Historical biogeography and molecular systematics of the Indo-Pacific genus Dascyllus (Teleostei: Pomacentridae)

The phylogeographical and systematic relationships among species in the tropical marine fish genus Dascyllus were inferred using mitochondrial DNA (mtDNA) sequence data. Although our results were generally consistent with previously published phylogenies based on both morphological and mitochondrial data, our broad taxonomic and geographical sampling design revealed novel insights into the phylogenetic history of Dascyllus that had escaped previous notice. These results include: (a) the polyphyletic nature of D. reticulatus mtDNAs, representing two divergent and geographically separated lineages, one shared with D. flavicaudus and the second forming the sister lineage of D. carneus; (b) the paraphyly of D. trimaculatus relative to the closely related D. abisella; and (c) phylogeographical structure within the widespread taxa D. aruanus and D. trimaculatus. Application of a molecular clock permits us to posit a causative role for tectonic and oceanic changes regarding some Dascyllus speciation events. Finally, we mapped body size and the presence or absence of protogynous sex change on the mtDNA tree, and tested published hypotheses regarding determinants of the evolution of mating system and protogyny in the genus. Our data rejected a model based on body size but not one based on phylogenetic inertia. The ability to change sex arose once in the ancestor to the entire genus, and was lost once in the ancestor of the D. trimaculatus complex. For taxa that are as geographically widespread as many Indo-Pacific genera, this study highlights the importance of adequate geographical sampling when inferring patterns of species diversification and life history evolution.     

Systematics and phylogeny of the tribe Paragini (Diptera: Syrphidae) based on molecular and morphological characters

We studied the phylogeny and systematics of the tribe Paragini (Diptera: Syrphidae) using morphological and molecular data. The paper presents separate parsimony analyses of both adult morphological characters and partial DNA sequence data from mitochondrial cytochrome c oxidase I and nuclear ribosomal 28S rRNA gene, as well as a combined analysis of all the data. The data set of morphological characters included some features of the male terminalia (i.e. shape of the ejaculatory apodeme; relative position of elements of the aedeagal complex; shape of surstylar apodeme; shape of the aedeagal apodeme) not previously used in the systematics of the Paragini. The trees obtained from separate parsimony analyses of molecular and morphological data produced almost identical topologies. Four lineages are supported by the combined data set, and we establish two new subgenera, i.e. Serratoparagus Vujić et Radenković subgen. nov., and Afroparagus Vujić et Radenković subgen. nov., and redefine Pandasyopthalmus Stuckenberg, 1954 stat. rev. and Paragus Latreille, 1804, stat. rev. The monophyly of the Pandasyopthalmus clade, including the species fitting neither of the current species groups ( jozanus -group) of Paragini, is established. Diagnoses of all known species groups are presented, including a new arrangement of almost all valid species of Paragini.  © 2008 The Linnean Society of London, Zoological Journal of the Linnean Society , 2008, 152 , 507–536.     

Systematics of the genus Capra inferred from mitochondrial DNA sequence data

Traditional classification in the genus Capra is based mainly on horn morphology. However, previous investigations based on allozyme data are not consistent with this classification. We thus reexamined the evolutionary history of the genus by analyzing mitochondrial DNA (mtDNA) sequence variation. We collected bone samples from museums or dead animals found in the field. Thirty-four individuals were successfully sequenced for a portion of the mtDNA cytochrome b gene and control region (500 bp in total). We obtained a star-like phylogeny supporting a rapid radiation of the genus. In accordance with traditional classification, mtDNA data support the presence of two clades in the Caucasus and the hypothesis of a domestication event in the Fertile Crescent. However, in conflict with morphology, we found that C. aegagrus and C. ibex are polyphyletic species, and we propose a new scenario for Capra immigration into Europe.     

A molecular phylogeny of warbling-finches (Poospiza): paraphyly in a neotropical Emberizid genus

We investigated the phylogenetic relationships of 12 species within a single genus of neotropical passerine (Poospiza) using 849 bp (283 codons) of the cytochrome b mitochondrial gene. We further explored evolutionary affinities of these taxa using sequence from an additional 47 thraupine (tanagers) and 7 emberizine (sparrows and buntings) genera, members of the predominantly New World family Emberizidae. Poospiza have traditionally been considered part of the emberizine radiation. However, our analyses suggest that members of this genus are more closely related to some thraupine lineages than they are to the other neotropical emberizine genera included in our study (Atlapetes, Embernagra, Melopyrrha, Phrygilus, Saltatricula, Tiaris). Although member taxa are closely related, the genus Poospiza appears to be paraphyletic with representatives of 6 thraupine genera (Cnemoscopus, Cypsnagra, Hemispingus, Nephelornis, Pyrrhocoma, Thylpopsis) interspersed among four well-supported Poospiza clades. The majority of species within this Poospiza-thraupine clade have geographic ranges that are exclusive to, or partially overlap with, the Andes Mountains. It is probable that these mountains have played an important role in driving cladogenesis within this group. Sequence divergence (transversions only; mean 4.7+/-1.3%) within the clade suggests that much of this diversification occurred within the late Miocene and Pliocene, a period coincident with major orogenic activity in central-western South America.     

One Species or Several? Discordant Patterns of Geographic Variation between Allozymes and mtDNA Sequences among Spiders in the Genus Metepeira (Araneae: Araneidae)

Paradoxically, an allozyme study of Metepeira “spinipes” (sensu lato) demonstrated extensive gene flow among four populations whose members are nevertheless morphologically and behaviorally distinct. Initially, the authors tentatively concluded that the populations exhibited panmixis and suggested that local environmental effects accounted for the apparent morphological and behavioral differences. However, they later concluded that such differences were too great to be accounted for by the environment alone and that the four populations actually represented three different species. To confirm that the allozyme results were, in fact, artifactual, we reexamined the relationships among these populations by sequencing a portion of the 12S mtDNA ribosomal subunit. In contrast to the allozyme result, our results demonstrate good agreement between patterns of genetic and morphological/behavioral variation. We suggest (1) that the allozyme allele frequencies are homogenized by balancing selection, not gene flow as was previously concluded, and therefore (2) that this study provides another instance in which inferences about population structures from allozyme data are misleading.     

Vegetative diversification and radiation in subtribeDendrobiinae (Orchidaceae): Evidence from chloroplast DNA phylogeny and anatomical characters

The data derived from a chloroplast DNA restriction site analysis of subtribeDendrobiinae (Orchidaceae) indicate that extreme vegetative diversification is concentrated in two limited parts of this group. Overlaying the vegetative character states onto the chloroplast DNA cladogram suggests that several xeromorphic, vegetative characters evolved in the lines leading to the above-mentioned clades. Several anatomical characters are also associated with xeromorphy. These vegetative and anatomical characters facilitated the establishment of this group in various dry habitats. On the other hand, the modifications of size and number of parenchymatous cells substantially contributed to the vegetative diversification. This fact implies that a simple structural adjustment can result in a major modification of growth habits in theDendrobiinae.     

Molecular evolution of tephritid fruit flies in the genus Bactrocera based on the cytochrome oxidase I gene

Fruit flies of the genus Bactrocera (Diptera: Tephritidae) are one of the major economically important insects in Asia and Australia. Little attention has been given to analyses of molecular phylogenetic relationships among Bactrocera subgenera. By using mitochondrial cytochrome oxidase I gene (COI) sequences, the phylogenetic relationships among four subgenera, Asiadacus, Bactrocera, Hemigymnodacus, and Zeugodacus, were investigated. Nucleotide diversity within subgenera ranged from 11.7 to 12.4%, and the net divergence among subgenera ranged from 11.2 to 15.7%. Phylogenetic trees calculated from both maximum parsimony and neighbor-joining phylogenetic analysis methods were highly congruent in terms of tree topologies. Phylogenetic analysis of mitochondrial COI sequences suggests that tephritid fruit fly species, which attack cucurbit plants, that is, Asiadacus, Hemigymnodacus and Zeugodacus, were more closely related to each other than to fruit fly species of the subgenus Bactrocera, which attack plants of numerous families. Our data supports previous classification of Bactrocera based on morphological characters. However, the phylogenetic tree showed the polyphyletic of fruit flies in subgenus Zeugodacus. Possible causes of speciation among fruit flies species in this genus were also discussed.     

A new endemic lineage of the Andean frog genus Telmatobius (Anura,Telmatobiidae) from the western slopes of the central Andes

The amphibian genus Telmatobius is a diverse group of species that inhabits the Andes. This study analysed the phylogenetic relationships of 19 species described from the central Andes of Chile and Bolivia, and 12 undescribed populations of Chile. A molecular phylogeny based on mitochondrial DNA 16S and cytochrome b shows that the Chilean species belong to three groups: (1) the Telmatobius marmoratus group, widespread in the Chilean and Bolivian Altiplano; (2) the Telmatobius hintoni group, including the species Telmatobius philippii, Telmatobius fronteriensis, and Telmatobius huayra, occurring in the south‐western Altiplano of Chile and Bolivia, and (3) the Telmatobius zapahuirensis group, a new clade which also includes Telmatobius chusmisensis, Telmatobius dankoi, and Telmatobius vilamensis, restricted to western slopes of the Andes, and which was recovered as more closely related to the T. hintoni group than the T. marmoratus group. The divergence times between clades were traced to the late Pleistocene. The molecular phylogeny also confirmed that the groups of the Altiplano and western Andes slopes form a clade separated from the species that inhabit the eastern Andes (Telmatobius verrucosus and Telmatobius bolivianus groups), supporting the forest origin of the Altiplano groups proposed by several previous authors. © 2014 The Linnean Society of London     

A new species of the genus Lightiella: the first record of Cephalocarida (Crustacea) in Europe

A new species of Cephalocarida belonging to the genus Lightiella is described. Like all known species of Lightiella , the new species is characterized by reduction of trunk segment 8, which also lacks both pleura and thoracopods. The diagnostic characters of the species are: (1) one seta on the inner distal corner of the penultimate endopodal segment of second maxilla and thoracopods 1–5; (2) only one claw on the distal segment of the endopod of thoracopod 6. A cladistic analysis of 27 morphological characters was used to estimate the phylogeny of all species of Lightiella , with all other cephalocarid species used as outgroups. The discovery of this species in the Mediterranean fills a gap in the distribution of the genus and of the entire class.  © 2006 The Linnean Society of London, Zoological Journal of the Linnean Society , 2006, 148 , 209–220.     

Evolution ofSedum seriesRupestria (Crassulaceae): Evidence from chloroplast DNA and biosystematic data

Evolutionary relationships within the compariumSedum seriesRupestria (Crassulaceae) were investigated by phylogenetic analyses of restriction site variation of the chloroplast genome and morphological variation. DNAs were digested with 21 restriction enzymes and hybridized withS. album cpDNA probes covering the entire genome. A total of 141 ingroup variable restriction sites was identified. Morphological variation was observed in a total of 66 characters. Both datasets were analysed using parsimony methods and compared with evidence from cytology, artificial hybridization and biogeography to infer evolutionary relationships. The results 1) indicate a relatively high level of nucleotide sequence divergence withinS. ser.Rupestria; 2) indicate three main lines of plastome differentiation, which are in agreement with morphology, basic chromosome numbers, and centres of diversity; 3) do not provide a compelling solution for basal relationships; 4) support an earlier hypothesis on reticulation and provide evidence for a third case of allopolyploidy in the series; 5) suggest that interspecific gene flow inS. ser.Rupestria is funnelled through the presumably allopolyploidS. rupestre subsp.erectum.     

A reappraisal of the genus Megacaryon (Boraginaceae,Lithospermeae) based on molecular,morphological, and karyological evidence

The systematic position and phylogenetic relationships of Echium orientale, a rare endemic of the mountains of northern Turkey, were elucidated based on morphological, molecular, and karyological evidence.

Using nuclear and plastid DNA sequences, we found that this species is not included in Echium, but is rather at least as divergent from it as other related lineages, namely the South African Lobostemon and Echiostachys. Pollen characters revealed a strong affinity with Onosma, especially in the non-reticulate ornamentation of the tectum. Fruit morphology is unique in the genera of the Echium ‘alliance' (e.g. Echium, Pontechium, Lobostemon, and Echiostachys), because of the large size and the smooth, glossy nutlet surface as in most species of Onosma. Karyological observations show that this species is diploid with 2n = 12, and differing from both Lobostemon or Echium, where nearly all species have higher numbers (usually 2n = 14 and 2n = 16, respectively). Combined with a ‘megaherb' habit, the weak zygomorphism of the large flowers and a restricted range in the humid mountain forests of the Black Sea region, fruit, pollen and chromosome characters suggest an isolated position for E. orientale in the Echium alliance. We therefore propose its placement in the monotypic Megacaryon, a genus originally described by Boissier, but largely disregarded by later botanists. An original specimen is designated as generic lectotype.     

Agouticarpa, a new neotropical genus of Tribe Gardenieae (Rubiaceae)

Agouticarpa, a new genus of the informalAlibertia group (Rubiaceae), is described and illustrated. It comprises six species, and occurs from Costa Rica to Bolivia. Three species are here described as new:Agouticarpa grandistipula, A. hirsuta, andA. velutina. Additionally, three new combinations are made:A. curvifolia andA. williamsii (previously inGenipa) andA. isernii (previously inAlibertia). Agouticarpa is characterized by being dioecious, having elliptic to abovate, membranaceous stipules, male flowers in a branched dichasial or thyrse-like inflorescence, a poorly developed cup-shaped calyx, pollen grains with 3–7 apertures, and large globose fruits.     

Four new species of the genus Perepsilonema Lorenzen, 1973 (Nematoda,Epsilonematidae) from the bay of Calvi (Corsica,Mediterranean)

Four new species of the genus Perepsilonema are described. They are characterized by general habitus, cuticular ornamentation, shape and sexual dimorphism of the amphideal fovea, shape and number of ventral copulatory spines and the shape of the spicules. The female genital system comprises two reflexed ovaries, a left and a right spermatheca and a median uterine chamber filled with sperm cells. The distal part of the uteri have secretory wall cells which contain in some specimen spherical refractive bodies.     

Phylogeny of ground beetles subgenus Nialoe (s. lat.) Tanaka (Coleoptera: Carabidae; genus Pterostichus): A molecular phylogenetic approach

We constructed a phylogeny of the ground beetle subgenus Nialoe ( s. lat. ), genus Pterostichus (Coleoptera: Carabidae) based on two mitochondrial (cytochrome oxidase I and 16S ribosomal DNA) and one nuclear (28S ribosomal DNA) gene sequences. Thirty-three representative species of the group and three outgroup species were analyzed. The resultant trees (maximum parsimonious, maximum likelihood and Bayesian trees of the combined data of the three gene sequences) indicated that there are two large and three small lineages in the group, some of which were supported by a previous morphology-based phylogeny. In all the analyses, the small lineage composed of two Korean species is sister to the rest of the subgenus, but relationships of other four lineages differed among the analyses and remained unresolved. The implications of the present results are discussed in terms of taxonomy and biogeography of the group.     

线粒体DNA序列在半翅目异翅亚目昆虫分子系统学上的应用

随着PCR技术的发展以及大量DNA序列的累积,昆虫分子系统学近年来快速发展。线粒体DNA(mtDNA)序列相对于核内DNA序列进化速率较快,常被用于昆虫的系统发育研究。本文综述了国内外学者利用各种线粒体DNA序列来研究半翅目异翅亚目昆虫系统发育的研究概况。总结发现,COⅠ、COⅡ、12S rDNA、16S rDNA、Cytb、ND1、ND2和ND5等线粒体区段被用于半翅目异翅亚目系统发育的研究,其中以COI、COⅡ、16S rDNA和Cytb应用最广泛,但目前尚缺乏不同分子标记间的联合分析。进一步的研究最好在选定半翅目异翅亚目昆虫的分类阶元(如科间、亚科间、科内属间、种间或种内)后,集中测定线粒体某几个区段的DNA序列,然后进行单一分析和联合分析,并与传统形态学研究结果进行比较,可望全面分析半翅目异翅亚目昆虫的系统发育关系。     

Evolutionary assessment of Artemia tibetiana (Crustacea, Anostraca) based on morphometry and 16S rRNA RFLP analysis

Over the last few years, molecular-based assays in the genus Artemia have considerably enriched prior systematic assessments based on morphometry. For the first time, morphometric and 16S rRNA PCR-RFLP analyses on all type-locality bisexual species of the genus have been employed here. Emphasis was put on the Asian species ( Artemia urmiana , A. tibetiana , A. sinica ) where patterns of divergence and reproductive isolation are rather discrete, and especially on A. tibetiana for which recent reports have questioned its specific status. Discriminant analysis of morphometric characters has shown significant differentiation among species. Classification scores were 99.4 and 100% for males and females, respectively. Mitochondrial DNA RFLP patterns have given indications for lower, albeit similar patterns of differentiation compared with those obtained by morphometry. Artemia tibetiana and A. urmiana are mitochondrially indistinguishable which is suggestive of recent ancestry. Our data, in conjunction with past evidence, are supportive of a significant amount of divergence between A. tibetiana and A. sinica . Morphometric and molecular assays can be reciprocally informative provided theory and patterns of speciation are incorporated into systematic assessments.     

Contribution to the taxonomy of Pinus uncinata (Pinaceae) based on cone characters

Eight natural populations of Pinus uncinata Ramond from the Spanish Pyrenees, five of P. mugo Turra from the Carpathians, the Sudethians and Abruzzian Apennines, three of P. sylvestris L. from the Central-European Lowland and the Iberian Peninsula and one of P. uliginosa Neumann from SW Poland have been compared biometrically in 16 cone characters. P. uncinata appears the most distant from all other taxa, differing by having the largest and most asymmetric cones and the thickest apophyses with the most prominent umbo. In cone characters, P. mugo is more similar to P. sylvestris than to P. uncinata. Nevertheless, P. mugo and P. sylvestris remain distant from each other in a number of morphological characters examined. P. uliginosa has cones intermediate between the other three taxa and is moreover very variable. The locality of P. uliginosa in the Silesian Lowland may be of a relict character and conserve genes from P. uncinata.     

A phylogenetic analysis of the palm subtribe Oncospermatinae (Arecaceae) based on morphological characters

Subtribe Oncospermatinae (Arecaceae: Arecoideae: Areceae) is a diverse group of spiny Old World palms. The subtribe includesOncosperma, a widespread Asian genus of five species, along with seven monotypic genera, all endemic to the Seychelles and Mascarene Islands of the western Indian Ocean. A phylogenetic analysis was conducted in order to test the monophyly of subtribe Oncospermatinae with respect to other Old World genera of tribe Areceae. A matrix of 38 morphological characters was scored for 29 taxa, including 11 species of the Oncospermatinae. A single most parsimonious tree was found, resolving the subtribe as a polyphyletic group of two distinct clades. One clade containingAcanthophoenix, Deckenia, Oncosperma, andTectiphiala was placed as sister to a large group that includes members of subtribes Archontophoenicinae, Arecinae, Iguanurinae, and Ptychospermatinae. The other clade of Oncospermatinae, including the Seychelles endemic generaNephrosperma, Phoenicophorium, Roscheria, andVerschaffeltia, was resolved as sister to the Madagascar endemic subtribe Masoalinae, and may have arisen in the western Indian Ocean region.