Noltea was placed as sister group to a well supported monophyletic Colletieae. Nineteen different in group topologies were found, with the additional analyses mainly supporting two of them. Within the Colletieae a basal dichotomy divides Trevoa and Retanilla from the remainder of the tribe. While the Trevoa-Retanilla clade is fully resolved, the second lacks detailed resolution. Within this clade the Colletia species from a well supported monophyletic group, while monophyly of the disjunct genus Discaria could not be confirmed.     

Phylogeny of mosquitoes of tribe Culicini (Diptera: Culicidae) based on morphological diversity

Harbach, R. E., Kitching, I. J., Culverwell, C. L., Dubois, J. & Linton, Y.‐M. (2012). Phylogeny of mosquitoes of tribe Culicini (Diptera: Culicidae) based on morphological diversity. —Zoologica Scripta, 41, 499–514. Relationships among taxa of the mosquito tribe Culicini are explored using 169 morphological characters from 86 exemplar species representing the four genera and 26 subgenera of Culicini, most species groups and subgroups of subgenus Culex and an outgroup of five species from five other tribes. We analysed the data set, with multistate characters treated as unordered, under implied weights with values of K ranging from 1 to 20, implemented by TNT. Each analysis, except K = 4, produced a single most parsimonious (fittest) cladogram (MPC). The topology of the ingroup was identical for K = 6–11, whereas the MPCs for K = 14–20 differed only in the position of a single species, which occupied the same position in the K = 16 and K = 6–11 topologies. The K = 9 and K = 16 trees were given further consideration. In both these cladograms, Lutzia is sister to a clade comprising genera Culex, Deinocerites and Galindomyia. The two topologies have 13 clades in common, but their arrangements differ primarily because of Culex (Culex) duttoni acting as a ‘rogue’ taxon. We evaluated the effect of removing this species from the K = 9 and K = 16 analyses and chose the refined K = 9 topology as the best hypothesis of relationships within Culicini. Genus Culex is not monophyletic because it includes Deinocerites and Galindomyia as derived members of the New World subgenera. With the exception of subgenera Culex, Eumelanomyia and Neoculex, there is strong support for the monophyly of all genera and subgenera. Subgenus Culex would be monophyletic were four other subgenera included and three other taxa (the Afrotropical Cx. duttoni, Neotropical Cx. apicinus and the Australasian Atriceps Group) excluded.     

Phylogeny and classification of diving beetles in the tribe Cybistrini (Coleoptera, Dytiscidae, Dytiscinae)

Phylogenetic relationships among members of the diving beetle tribe Cybistrini (Coleoptera: Dytiscidae) were inferred from analysis of 47 adult and larval morphological characters and sequences from portions of the genes cytochrome oxidase I (COI) and II (COII), histone III (H3) and wingless. Thirty‐three species of Cybistrini were included, representing all genus‐groups except Regimbartina Chatanay and Megadytes (Bifurcitus) Brinck, and most historically recognized species groups and subgenera used in the tribe. Outgroups include six species from other tribes within Dytiscinae and Lancetinae. Analyses included parsimony analysis of the combined data, likelihood analysis of combined molecular data and partitioned Bayesian analysis of the combined data. Results indicate that Cybistrini is well supported as a monophyletic group. Within the tribe, all currently recognized genus groups were found to be monophyletic with the exception of Onychohydrus Schaum, which is paraphyletic with respect to Austrodytes Watts in the parsimony analysis, but monophyletic in the likelihood and Bayesian analyses, and Cybister sensu stricto, which is paraphyletic with respect to C. (Melanectes) Brinck and C. (Scaphinectes) Ádám in the parsimony analysis or only the latter in the likelihood and Bayesian analyses. Results also suggest that some, but not all, historically recognized species groups or subgenera in the large genus Cybister Curtis are monophyletic, and this is discussed and compared. To improve the classification, the name Sternhydrus Brinck is elevated from subgenus to genus rank ( new status ). Four subgenera in the genus Cybister are recognized: C. (Melanectes) Brinck, C. (Megadytoides) Brinck ( resurrected ), C. (Neocybister) Miller, Bergsten and Whiting ( new subgenus ) and C. (Cybister) Curtis. The following new synonyms are established: Trochalus Dejean ( new synonym ), and ScaphinectesÁdám = Cybister (Cybister) ( new synonym ). The Neotropical species Cybister parvus Trémouilles (not examined) apparently does not fit any historical or currently recognized genus‐group diagnosis in Cybistrini, so it is retained in Cybister but incertae sedis with respect to subgenus. In addition to classification, the evolution of the unique character combinations present in cybistrines are discussed. A key to the adults of genera and subgenera is presented.     

Phylogeny and morphological evolution of tribe Menispermeae (Menispermaceae) inferred from chloroplast and nuclear sequences

The Menispermaceae family contains ca. 72 genera with 450 species that are almost entirely tropical. Its phylogeny at the tribal level has never been examined using molecular data. Here we used DNA sequences of the chloroplast matK gene and trnL-F regions, and the nuclear ITS region to study the delimitation and position of the tribe Menispermeae within the family and its subtribal monophyletic groups. Family-wide phylogenetic analyses of the chloroplast data produced two strongly supported clades. The first clade contains two subclades: Coscinieae including Arcangelisia and Anamirta, and Tinosporeae sensu lato including Fibraureae, supported by morphological characters, such as traits of the cotyledon, stylar scar and embryo. The second clade consists of the tribes Menispermeae sensu DC. and Tiliacoreae Miers. All our analyses surprisingly recognized that tribe Menispermeae is not monophyletic unless tribe Tiliacoreae is included, suggesting that characters of cotyledon and stylar scar are very important for the infrafamilial classification, and that endosperm presence vs. absence was over-emphasized in traditionally tribal division of the family. Our topologies indicate a secondary loss of endosperm. The monophyly of two subtribes of the tribe Menispermeae, Stephaniinae and Cissampelinae, is supported by the cpDNA and ITS data, as well as by morphological characters, including aperture types and shapes, and colpal membrane features of pollen grains, and sepal number of male flowers. The Cocculinae was recognized as a paraphyletic group containing the remaining genera of the tribe Menispermeae.     

Phylogeny of the Southeast Asian endemic genus Neocinnamomum H. Liu (Lauraceae)

A phylogenetic analysis of Neocinnamomum H. Liu and related genera was conducted using psbA–trnH, trnK cpDNA regions, and the ITS nrDNA segment. Neocinnamomum was confirmed to be monophyletic, and an evolutionary series of inflorescence development within the genus was recognized. The compound thyrse seen in N. caudatum is reduced to the few- to many-flowered condensed inflorescences with a poorly defined branching system seen in most species and ultimately to the 1-flowered inflorescence seen in N. atjehense. Consensus network analysis (CNA) suggested that long-branch attraction is responsible for the observed close relationship between Neocinnamomum and Cassytha L. in a combined analysis of the complete data. In contrast, the sister relationship of Neocinnamomum and Caryodaphnopsis seen in the Bayesian analyses of the partial combined matrix was supported by CNA and is also supported by morphology and wood and bark anatomy. The close similarity of the compound thyrse of less derived Neocinnamomum species to the thyrsoid inflorescences of some Caryodaphnopsis species is also seen as strong support for their affinity.     

Phylogeny and molecular evolution of the tribe Harpalini (Coleoptera, Carabidae) inferred from mitochondrial cytochrome-oxidase I

The tribe Harpalini is a group of ground beetles with a world-wide distribution that comprises approximately 2000 species and about 238 genera and subgenera. Hypotheses about the phylogenetic relationships of the subtribes of Harpalini are implicit within the systematic criteria put forward by different authors. A 759 bp fragment of the mitochondrial COI was sequenced in 119 specimens (107 species) of 52 genera and subgenera that represent the main lineages of Harpalines, and 3 species of other tribes used as outgroups. A hierarchical study of sequence divergence (under uncorrected and corrected models) and ts:tv ratio pattern analyses were carried out at different taxonomic levels. A low saturation rate was detected at first and second codon positions, whereas A+T richness causes a low transitions:transversions ratio, which suggests--a priori--a high rate of saturation at the third codon position. A progressive accumulation of sequence divergence and a decreasing ts:tv ratio were found from lower to higher taxonomic levels. MP strict consensus, ML, and minimum evolution distance (under ts+tv and tv only schemes) trees showed similar major clades within the tribe. The subtribe Ditomina is a monophyletic lineage with close affinities to the subtribe Harpalina. Harpalina is a polyphyletic lineage as the genus Daptus is always related to members of the subtribe Stenolophina, and the Selenophorines resulted a polyphyletic group related to the subtribe Anisodactylina. Main lineages proposed by Noonan [Quaest. Entomol. 9 (1973) 266] within the subtribe Anisodactylina have been corroborated in this study. The Australian genus Phorticosomus is not related to Ditomina but to the Australian Notiobioids lineage. Most taxa of the subtribe Stenolophina are always included in the same clade, together with taxa of the subtribe Pelmatellina, which might be considered as a lineage of Stenolophina related to Bradycellus and Dicheirotrichus. The subtribe Amblystomina lacks a well-supported relationship to the other subtribes of Harpalini and could not be consistently related to any of them.     

Phylogeny of the tribe Aveneae (Pooideae, Poaceae) inferred from plastid trnT-F and nuclear ITS sequences

New insights into evolutionary trends in the economically important oat tribe (Aveneae) are presented. Plastid trnT-F and nuclear ribosomal ITS sequences were used to reconstruct the phylogeny of the Aveneae-Poeae-Seslerieae complex (Pooideae, Poaceae) through Bayesian- and maximum parsimony-based analyses, separately and in combination. The plastid data identified a strongly supported core Aveneae lineage that separated from other former Aveneae and Poeae groups. Koeleriinae, Aveninae, and Agrostidinae emerged as the main groups of this core Aveneae, which also included other minor subgroups with uncertain relationships and a few former Poeae members. Several former Aveneae representatives were also placed in independent sublineages in Poeae. Seslerieae resolved as close allies of Poeae or Aveneae in the plastid and nuclear topologies, respectively. Because of the intermingling of some Aveneae and Seslerieae lineages in Poeae and vice versa, we propose to expand Poeae to include all the aforementioned lineages. This best reflects our current understanding of the phylogeny of these important temperate grasses and sheds light on their evolutionary history.     

Phylogeny and Cladistic Classification of the Paramonostiliferous Family Plectonemertidae (Phylum Nemertea)

Abstract— Numerical phylogenetic analysis of nemertean species from the genera Plectonemertes, Katechonemertes and Acteonementes (marine), Argonemertes, Antiponemertes and Leptonemertes (terrestrial), Potamonemertes and Campbellonemertes (freshwater) in the family Plectonemertidae was carried out with the following aims. (1) To estimate the evolutionary relationships between and among these species. (2) To lest the hypothesis of Moore and Gibson that the analysed freshwater species originated from a terrestrial ancestor. (3) To classify the species in monophyletic genera. The analysis did not confirm the hypothesis that the freshwater habitat has been colonised via land. Instead, it suggests that both terrestrial and freshwater species within this family have evolved from a marine ancestor. The cladogram suggests that Antiponemetes is paraphyletic, and it is combined with Argonemertes to form a monophyletic genus.     

Phylogeny of the Southeast Asian freshwater fish genus Pangio (Cypriniformes; Cobitidae)

The genus Pangio is one of the most species-rich of the loach family Cobitidae and widespread across South and Southeast Asia. Its species diversity has never been studied under a clear phylogenetic approach, but four 'species-groups' were proposed according to the most obvious morphological characters. We present here phylogenetic analyses of the genus Pangio based on sequence data of the mitochondrial cytochrome b gene, the nuclear recombination-activating gene 1 (RAG 1) and a combined dataset of 109 specimens from 18 morphologically identified species across the whole distribution area of the genus. Our data reveal the existence of three major lineages within Pangio. Two of our major lineages were congruent with formerly proposed species-groups, the remaining two species-groups together formed the third major lineage; herein we refer to the lineages as to anguillaris-group, kuhlii-oblonga group and shelfordii-group. The application of a molecular clock dated the age of the three lineages to 33-29 million years. At the species level, our data suggest about 30 distinct lineages, indicating that there is a high number of undescribed species within Pangio. The use of Pangio to address biogeographic questions is demonstrated with the example of the shelfordii-group, which is distributed across Sundaland.     

Phylogeny and biogeography of the rice tribe (Oryzeae): Evidence from combined analysis of 20 chloroplast fragments

Based on sequences of 20 chloroplast fragments, we generated a fully resolved phylogeny of Oryzeae and estimated divergence times of its major lineages as well as explored the historical biogeography of the tribe. Our results (1) confirmed the monophyly of Oryzeae and two-subtribe subdivision; (2) indicated that Maltebrunia, Potamophila and Prosphytochloa were genetically distinct enough to deserve generic status but Maltebrunia and Prosphytochloa were sister groups in the subtribe Oryzinae while Potamophila was a member in the subtribe Zizaniinae; (3) suggested that the previously unresolved phylogeny of the subtribe Zizaniinae was most likely explained by insufficient data due to rapid radiation; (4) provided the first well-corroborated timescale for the origin and divergence of Oryzeae, with the crown node of Oryzeae and the deepest split of Oryza at ～24 and 15 MYA, respectively; (5) developed a biogeographic history of the tribe and substantiated the important roles of long-distance dispersal in the origin and diversification of the tribe Oryzeae.     

Phylogeny of the Neotropical moth tribe Josiini (Notodontidae: Dioptinae): a hidden case of Miillerian mimicry

The Neotropical moth tribe Josiini (Notodontidae: Dioptinae) contains over 100 described species in 11 genera. All are diurnal, with brightly-coloured, presumably aposematic wing patterns. Larval hostplants are exclusively in the genus Passiflora (Passifloraceae) except for two new records, reported here, from Tumera (Turneraceae). A comparative morphological study of 26 representative josiine species yielded 86 characters from adults, larvae and pupae, all of which are figured and discussed. Phylogenetic analysis of these data produced a single most-parsimonious cladogram. According to the phylogenetic results: (1) monophyly of the Josiini is strongly supported; (2) the currently accepted generic classification is in disarray; (3) morphological character variation is extensive, and adult traits reflect phylogeny more effectively than do those of immature stages; (4) wing pattern types have undergone convergent evolution. A rare phenotype, longitudinal wing stripes, appears in two widely divergent clades, suggesting the evolution of Miillerian mimicry within the Josiini.