Construction of the phylogenetic model for the genera of the tribe Arctiini (Lepidoptera,Arctiidae) with the SYNAP method

A new scheme of the phylogeny of the tribe Arctiini is proposed. The Western Mediterranean genus Atlantarctia is considered the most primitive one in the tribe; the rest of genera form two large clades Arctia-Pericallia and Gonerda-Platyprepia. The first clade is supposed to have been subjected to radiation in western Eurasia, and the second clade, in Asia and North America in the Palaeogene when the eastern part of Asia was isolated from western Eurasia. Subsequently, most probably in the Neogene-Pleistocene, representatives of both clades spread over the whole Eurasia and North America. The Arctiini fauna of the tundra zone, which includes the genera Acerbia and Pararctia, was formed in Asia and North America, whereas the subboreal fauna (both steppe and nemoral) originated in western Eurasia. The boreal genus Borearctia has most likely also originated in Asia.     

Apotrachelocerca arenicola (Kahl, 1933) n. g., comb. n. (Protozoa, Ciliophora, Trachelocercidae): morphology and phylogeny

During faunistic study on psammophilic ciliates along the coast of Qingdao, China, a population of Trachelocerca arenicola Kahl, 1933 was found and then investigated using silver staining and gene sequencing methods. The results indicated that it represented a new genus Apotrachelocerca characterized by uninterrupted circumoral kineties composed of two rows of dikinetids and no brosse or ciliary tuft in the oral cavity. This new genus should be assigned to the family Prototrachelocercidae Foissner, 1996. Based on the small subunit rRNA gene sequence, phylogenetic trees revealed that Apotrachelocerca arenicola occupied a basal position to other trachelocercids.     

Phylogenetic position of Licnophora,Lechriopyla, and Schizocaryum,three unusual ciliates (phylum Ciliophora) endosymbiotic in echinoderms (phylum Echinodermata)

Various echinoderms are colonized by species from several classes of the Phylum Ciliophora, indicating that the echinoderm "habitat" has been invaded independently on numerous occasions throughout evolutionary history. Two "echinoderm" ciliates whose phylogenetic positions have been problematic are Licnophora macfarlandi Stevens, 1901 and Schizocaryum dogieli Poljansky and Golikova, 1957. Licnophora macfarlandi is an endosymbiont of the respiratory trees of holothuroids, and S. dogieli is found in the esophagus of echinoids. A third species, Lechriopyla mystax Lynch, 1930, is a plagiopylid ciliate found in the intestine of echinoids. Host echinoderms were collected near the Friday Harbor Laboratories, San Juan Island, WA. Specimens of S. dogieli and L. mystax were obtained from the esophagus and intestine, respectively, of the sea urchin Strongylocentrotus pallidus. Specimens of L. macfarlandi were collected from the fluid obtained from the respiratory trees of Parastichopus californicus. Using small subunit ribosomal RNA (SSrRNA) sequences of these three ciliates and a global alignment of SSrRNA sequences of other ciliates, we established the following. 1) Licnophora is a spirotrich ciliate, clearly related to the hypotrichs and stichotrichs; this is corroborated by its possession of macronuclear replication bands. 2) Lechriopyla is the sister genus to Plagiopyla and is a member of the Class Plagiopylea, which was predicted based on its cytology. 3) Schizocaryum clusters in the Class Oligohymenophorea and is most closely related to the scuticociliates; there are currently no morphological features known to relate Schizocaryum to the scuticociliates.     

Phylogenetic analysis of anostracans (Branchiopoda: Anostraca) inferred from nuclear 18S ribosomal DNA (18S rDNA) sequences

The nuclear small subunit ribosomal DNA (18S rDNA) of 27 anostracans (Branchiopoda: Anostraca) belonging to 14 genera and eight out of nine traditionally recognized families has been sequenced and used for phylogenetic analysis. The 18S rDNA phylogeny shows that the anostracans are monophyletic. The taxa under examination form two clades of subordinal level and eight clades of family level. Two families the Polyartemiidae and Linderiellidae are suppressed and merged with the Chirocephalidae, of which together they form a subfamily. In contrast, the Parartemiinae are removed from the Branchipodidae, raised to family level (Parartemiidae) and cluster as a sister group to the Artemiidae in a clade defined here as the Artemiina (new suborder). A number of morphological traits support this new suborder. The Branchipodidae are separated into two families, the Branchipodidae and Tanymastigidae (new family). The relationship between Dendrocephalus and Thamnocephalus requires further study and needs the addition of Branchinella sequences to decide whether the Thamnocephalidae are monophyletic. Surprisingly, Polyartemiella hazeni and Polyartemia forcipata ("Family" Polyartemiidae), with 17 and 19 thoracic segments and pairs of trunk limb as opposed to all other anostracans with only 11 pairs, do not cluster but are separated by Linderiella santarosae ("Family" Linderiellidae), which has 11 pairs of trunk limbs. All appear to be part of the Chirocephalidae and share one morphological character: double pre-epipodites on at least part of their legs. That Linderiella is part of the Polyartemiinae suggests that multiplication of the number of limbs occurred once, but was lost again in Linderiella. Within Chirocephalidae, we found two further clades, the Eubranchipus-Pristicephalus clade and the Chirocephalus clade. Pristicephalus is reinstated as a genus.     

Phylogenetic relationships among species of Hypochaeris (Asteraceae, Cichorieae) based on ITS, plastid trnL intron, trnL-F spacer, and matK sequences

Nuclear internal transcribed spacer (ITS) regions and chloroplast trnL intron and trnL/trnF spacer and matK sequences were used from 86 accessions to assess relationships among 31 European and South American species of Hypochaeris plus 18 representatives of related genera of tribe Cichorieae. The ITS tree shows high resolution compared to that of the maternally inherited trnL intron, trnL/F spacer, and matK sequences. The ITS and the combined tree reveal clades that agree well with sections of the genus established previously on morphological and cytological grounds, except for H. robertia, which groups with Leontodon helveticus and L. autumnalis. Monophyly of species of Hypochaeris from South America is strongly supported by both ITS and the joint matrix of ITS, trnL, and matK data. European species lie basal to South American taxa, which suggests that species in South America evolved from a single introduction from European progenitors and not from H. robertia as suggested previously. Low levels of sequence divergence among South American taxa suggest a pattern of rapid speciation, in contrast to much greater divergence among European representatives. Different species of Leontodon form two different clades that are also supported by chromosome numbers and morphology. Both nuclear and chloroplast markers suggest that Helminthotheca, Leontodon, and Picris are closely related to each other as well as to Hypochaeris.     

Phylogenetic analysis of the genus <Emphasis Type="Italic">Argia</Emphasis> Rambur, 1842 (Odonata: Coenagrionidae), based on morphological characters of larvae and mitochondrial DNA sequences

The study of the evolutionary interrelationships among the species encompassed in the Neotropical genus Argia (Zygoptera: Coenagrionidae) has been neglected. The goal of this study is to infer the phylogenetic relationships among 36 species of Argia Rambur, 1842, using complementary data sets (i.e., larval morphology and mitochondrial DNA). The morphological data set comprises 76% of the larvae currently described for this genus and includes 97 morphological characters. From those, 47 characters have not been previously used in taxonomic studies involving dragonflies’ larvae. This is the first cladistic study based on larvae morphology for species within the suborder Zygoptera. Data partitions were analyzed individually, as well as total evidence, using parsimony and Bayesian inference as criteria for optimal-tree selection. The results support the monophyly of the North American species of Argia. This genus can be identified by the combination of eight synapomorphies, four of which are exclusively found in Argia. According to the optimal trees, the individual data sets (i.e., morphology and DNA sequences) have a high level of homoplasy, resulting in soft polytomies and low support for several nodes. The specific relationships of the terminal units differ between the phylogenies; nonetheless, there is historical congruence among them. Within Argia, five clades were consistently recovered. Most of those clades have been identified, at least in part, in previous phylogenetic and taxonomic studies. Indubitably, the morphological characters from larvae have historical signal useful for cladistic and taxonomic inference. Therefore, it should be a priority to pay more attention to this source of characters.     

Multiple data sets,congruence, and hypothesis testing for the phylogeny of basal groups of the lizard genus Sceloporus (Squamata,Phrynosomatidae)

Several data partitions, including nuclear and mitochondrial gene sequences, chromosomes, isoenzymes, and morphological characters, were used to propose a new phylogeny and to test previously published hypotheses about the phylogenetic positions of basal clades of the lizard genus Sceloporus and the relationship of Sceloporus to the former genus "Sator". In accord with earlier studies, our results grouped "Sator" as internal to Sceloporus, and both support a hypothesis of transgulfian vicariance for the origin of the former genus "Sator" on islands in the Sea of Cortez. Robustness of support for internal nodes in our best tree was established though widely used indices (bootstrap proportions, decay values) but also through congruence among independent data partitions. Several deep nodes in the tree recovered by several methods, including equally weighted and differentially weighted parsimony and maximum likelihood models, are only weakly supported by the traditional indices. This methodological concordance is taken as evidence for insensitivity of the deep structure of the topology to alternative assumptions.     

<Emphasis Type="Italic">Foxtosognus rarus</Emphasis> gen. n., sp. n.—A new genus and species of copepods (Copepoda: Calanoida) from the abyssopelagic zone of the Kuril-Kamchatka Trench

A female of Foxtosognus rarus gen. n., sp. n., a new genus and species of copepods, is described from the abyss of the Kuril-Kamchatka Trench. The new genus is placed in the family Arctokonstantinidae, whose diagnosis is emended and supplemented with the following characters: mandibular basis with one to two setae; mandibular endopod one without setae; maxillular distal basal endite plus endopod with two to four setae or without setae. The features that distinguish Foxtosognusgen. n. from other representatives of this family are as follows: mandibular palp with a long endopod segment one, endopod segment two with seven setae, and exopod segment five with two setae; maxillula with distal basal endite lacking setae and separated from endopod bearing three setae; maxillular precoxal arthrite with seven to eight setae and exopod with four setae; maxilliped syncoxa without setae on precoxal endites and endopod of three segments. The genera Sognocalanus and Foxtonia earlier included in the Spinocalanidae are herein transferred to the Arctokonstantinidae.     

Utility of low-copy nuclear markers in phylogenetic reconstruction of Hypericum L. (Hypericaceae)

Primers and sequence variation for two low-copy nuclear genes (LCG) not previously used for phylogenetic inference in the genus Hypericum, PHYC and EMB2765, are presented here in comparison with the fast-evolving nuclear intergenic spacer ITS. Substitution rates in the LCG markers were half those reported in ITS for Hypericum, which might help avoid the problems caused by substitution saturation and difficulties to establish homologies that afflict the latter marker. We included representatives of all major clades within Hypericum and found that levels of phylogenetic resolution, clade support values and internal character consistency were similar to, or even higher than, those of ITS-based phylogenies. The presence of at least two copies in EMB2765 in Hypericum imposed a methodological challenge that was circumvented by the design of an effective clade-specific primer. Both EMB2765 and, especially, PHYC appear to be good alternatives to the ITS marker, confirming the main phylogenetic relationships found in previous studies, but with improved resolution and support values for some basal relationships.     

Phylogenetic relationships among families of the Scaphopoda (Mollusca)

Phylogenetic relationships among families in the molluscan class Scaphopoda were analysed using morphological characters and cladistic parsimony methods. A maximum parsimony analysis of 34 discrete characters, treated as unordered and equally weighted, from nine ingroup terminal taxa produced a single most parsimonious tree; supplementary analyses of tree length frequency distribution and Bremer support indices indicate a strong phylogenetic signal from the data and moderate to minimally supported clades. The traditional major division of the class, the orders Dentaliida and Gadilida, is supported as both taxa are confirmed as monophyletic clades. Within the Dentaliida, two clades are recognized, the first comprised of the families Dentaliidae and Fustiariidae, the second of the Rhabdidae and Calliodentaliidae; together, these groups comprise a third clade, which has the Gadilinidae as sister. Within the Gadilida, a nested series of relationships is found among [Entalinidae, [Pulsellidae, [Wemersoniellidae, Gadilidae]]]. These results lend cladistic support to earlier hypotheses of shared common ancestry for some families, but are at variance with other previous hypotheses of evolution in the Scaphopoda. Furthermore, analysis of constituent Gadilinidae representatives provide evidence for paraphyly of this family. The relationships supported here provide a working hypothesis that the development of new characters and greater breadth of taxonomic sampling can test, with a suggested primary goal of establishing monophyly at the family level.     

Insights into the phylogeny of systematically controversial haptorian ciliates (Ciliophora, Litostomatea) based on multigene analyses

The ciliate subclass Haptoria is a diverse taxon that includes most of the free-living predators in the class Litostomatea. Phylogenetic study of this group was initially conducted using a single molecular marker small-subunit ribosomal RNA (SSU rRNA genes). Multi-gene analysis has been limited because very few other sequences were available. We performed phylogenetic analyses of Haptoria incorporating new SSU rRNA gene sequences from several debated members of the taxon, in particular, the first molecular data from Cyclotrichium. We also provided nine large-subunit ribosomal RNA (LSU rRNA) gene sequences and 10 alpha-tubulin sequences from diverse haptorians, and two possible relatives of controversial haptorians (Plagiopylea, Prostomatea). Phylogenies inferred from the different molecules showed the following: (i) Cyclotrichium and Paraspathidium were clearly separated from the haptorids and even from class Litostomatea, rejecting their high-level taxonomic assignments based on morphology. Both genera branch instead with the classes Plagiopylea, Prostomatea and Oligohymenophora. This raises the possibility that the well-known but phylogenetically problematic cyclotrichiids Mesodinium and Myrionecta may also have affinities here, rather than with litostomes; (ii) the transfer of Trachelotractus to Litostomatea is supported, especially by the analyses of SSU rRNA and LSU rRNA genes, however, Trachelotractus and Chaenea (more uncertainly) generally form the two deepest lineages within litostomes; and (iii) phylogenies of the new molecular markers are consistent with SSU rRNA gene information in recovering order Pleurostomatida as monophyletic. However, Pleurostomatida branches cladistically within order Haptorida, as does subclass Trichostomatia (on the basis of SSU rRNA phylogenies). Our results suggest that the class-level taxonomy of ciliates is still not resolved, and also that a systematic revision of litostomes is required, beginning at high taxonomic levels (taxa currently ranked as subclasses and orders).     

Mitochondrial phylogeny of leaf monkeys (genus Presbytis, Eschscholtz, 1821) with implications for taxonomy and conservation

The langurs of the genus Presbytis inhabit tropical rainforests of Sundaland, and with more than 50 color variants grouped in up to eleven species, Presbytis is one of the most diverse Old World monkey genera. The number of taxa and their phylogenetic relationships however remain controversial. To address these issues, we analyzed a 1.8 kb long fragment of the mitochondrial genome, including the cytochrome b gene, the hypervariable region I of the D-loop and the intermediate tRNAs, from individuals representing nine species. Based on our data, we obtained various well-supported terminal clades, which refer mainly to described taxa. Relationships among these clades are not fully resolved, suggesting at least two radiations in the evolutionary history of the genus. According to divergence age estimates, radiations occurred in the late Miocene and the early to middle Pleistocene. Our findings support the revision of the current classification of the genus Presbytis and enable us to discuss implications for conservation. However, further studies including nuclear sequence data are necessary to completely understand the evolutionary history of the genus, and to address possible hybridization events among taxa.     

Scuticociliate endosymbionts of echinoids (phylum Echinodermata): phylogenetic relationships among species in the genera Entodiscus, Plagiopyliella, Thyrophylax, and Entorhipidium (phylum Ciliophora)

Morphological research on over 50 species of ciliates recorded as endosymbionts of echinoids suggests that invasion of the echinoid microhabitat occurred on at least 4 occasions. Gene sequence data confirm the phylogenetic distinctness of spirotrichean, armophorean, plagiopylean, and oligohymenophorean endosymbionts. It is also likely that oligohymenophoreans have repeatedly invaded the gut habitat. To test this hypothesis, we sequenced small subunit rRNA (SSrRNA) genes of 6 species representing the larger scuticociliate species found in the intestine of Strongylocentrotus pallidus from the northeast Pacific Ocean: Entodiscus borealis (Entodiscidae); Plagiopyliella pacifica and Thyrophylax vorax (Thyrophylacidae); and Entorhipidium pilatum, Entorhipidium tenue, and Entorhipidium sp. (Entorhipidiidae). SsrRNA genes were amplified by PCR, and sequences obtained in both directions. In all phylogenetic analyses, the scuticociliates are well supported as a clade. Entodiscus is distinct from these other echinoid taxa and is the sister taxon to the facultatively parasitic Uronema marinum. The other 5 echinoid species always form a clade whose basal species is the free-living Parauronema longum. The greatest genetic distance among these latter 5 species is less than 1.5%. This probably explains why the Thyrophylacidae and Entorhipidiidae are paraphyletic based on the SSrRNA gene sequences.     

Phylogenetic relationships in the subgenus Mus (genus Mus, family Muridae, subfamily Murinae): examining gene trees and species trees

Over eight kilobases (kb) of sequence from eight genes including two mitochondrial loci, Cyt b and 12S, and six nuclear loci, B2m , Zp3 , Tcp1, Sry, Smcx and Smcy , were used to investigate phylogenetic relationships among 11 taxa representing eight species within the rodent genus Mus . Particular attention was given to discerning relationships among species within the subgenus Mus including members of a Palearctic clade ( M. musculus , M. spicilegus , M. macedonicus and M. spretus ) and members of an Asian clade ( M. caroli , M. cookii and M. cervicolor ), as previous studies using different datasets have produced different topologies for taxa within these two groups. While parsimony analyses of the combined eight-gene dataset yielded a single, fully resolved tree, support values were lower for nodes resolving relationships within the Palearctic and Asian clades than they were elsewhere in the tree. In addition, a maximum likelihood analysis of the same eight-gene dataset yielded different topologies for both the Palearctic and the Asian clades. Both observations are indicative of clade instability. The nature of this instability was explored through a comparison with our previous study in which we included the two mitochondrial loci and only four of the six nuclear genes, and through an analysis of partitioned data, specifically mitochondrial vs. nuclear genes. This study underscores the importance of considering among-site rate variation in phylogeny reconstruction. © 2005 The Linnean Society of London, Biological Journal of the Linnean Society , 2005, 84 , 653–662.     

Molecular phylogeny of the Barnadesioideae (Asteraceae)

The small but morphologically diverse subfamily Barnadesioideae of the sunflower family, Asteraceae, is of special interest as it constitutes the sister-group to the rest of the family. Therefore it is of critical importance for elucidating the origin and early evolution of Asteraceae. Cladistic analyses of DNA sequence variation in the trnL intron and nuclear ribosomal ITS regions strongly support five major clades in the subfamily: Schlechtendalia, Chuquiraga-Doniophyton, Barnadesia-Huarpea, Dasyphyllum subgenus Dasyphyllutn and a clade comprising Dasyphyllum subgenus Archidasyphyllum, Arnaldoa and Fulcaldea. Within Dasyphyllum subgenus Dasyphyllum, D. hystrix has a basal position, and sect. Macrocephala is supported as monophyletic, while sect. Microcephala lacks jackknife support. Within Barnadesia, B. parviflora has a very divergent ITS sequence and a basal position in the genus. The phylogenetic trees make some sense of the great morphological variation within the subfamily, although some clades identified here lack obvious defining morphological characteristics. Optimisation of geographical distributions onto the molecular phylogenies shows that the Barnadesioideae most likely originated in southern South America.     

Molecular evolution of the Lake Baikal endemic caddisflies (Trichoptera)

Phylogenetic relationships of the nine Lake Baikal endemic caddisfly species with the representatives of the genus Apatania (Apataniidae) were reconstructed on the basis on nucleotide sequences of the mitochondrial COI gene. The results of Bayesian analysis pointed to the relationships of the endemics with the North American Apatania incerta (Banks, 1897) and A. sorex (Ross, 1941). The divergence of the genetic lineages of the Baikalian and Nearctic apataniids occurred in the Late Oligocene–Early Miocene. On the dendrogram, endemic species formed two monophyletic clades corresponding to the tribes Thamastini and Baicalinini. It was also found that the genus Protobaicalina was polyphyletic, while the genus Baicalina was a species flock. Our analysis showed that the nearest common ancestor of the studied Baikal caddisfly species existed about 21 Mya, while the modern species composition of endemic fauna dates back to Pliocene–Pleistocene age (2.5–0.7 million years).     

In search of monophyletic taxa in the family Desmidiaceae (Zygnematophyceae, Viridiplantae): the genus Cosmarium

Nuclear-encoded small subunit (SSU) rDNA, 1506 group I introns, and chloroplast rbcL genes were sequenced from 97 strains representing the largest desmid genus Cosmarium (45 spp.), its putative relatives Actinotaenium (5 spp.), Xanthidium (4 spp.), Euastrum (9 spp.), Staurodesmus (13 spp.), and other Desmidiaceae (Zygnematophyceae, Streptophyta) and used to assess phylogenetic relationships in the family. Analyses of single genes and of a concatenated data set (3260 nt) established 10 well-supported clades in the family with Cosmarium species distributed in six clades and one nonsupported assemblage. Most of the clades contained representatives of at least two genera highlighting the polyphyletic nature of the genera Cosmarium, Euastrum, Staurodesmus, and Actinotaenium. To enhance resolution between clades, we extended the data set by sequencing the slowly evolving chloroplast-encoded large subunit (LSU) rRNA gene from 40 taxa. Phylogenetic analyses of a concatenated data set (5509 nt) suggested a sister relationship between two clades that consisted mainly of Cosmarium species and included C. undulatum, the type species of the genus. We describe molecular signatures in the SSU rRNA for two clades and conclude that more studies involving new isolates, additional molecular markers, and reanalyses of morphological traits are necessary before the taxonomic revision of the genus Cosmarium can be attempted.     

Relationships within the Munnopsidae (Crustacea, Isopoda, Asellota) based on three genes

The Munnopsidae are a diverse group of asellote isopods that are an important component of deep‐sea fauna. Morphologically‐based phylogenetic inference attempts have proven to be of limited use due to the ecological and morphological diversity within the clade. Monophyly of the family is well‐established but relationships within the group remain unresolved. This project is the first molecularly‐based effort focused specifically on resolving phylogenetic relationships within the Munnopsidae. Partial 28S and COI and complete 18S genes were sequenced for 28 asellotes, 15 additional taxa were included from which only one or two of the three target sequences could be obtained, and 18S sequences for five additional taxa were available from GenBank. Sequences were analysed both as individual genes and in combination using Bayesian and maximum parsimony approaches. Each gene provided a phylogenetic signal that could be identified in the combined analyses, with 18S analyses providing the most resolution of phylogenetic relationships. The available representatives of subfamilies Munnopsinae and Ilyarachninae were monophyletic, as was the genus Munneurycope. Relationships within the subfamily Munnopsinae were well‐resolved by thorough taxon sampling, several new species were placed, and the need for taxonomic revision of Munnopsis/Munnopsoides was supported. These analyses supported putative Eurycope paraphyly and emphasized the need for careful revision of this highly variable genus. Tytthocope was sister to Munnopsurus. Syneurycope was suggested as the sister group to the ilyarachnines. Combined analyses provided increased support for clades suggested in at least two individual gene analyses and for clades not strongly contradicted by individual analyses. Further work is required to fully resolve the munnopsid phylogeny and should consist of increased taxon sampling for the complete 18S sequence and possibly identification of at least one slowly evolving, nuclear protein‐coding gene to resolve the basal polytomy and enable placement of the root.     

A New Eocene Dasypodid with Caniniforms (Mammalia,Xenarthra, Cingulata) from Northwest Argentina

The aim of this work is to present a new genus and species of Dasypodidae from the Lumbrera Formation (“lower Lumbrera”), early-middle Eocene of Salta Province, northwest Argentina. The new taxon, documented by one specimen, consists of an incomplete skull and jaw with teeth housed in their alveoli, postcranial remains, and isolated osteoderms. Lumbreratherium oblitum, gen. et sp. nov., is characterized by heterodont dentition, with a caniniform as the first tooth, diastema between caniniform and first molariform, teeth with closed roots, and a peculiar morphology of the osteoderms. A phylogenetic analysis indicates that Lumbreratherium oblitum, gen. et sp. nov., and Pucatherium parvum belong to a monophyletic clade in a basal position within the Cingulata. The singularity of the morphological characteristics of these Paleogene armadillos of northwest Argentina reinforces the hypothesis of an intertropical origin of mammal clades different from those of the Paleogene in more austral regions of Argentina.