Phylogenetic relationships of the New World Troidini swallowtails (Lepidoptera: Papilionidae) based on COI, COII, and EF-1α genes

A phylogeny of the Neotropical members of the Tribe Troidini (Lepidoptera: Papilionidae) was obtained with sequences of three protein-coding genes: two mitochondrial (COI and COII), and one nuclear (EF-1α). Parsimony and Bayesian analyses of 33 taxa resulted in very similar trees regardless of method used with the 27 troidines always forming a monophyletic clade. Within Troidini, the genus Battus is sister group to the remaining troidines, followed by a clade formed by the Paleotropical taxa (here represented by three exemplars). The genus Euryades is the next branch, and sister group of Parides. The genus Parides is monophyletic, and is divided into four main groups by Maximum Parsimony analysis, with the most basal group composed of tailed species restricted to SE Brazil. Character optimization of ecological and morphological traits over the phylogeny proposed for troidines indicated that the use of several species of Aristolochia is ancestral over the use of few or a single host-plant. For the other three characters, the ancestral states were the absence of long tails, forest as the primary habitat and oviposition solitary or in loose group of several eggs.     

Phylogenetic relationship among Libellula, Ladona and Plathemis (Odonata: Libellulidae) based on DNA sequence of mitochondrial 16S rRNA gene

Abstract. The type genus for the dragonfly family Libellulidae is Libellula. At present, Libellula s.l. includes twenty-nine species, whose distribution is largely Nearctic. Whether two other libellulid taxa, Ladona and Plathemis, should be considered synonyms of Libellula, subgenera of Libellula, or separate genera, has been a subject of intermittent debate for over a century. Earlier proposals concerning Ladona and Plathemis were based on a limited number of morphological characters and lacked rigorous phylogenetic analyses. Therefore, we used the DNA sequence of a portion of the mitochondrial 16S rRNA gene and parsimony, maximum likelihood and neighbour-joining analyses to explore whether Ladona and Plathemis are monophyletic lineages distinct from Libellula. We obtained ≈ 415 bp of DNA sequence from twenty-three taxa including thirteen species of Libellula s.s., all three recognized species of Ladona, the two species of Plathemis and representatives of four other libellulid genera. Tetragoneuria williamsoni (Odonata: Corduliidae) was included as the outgroup. Parsimony analysis suggested that Ladona and Plathemis are monophyletic lineages distinct from Libellula s.s. with a sister group relationship between Libellula and Ladona. The monophyly of Ladona, Plathemis and Libellula was supported in > 90% of bootstrap replications and in trees five to ten steps longer than the most parsimonious trees. Relationships inferred from maximum likelihood and neighbour-joining analyses also supported the monophyly of Ladona and Plathemis. The four other libellulid genera included in the study formed a monophyletic clade distinct from Libellula, Ladona and Plathemis. Based on our analysis, we propose that Ladona and Plathemis be considered either genera or subgenera within Libellulidae.     

Phylogeny of extant genera in the family Characeae (Charales,Charophyceae) based on rbcL,sequences and morphology

Extant genera of Characeae have been assigned to two tribes: Chareae (Chara, Lamprothamnium, Nitellopsis, and Lychnothamnus) and Nitelleae (Nitella and Tolypella), based on morphology of the thallus and reproductive structures. Character analysis of fossil and extant oogonia suggest that Tolypella is polyphyletic, the genus comprising two sections, one in each of the two tribes. Eleven morphological characters and sequence data for the Rubisco large subunit (rbcL) were used to reconstruct the phylogeny of genera, including the two sections of Tolypella. Parsimony analysis of the rbcL data, with all positions and changes weighted equally, strongly supports the monophyly of the Characeae. The two Tolypella sections form a robust monophyletic group basal to the family. Transversion weighting yielded the same tree but with a paraphyletic Tolypella. The rbcL data strongly support monophyly of tribe Chareae but tribe Nitelleae is paraphyletic. Parsimony analysis of morphological data produced one unrooted tree consistent with monophyly of the two tribes; on this tree the Tolypella sections were paraphyletic. Combining morphological with rbcL data did not change the results derived from rbcL sequences alone. The rbcL data support the monophyly of the Characeae and Coleochaete, which together form a monophyletic sister group to embryophytes.     

PHYLOGENETIC ANALYSES OF THE BRYOPSIDALES (ULVOPHYCEAE,CHLOROPHYTA) BASED ON RUBISCO LARGE SUBUNIT GENE SEQUENCES1

Current taxonomy of the Bryopsidales recognizes eight families; most of which are further categorized into two suborders, the Bryopsidineae and Halimedineae. This concept was supported by early molecular phylogenetic analyses based on rRNA sequence data, but subsequent cladistic analyses of morphological characters inferred monophyly in only the Halimedineae. These conflicting results prompted the current analysis of 32 taxa from this diverse group of green algae based on plastid‐encoded RUBISCO large subunit (rbcL) gene sequences. Results of these analyses suggested that the Halimedineae and Bryopsidineae are distinct monophyletic lineages. The families Bryopsidaceae, Caulerpaceae, Codiaceae, Derbesiaceae, and Halimediaceae were inferred as monophyletic, however the Udoteaceae was inferred as non‐monophyletic. The phylogenetic position of two taxa with uncertain subordinal affinity, Dichotomosiphon tuberosus Lawson and Pseudocodium floridanum Dawes & Mathieson, were also inferred. Pseudocodium was consistently placed within the halimedinean clade suggesting its inclusion into this suborder, however familial affinity was not resolved. D. tuberosus was the inferred sister taxon of the Halimedineae based on analyses of rbcL sequence data and thus a possible member of this suborder.     

Tales of dracula ants: the evolutionary history of the ant subfamily Amblyoponinae (Hymenoptera: Formicidae)

The ants in the subfamily Amblyoponinae are an old, relictual group with an unusual suite of morphological and behavioural features. Adult workers pierce the integument of their larvae to imbibe haemolymph, earning them the vernacular name ‘dracula ants’. We investigate the phylogeny of this group with a data set based on 54 ingroup taxa, 23 outgroups and 11 nuclear gene fragments (7.4 kb). We find that the genus Opamyrma has been misplaced in this subfamily: it is a member of the leptanilline clade and sister to all other extant Leptanillinae. Transfer of Opamyrma to Leptanillinae renders the Amblyoponinae monophyletic. The enigmatic Afrotropical genus Apomyrma is sister to all other amblyoponines, and the latter cleave into two distinct and well‐supported clades, here termed POA and XMMAS. The POA clade, containing Prionopelta, Onychomyrmex and Amblyopone, is well resolved internally, and its structure supports synonymy of the genus Concoctio under Prionopelta ( syn.n. ). The XMMAS clade comprises two well‐supported groups: (i) a predominantly Neotropical clade, for which we resurrect the genus name Fulakora ( stat.r., stat.n. ), with junior synonyms Paraprionopelta ( syn.n. ) and Ericapelta ( syn.n. ); and (ii) the remaining taxa, or ‘core XMMAS’, which are manifested in our study as a poorly resolved bush of about a dozen lineages, suggesting rapid radiation at the time of their origin. Most of these XMMAS lineages have been assigned to the catch‐all genus Stigmatomma, but the more distinctive elements have been treated as separate genera (Xymmer, Mystrium, Myopopone and Adetomyrma). Resolution of basal relationships in the core XMMAS clade and reconfiguration of ‘Stigmatomma’ to restore monophyly of all named genera will require more extensive genetic data and additional morphological analysis. However, the genus Bannapone can be synonymized under Stigmatomma ( syn.n. ) because it is embedded within a clade that contains S. denticulatum, the type species of Stigmatomma. Divergence dating analysis indicates that crown Amblyoponinae arose in the mid‐Cretaceous, about 107 Ma (95% highest probability density: 93–121 Ma). The POA and XMMAS clades have estimated crown ages of 47 and 73 Ma, respectively. The initial burst of diversification in the core XMMAS clade occurred in the Late Paleocene/Early Eocene (50–60 Ma). Ancestral range reconstruction suggests that amblyoponines originated in the Afrotropics, and dispersed to the Indo‐Malayan region and to the New World. During none of these dispersal events did the ants break out of their cryptobiotic lifestyle.     

A morphological phylogeny of Agrotis Ochsenheimer (Lepidoptera,Noctuidae), with emphasis on the South American species

The monophyly of Agrotis Ochsenheimer in addition to the relationships among the South American species of the genus and the relationship between Agrotis and Feltia Walker are examined. A cladistic analysis was performed based on 45 terminals, with 28 ingroup and 17 outgroup taxa, and 126 characters (two continuous and 124 discrete) from adult morphology, including male and female genitalia. Parsimony analyses were performed under equal and implied weighting. Results support Agrotis as a monophyletic group, sister to the South American species of Feltia (Feltia tent.), and the latter being more closely related to Agrotis than to the ‘true’ Feltia. Species of Agrotis that branched off first (including the type species) have characters shared with both Feltia and Agrotis. South American species of Agrotis (with some proviso) form a clade that branched off later, with some weakly supported species groups that had been proposed in previous works. Biogeographical aspects of the group are discussed after optimizing species distributions on the tree. Trees obtained after analyses using implied weights show similar relationships to those under equal weights, particularly regarding Feltia tent., showing Feltia tent. plus Agrotis forming a monophyletic group, sister to the ‘true’ Feltia.     

Phylogenetic relationships of the New World Troidini swallowtails (Lepidoptera: Papilionidae) based on COI, COII, and EF-1alpha genes

A phylogeny of the Neotropical members of the Tribe Troidini (Lepidoptera: Papilionidae) was obtained with sequences of three protein-coding genes: two mitochondrial (COI and COII), and one nuclear (EF-1alpha). Parsimony and Bayesian analyses of 33 taxa resulted in very similar trees regardless of method used with the 27 troidines always forming a monophyletic clade. Within Troidini, the genus Battus is sister group to the remaining troidines, followed by a clade formed by the Paleotropical taxa (here represented by three exemplars). The genus Euryades is the next branch, and sister group of Parides. The genus Parides is monophyletic, and is divided into four main groups by Maximum Parsimony analysis, with the most basal group composed of tailed species restricted to SE Brazil. Character optimization of ecological and morphological traits over the phylogeny proposed for troidines indicated that the use of several species of Aristolochia is ancestral over the use of few or a single host-plant. For the other three characters, the ancestral states were the absence of long tails, forest as the primary habitat and oviposition solitary or in loose group of several eggs.     

PHYLOGENETIC ANALYSIS OF MORPHOLOGICAL SPECIES OF CARTERIA (VOLVOCALES,CHLOROPHYTA) BASED ON rbcL GENE SEQUENCES1

Four related species in the unicellular volvocalean genus Carteria [C. crucifera Pascher, C. eugametos Mitra, C. inversa (Korshikov) Bourrelly and C. cerasiformis Nozaki et al.] were delineated on the basis of recent comparative light and electron microscopy of a large number of culture strains. However, the species thus delineated may not represent natural or monophyletic entities. In the present study, 1128 base pairs of the chloroplast protein-coding gene (large subunit of ribulose-1,5-bisphosphate carboxylase/oxygenase gene) from 12 Carteria strains representing the four species as well as from related volvocalean species were analyzed to elucidate the phylogenetic status of the taxonomic or morphologic species of Carteria. The sequence data showed that the 12 Carteria strains exhibit four robust monophyletic groups which are strictly consistent with the four taxonomic species. These results are discussed in relation to contrasting results found in other microalgal genera. It is concluded that phylogenetic analysis, based on DMA sequence data and comparative morphologic characterization of species and using a large number of culture strains, is essential to a natural system of microalgal species taxonomy.     

PHYLOGENY OF THE EUGLENOID LORICATE GENERA TRACHELOMONAS AND STROMBOMONAS (EUGLENOPHYTA) INFERRED FROM NUCLEAR SSU AND LSU rDNA1

Previous studies using the nuclear SSU rDNA and partial LSU rDNA have demonstrated that the euglenoid loricate taxa form a monophyletic clade within the photosynthetic euglenoid lineage. It was unclear, however, whether the loricate genera Trachelomonas and Strombomonas were monophyletic. In order to determine the relationships among the loricate taxa, SSU and LSU nuclear rDNA sequences were obtained for eight Strombomonas and 25 Trachelomonas strains and combined in a multigene phylogenetic analysis. Conserved regions of the aligned data set were used to generate maximum‐likelihood (ML) and Bayesian phylogenies. Both methods recovered a strongly supported monophyletic loricate clade with Strombomonas and Trachelomonas species separated into two sister clades. Taxa in the genus Strombomonas sorted into three subclades. Within the genus Trachelomonas, five strongly supported subclades were recovered in all analyses. Key morphological features could be attributed to each of the subclades, with the major separation being that all of the spine‐bearing taxa were located in two sister subclades, while the more rounded, spineless taxa formed the remaining three subclades. The separation of genera and subclades was supported by 42 distinct molecular signatures (33 in Trachelomonas and nine in Strombomonas). The morphological and molecular data supported the retention of Trachelomonas and Strombomonas as separate loricate genera.     

Molecular phylogenetic analysis of the dragonfly genera Libellula, Ladona, and Plathemis (Odonata: Libellulidae) based on mitochondrial cytochrome oxidase I and 16S rRNA sequence data

Molecular phylogenetic relationships among members of the odonate genus Libellula (Odonata: Anisoptera: Libellulidae) were examined using 735 bp of mitochondrial COI and 416 bp of 16S ribosomal RNA gene sequences. Considerable debate exists over several relationships within Libellula, as well over the status of two putative genera often placed as subgenera within Libellula: Ladona and Plathemis. Parsimony and maximum-likelihood analyses of the separate and combined data sets indicate that Plathemis is basal and monophyletic and that Ladona is the sister clade to the remainder of Libellula sensu stricto (s.s.) (all species within the genus Libellula, excluding Plathemis and Ladona). Moreover, two European taxa, Libellula fulva and L. depressa, were found to occupy a sister group relationship within the Ladona clade. Relationships within Libellula s.s. are less well resolved. However, monophyletic lineages within the genus are largely consistent with morphologically based subgeneric classifications. Although tree topologies from each analysis differed in some details, the differences were in no case statistically significant. The analysis of the combined COI and 16S data yielded trees with overall stronger support than analyses of either gene alone. Several analyses failed to support the monophyly of Libellula sensu lato due to the inclusion of one or more outgroup species. However, statistical comparisons of topologies produced by unconstrained analyses and analyses in which the monophyly of Libellula was constrained indicate that any differences are nonsignificant. Based on morphological data, we therefore reject the paraphyly of Libellula and accept the outgroup status of Orthemis ferruginea and Pachydiplax longipennis.     

Phylogenetics of the common raven complex (Corvus: Corvidae) and the utility of ND4, COI and intron 7 of the β-fibrinogen gene in avian molecular systematics

The common raven (Corvus corax) is one of the most widely distributed and recognizable avian species in the world. Recent molecular work, however, described two mitochondrial lineages of the common raven, termed the Holarctic clade and the California clade, and questioned the monophyly of this taxon by placing the Chihuahuan raven (C. cryptoleucus) sister to the California clade. We evaluated this phylogenetic hypothesis with additional sequence data and increased taxon sampling. We used ～3.7 kb of DNA sequence data from sections of the mitochondrial coding genes COI, cyt b and ND4, a fragment of the non‐coding mitochondrial DNA control region, and the entire intron 7 of the nuclear β‐fibrinogen gene (β‐fibint 7). We combined these DNA sequence data to erect hypotheses of relationships for lineages of the common raven and related taxa. Maximum parsimony, maximum likelihood, and Bayesian methods yield a paraphyletic common raven. These analyses nest the Chihuahuan raven within the common raven, with strong support for a sister relationship between the Chihuahuan raven and the California clade. In addition, the pied crow (C. albus) is also nested within the common raven, and is sister to the Holarctic clade. Our analyses reveal the challenge of determining phylogenetic relationships and species boundaries in this morphologically conservative genus, and suggest that future molecular work with increased taxon sampling will uncover cryptic species and novel evolutionary relationships. Lastly, this survey is one of a growing number of avian phylogenetic studies to employ either β‐fibint 7 or COI, and the first to use ND4. We developed a simple procedure for comparing rates of evolution in molecular markers, and show that in Corvus the nuclear intron β‐fibint 7 is evolving at a considerably slower pace than the mitochondrial markers, while COI is evolving at a slower rate than cyt b, and ND4 approximately the same rate as cyt b. Hence, β‐fibint 7 and other individual nuclear introns may have limited utility in resolving relationships among recently evolved taxa, whereas both COI and ND4 should be useful in a wide range of avian molecular genetic investigations.     

Molecular phylogenetics of the giant genus Croton and tribe Crotoneae (Euphorbiaceae sensu stricto) using ITS and TRNL-TRNF DNA sequence data

Parsimony, likelihood, and Bayesian analyses of nuclear ITS and plastid trnL-F DNA sequence data are presented for the giant genus Croton (Euphorbiaceae s.s.) and related taxa. Sampling comprises 88 taxa, including 78 of the estimated 1223 species and 29 of the 40 sections previously recognized of Croton. It also includes the satellite genus Moacroton and genera formerly placed in tribe Crotoneae. Croton and all sampled segregate genera form a monophyletic group sister to Brasiliocroton, with the exception of Croton sect. Astraea, which is reinstated to the genus Astraea. A small clade including Moacroton, Croton alabamensis, and C. olivaceus is sister to all other Croton species sampled. The remaining Croton species fall into three major clades. One of these is entirely New World, corresponding to sections Cyclostigma, Cascarilla, and Velamea sensu Webster. The second is entirely Old World and is sister to a third, also entirely New World clade, which is composed of at least 13 of Webster's sections of Croton. This study establishes a phylogenetic framework for future studies in the hyper-diverse genus Croton, indicates a New World origin for the genus, and will soon be used to evaluate wood anatomical, cytological, and morphological data in the Crotoneae tribe.     

Probing the Monophyly of the Sphaeropleales (Chlorophyceae) Using Data From Five Genes

Molecular phylogenetic analyses have had a major impact on the classification of the green algal class Chlorophyceae, corroborating some previous evolutionary hypotheses, but primarily promoting new interpretations of morphological evolution. One set of morphological traits that feature prominently in green algal systematics is the absolute orientation of the flagellar apparatus in motile cells, which correlates strongly with taxonomic classes and orders. The order Sphaeropleales includes diverse green algae sharing the directly opposite (DO) flagellar apparatus orientation of their biflagellate motile cells. However, algae across sphaeroplealean families differ in specific components of the DO flagellar apparatus, and molecular phylogenetic studies often have failed to provide strong support for the monophyly of the order. To test the monophyly of Sphaeropleales and of taxa with the DO flagellar apparatus, we conducted a molecular phylogenetic study of 16 accessions representing all known families and diverse affiliated lineages within the order, with data from four plastid genes (psaA, psaB, psbC, rbcL) and one nuclear ribosomal gene (18S). Although single‐gene analyses varied in topology and support values, analysis of combined data strongly supported a monophyletic Sphaeropleales. Our results also corroborated previous phylogenetic hypotheses that were based on chloroplast genome data from relatively few taxa. Specifically, our data resolved Volvocales, algae possessing predominantly biflagellate motile cells with clockwise (CW) flagellar orientation, as the monophyletic sister lineage to Sphaeropleales, and an alliance of Chaetopeltidales, Chaetophorales, and Oedogoniales, orders having multiflagellate motile cells with distinct flagellar orientations involving the DO and CW forms.     

The monophyly and evolution of Cynara L. (Asteraceae) sensu lato: evidence from the Internal Transcribed Spacer region of nrDNA

The monophyly and evolution of Cynara was investigated using ITS sequence data. Parsimony analysis supports the monophyly of Cynara sensu lato, i.e. including the distinctive taxa C. humilis and C. tournefortii. This contradicts the recent decision to create a new monotypic genus Arcyna for C. tournefortii. A hypothesised close relationship between C. tournefortii and Silybum Adans. is also refuted. Four of the five species of Cynara, for which multiple accessions were sequenced, were shown to be monophyletic but C. baetica was found to be non-monophyletic. Free energy estimates for ITS1 secondary structure and conservation of the 5.8S region suggest that this is not due to the occurrence of pseudogenes. Hybridisation is a plausible explanation but evidence for the likely parents involved in such an event is inconclusive.     

MOLECULAR PHYLOGENY OF THE GENUS CAULERPA (CAULERPALES,CHLOROPHYTA) INFERRED FROM CHLOROPLAST tufA GENE1

The genus Caulerpa consists of about 75 species of tropical to subtropical siphonous green algae. To better understand the evolutionary history of the genus, a molecular phylogeny was inferred from chloroplast tufA sequences of 23 taxa. A sequence of Caulerpella ambigua was included as a potential outgroup. Results reveal that the latter taxon is, indeed, sister to all ingroup sequences. Caulerpa itself consists of a series of relatively ancient and species‐poor lineages and a relatively modern and rapidly diversifying clade, containing most of the diversity. The molecular phylogeny conflicts with the intrageneric sectional classification based on morphological characters and an evolutionary scheme based on chloroplast ultrastructure. High bootstrap values support monophyly of C. mexicana, C. sertularioides, C. taxifolia, C. webbiana, and C. prolifera, whereas most other Caulerpa species show para‐ or polyphyly.     

Phylogenetic relationships of the anamorphic genus <Emphasis Type="Italic">Fusicladium</Emphasis> s. lat. as inferred by ITS nrDNA data

The genus Fusicladium s. lat. (incl. Pollaccia and Spilocaea) was phylogenetically analysed using ITS nrDNA sequences. Pollaccia and Spilocaea did not form monophyletic groups of their own, but were intermingled between Fusicladium species, together with which they formed a monophyletic clade. Thus, Pollaccia and Spilocaea should be included in a wider genus concept of Fusicladium, constituting a morphologically variable genus. Furthermore, all Venturia and Fusicladium isolates clustered together on the bases of available ITS data, providing support for the monophyly of the anamorphic genus Fusicladium and the teleomorphic genus Venturia. Within this clade several subclades can be recognized. All taxa on the host family Salicaceae were found in one subclade. Three other subclades comprised taxa on Rosaceae whereas taxa on other host families all clustered separately. Geographic specializations were not observed. Two examples of host switching could be demonstrated, but these were confined to instances involving host species belonging to the same family. Fusicladium convolvularum and F. effusum, two species with unknown teleomorphs, clustered within the Fusicladium/Venturia clade, supporting the correct placement of these taxa in Fusicladium. The placement of Pseudocladosporium hachijoense within the family Venturiaceae was also supported.     

Phylogenetic reticulation in subtribe Helianthinae

Incongruence between phylogenetic estimates based on nuclear and chloroplast DNA (cpDNA) markers was used to infer that there have been at least two instances of chloroplast transfer, presumably through wide hybridization, in subtribe Helianthinae. One instance involved Simsia dombeyana, which exhibited a cpDNA restriction site phenotype that was markedly divergent from all of the other species of the genus that were surveyed but that matched the restriction site pattern previously reported for South American species of Viguiera. In contrast, analysis of sequence data from the nuclear ribosomal DNA internal transcribed spacer (ITS) region showed Simsia to be entirely monophyletic and placed samples of S. dombeyana as the sister group to the relatively derived S. foetida, a result concordant with morphological information. A sample of a South American species of Viguiera was placed by ITS sequence data as the sister group to a member of V. subg. Amphilepis, which was consistent with cpDNA restriction site data. Samples of Tithonia formed a single monophyletic clade based on ITS sequence data, whereas they were split between two divergent clades based on cpDNA restriction site analysis. The results suggested that cpDNA transfer has occurred between taxa diverged to the level of morphologically distinct genera, and highlight the need for careful and complete assessment of molecular data as a source of phylogenetic information.     

PHYLOGENY OF CHLAMYDOMONAS (CHLOROPHYTA) BASED ON CLADISTIC ANALYSIS OF NUCLEAR 18S rRNA SEQUENCE DATA1

The genus Chlamydomonas Ehrenberg may contain as many as 450 described species. Morphological, physiological and molecular data show that variation among some Chlamydomonas species can he great, leading to speculation that multiple, generic-level lineages exist within this genus. The most recent systematic studies of Chlamydomonas have led to proposals of nine distinct morphological and 15 distinct sporangial autolysin groups. Partial sequences from the nuclear small subunit rRNAs from 14 Chlamydomonas species representing 12 autolysin and four morphological groups, and from three flagellates thought to he related to Chlamydomonas were determined in a phylogenetic study of relationships among these algae. Sequence comparisons among some Chlamydomonas species revealed differences comparable to the sequence divergence between soybeans and cycads. Cladistic analysis of the sequence data suggests that multiple lineages exist among species of Chlamydomonas. Some of these lineages represent alliances of both Chlamydomonas and non-Chlamydomonas taxa; thus, the current taxonomy does not reflect natural, or monophyletic, groups. Collectively, these lineages may represent distinct families or even orders.     

Phylogeny of carabid beetles as inferred from 18S ribosomal DNA (Coleoptera: Carabidae)

The phylogeny of carabid tribes is examined with sequences of 18S ribosomal DNA from eighty-four carabids representing forty-seven tribes, and fifteen outgroup taxa. Parsimony, distance and maximum likelihood methods are used to infer the phylogeny. Although many clades established with morphological evidence are present in all analyses, many of the basal relationships in carabids vary from analysis to analysis. These deeper relationships are also sensitive to variation in the sequence alignment under different alignment conditions. There is moderate evidence against the monophyly of Migadopini + Amarotypini, Scaritini + Clivinini, Bembidiini and Brachinini. Psydrini are not monophyletic, and consist of three distinct lineages (Psydrus, Laccocenus and a group of austral psydrines, from the Southern Hemisphere consisting of all the subtribes excluding Psydrina). The austral psydrines are related to Harpalinae plus Brachinini. The placements of many lineages, including Gehringia, Apotomus, Omophron, Psydrus and Cymbionotum, are unclear from these data. One unexpected placement, suggested with moderate support, is Loricera as the sister group to Amarotypus. Trechitae plus Patrobini form a monophyletic group. Brachinini probably form the sister group to Harpalinae, with the latter containing Pseudomorpha, Morion and Cnemalobus. The most surprising, well supported result is the placement of four lineages (Cicindelinae, Rhysodinae, Paussinae and Scaritini) as near relatives of Harpalinae + Brachinini. Because these four lineages all have divergent 18S rDNA, and thus have long basal branches, parametric bootstrapping was conducted to determine if their association and placement could be the result of long branch attraction. Simulations on model trees indicate that, although their observed association might be due to long branch attraction, there was no evidence that their placement near Harpalinae could be so explained. These simulations also suggest that 18S rDNA might not be sufficient to infer basal carabid relationships.     

PHYLOGENY OF THE EUGLENALES BASED UPON COMBINED SSU AND LSU RDNA SEQUENCE COMPARISONS AND DESCRIPTION OF DISCOPLASTIS GEN. NOV. (EUGLENOPHYTA)1

A Bayesian analysis, utilizing a combined data set developed from the small subunit (SSU) and large subunit (LSU) rDNA gene sequences, was used to resolve relationships and clarify generic boundaries among 84 strains of plastid‐containing euglenophytes representing 11 genera. The analysis produced a tree with three major clades: a Phacus and Lepocinlis clade, a Discoplastis clade, and a Euglena, Colacium, Trachelomonas, Strombomonas, Monomorphina, and Cryptoglena clade. The majority of the species in the genus Euglena formed a well‐supported clade, but two species formed a separate clade near the base of the tree. A new genus, Discoplastis, was erected to accommodate these taxa, thus making the genus Euglena monophyletic. The analysis also supported the monophyly of Colacium, Trachelomonas, Strombomonas, Monomorphina, and Cryptoglena, which formed two subclades sister to the Euglena clade. Colacium, Trachelomonas, and Strombomonas, all of which produce copious amounts of mucilage to form loricas or mucilaginous stalks, formed a well‐supported lineage. Our analysis supported retaining Strombomonas and Trachelomonas as separate genera. Monomorphina and Cryptoglena formed two well‐supported clades that were sister to the Colacium, Trachelomonas, and Strombomonas clade. Phacus and Lepocinclis, both of which have numerous small discoid chloroplasts without pyrenoids and lack peristaltic euglenoid movement (metaboly), formed a well‐supported monophyletic lineage that was sister to the larger Euglena through Cryptoglena containing clade. This study demonstrated that increased taxon sampling, multiple genes, and combined data sets provided increased support for internal nodes on the euglenoid phylogenetic tree and resolved relationships among the major genera in the photosynthetic euglenoid lineage.