Mitochondrial DNA phylogeny of West African aplocheiloid killifishes (Cyprinodontiformes, Aplocheilidae)

African killifishes (Cyprinodontiformes, Aplocheilidae) historically associated with the genus Aphyosemion occur in two geographically distinct regions. One assemblage from far West Africa has been previously shown to be monophyletic and not closely related to the remaining eastern species of Aphyosemion (W. J. Murphy and G. E. Collier, 1997, Mol. Biol. Evol. 14, 790-799). This is supported by further analysis of mitochondrial DNA sequences from 19 species from 21 different localities, representing 19 of the putative 22 species of this western group. Phylogenetic analyses of these data corroborate the monophyly and sister-group relationship of two distinct groups of taxa: Callopanchax and Scriptaphyosemion. Many of the relationships within Scriptaphyosemion suggest that these taxa may have radiated within a short period of time relative to the rate of substitutions within these sequences. A third, and possibly paraphyletic group of species, Archiaphyosemion, is suggested to be the sister taxon to the first two groups. These three groups are elevated to generic rank and together represent the sister group to the genus Epiplatys. Biogeographic inference suggests that the ancestors of this group diversified westward through upland habitat and have only relatively recently entered the lowland habitats in which Scriptaphyosemion and Callopanchax have diversified, with the latter genus reacquiring a suite of traits collectively referred to as annualism.     

EVOLUTION OF THE FUCACEAE (PHAEOPHYCEAE) INFERRED FROM nrDNA-ITS

Sequences of the internal transcribed spacer region (ITS-1, 5.8S, and ITS-2) of nuclear ribosomal DNA were obtained from 16 species representing all six genera of Fucaceae ( Ascophyllum, Fucus, Hesperophycus, Pelvetia, Pelvetiopsis, and Xiphophora ) plus one outgroup ( Hormosira ). Parsimony analysis indicated that the family Fucaceae is monophyletic and that the northern hemisphere taxa are highly divergent from the only southern hemisphere genus, Xiphophora. The genus Pelvetia is not monophyletic because the European P. canaliculata is more closely related to Fucus, Hesperophycus, and Pelvetiopsis than to other Pelvetia species. We establish Silvetia, gen. nov. and transfer the 3 Pacific species of Pelvetia to the new genus. Fucus is monophyletic and not ancestral in the Fucaceae. The ITS sequences identified two strongly supported lineages within Fucus, one with F. serratus sister to the clade containing F. gardneri, F. distichus, and F. evanescens and a second including F. vesiculosus, F. spiralis, F. ceranoides, and F. virsoides. The ITS was not useful for resolving relationships within each of these clusters and between populations of F. vesiculosus. Within-individual variation in ITS sequences is high in Fucus, a derived genus, compared to Ascophyllum, a more ancestral genus. Mapping of the two characters that form the basis of Powell's model for speciation in the Fucaceae showed that 1) number of eggs per oogonium has not followed a gradual reduction and that 2) monoecy/dioecy has changed several times during evolution of this family.     

Phylogenetic relationships of the bulbuls (Aves: Pycnonotidae) based on mitochondrial and nuclear DNA sequence data

Bulbuls (Aves: Pycnonotidae) are a fairly speciose (ca. 130 sp.) bird family restricted to the Old World. Family limits and taxonomy have been revised substantially over the past decade, but a comprehensive molecular phylogeny for the family has not been undertaken. Using nuclear and mitochondrial DNA sequences, we reconstructed a well-supported phylogenetic hypothesis for the bulbuls. Three basal lineages were identified: a large African clade, a large Asian clade that also included African Pycnonotus species, and the monotypic African genus Calyptocichla. The African clade was sister to the other two lineages, but this placement did not have high branch support. The genus Pycnonotus was not monophyletic because three species (eutilotus, melanoleucos, and atriceps) were highly diverged from the other species and sister to all other Asian taxa. Additional taxon sampling is needed to further resolve relationships and taxonomy within the large and variable Hypsipetes complex.     

Phylogenetic Analysis of Heterothallic Neurospora Species

We examined the phylogenetic relationships among five heterothallic species of Neurospora using restriction fragment polymorphisms derived from cosmid probes and sequence data from the upstream regions of two genes, al-1 and frq. Distance, maximum likelihood, and parsimony trees derived from the data support the hypothesis that strains assigned to N. sitophila, N. discreta, and N. tetrasperma form respective monophyletic groups. Strains assigned to N. intermedia and N. crassa, however, did not form two respective monophyletic groups, consistent with a previous suggestion based on analysis of mitochondrial DNAs that N. crassa and N. intermedia may be incompletely resolved sister taxa. Trees derived from restriction fragments and the al-1 sequence position N. tetrasperma as the sister species of N. sitophila. None of the trees produced by our data supported a previous analysis of sequences in the region of the mating type idiomorph that grouped N. crassa and N. sitophila as sister taxa, as well as N. intermedia and N. tetrasperma as sister taxa. Moreover, sequences from al-1, frq, and the mating-type region produced different trees when analyzed separately. The lack of consensus obtained with different sequences could result from the sorting of ancestral polymorphism during speciation or gene flow across species boundaries, or both.     

Phylogenetic relationships of Loxosceles and Sicarius spiders are consistent with Western Gondwanan vicariance

The modern geographic distribution of the spider family Sicariidae is consistent with an evolutionary origin on Western Gondwana. Both sicariid genera, Loxosceles and Sicarius are diverse in Africa and South/Central America. Loxosceles are also diverse in North America and the West Indies, and have species described from Mediterranean Europe and China. We tested vicariance hypotheses using molecular phylogenetics and molecular dating analyses of 28S, COI, 16S, and NADHI sequences. We recover reciprocal monophyly of African and South American Sicarius, paraphyletic Southern African Loxosceles and monophyletic New World Loxosceles within which an Old World species group that includes L. rufescens is derived. These patterns are consistent with a sicariid common ancestor on Western Gondwana. North American Loxosceles are monophyletic, sister to Caribbean taxa, and resolved in a larger clade with South American Loxosceles. With fossil data this pattern is consistent with colonization of North America via a land bridge predating the modern Isthmus of Panama.     

Relationships among characiform fishes inferred from analysis of nuclear and mitochondrial gene sequences

Suprafamilial relationships among characiform fishes and implications for the taxonomy and biogeographic history of the Characiformes were investigated by parsimony analysis of four nuclear and two mitochondrial genes across 124 ingroup and 11 outgroup taxa. Simultaneous analysis of 3660 aligned base pairs from the mitochondrial 16S and cytochrome b genes and the nuclear recombination activating gene (RAG2), seven in absentia (sia), forkhead (fkh), and alpha-tropomyosin (trop) gene loci confirmed the non-monophyly of the African and Neotropical assemblages and corroborated many suprafamilial groups proposed previously on the basis of morphological features. The African distichodontids plus citharinids were strongly supported as a monophyletic Citharinoidei that is the sistergroup to all other characiforms, which form a monophyletic Characoidei composed of two large clades. The first represents an assemblage of both African and Neotropical taxa, wherein a monophyletic African Alestidae is sister to a smaller clade comprised of the Neotropical families Ctenolucidae, Lebiasinidae, and the African Hepsetidae, with that assemblage sister to a strictly Neotropical clade comprised of the Crenuchidae and Erythrinidae. The second clade within the Characoidei is strictly Neotropical and includes all other Characiformes grouped into two well supported major clades. The first, corresponding to a traditional definition of the Characidae, is congruent with some groupings previously supported by morphological evidence. The second clade comprises a monophyletic Anostomoidea that is sister to a clade formed by the families Hemiodontidae, Parodontidae, and Serrasalmidae, with that assemblage, in turn, the sistergroup of the Cynodontidae. Serrasalmidae, traditionally regarded as a subfamily of Characidae, was recovered as the sistergroup of (Anostomoidea (Parodontidae+Hemiodontidae)) and the family Cynodontidae was recovered with strong support as the sistergroup to this assemblage. Our results reveal three instances of trans-continental sistergroup relationships and, in light of the fossil evidence, suggest that marine dispersal cannot be ruled out a priori and that a simple model of vicariance does not readily explain the biogeographic history of the characiform fishes.     

Molecular evolution and phylogenetic implications of internal transcribed spacer sequences of nuclear ribosomal DNA in the Phaseolus-Vigna complex.

Molecular phylogeny based on internal transcribed spacer (ITS) sequences was studied to resolve the taxonomic contradiction in Vigna and its relation to Phaseolus. The ITS region of the 18S-26S nuclear ribosomal DNA repeat was sequenced for 29 Vigna species, selected from five of the nine subgenera, and 9 species of Phaseolus. The length of ITS-1 ranged from 187 to 243 bp and 217 to 290 bp, and that of ITS-2 from 187 to 219 bp and 225 to 243 bp, within Vigna and Phaseolus species, respectively. Phylogenies derived from ITS sequences based on maximum-parsimony and neighbor-joining methods gave trees essentially of similar topology. The ITS phylogeny was generally congruent with recent classifications based largely on morphological, biochemical, cytogenetical, and palynological features, except that subgenus Plectotropis of Neotropical origin was revealed to be closely related to subgenus Vigna instead of forming a link between African (subgenus Vigna) and Asiatic (subgenus Ceratotropis) vignas, and subgenus Sigmoidotropis, featuring morphological characters of both Vigna and Phaseolus, was placed as the sister group to the Phaseolus taxa. The ITS sequences were shown to be useful for identifying wild progenitors of V. mungo, V. radiata, V. umbellata, and V. unguiculata and for clarifying taxonomy-related problems in many previously controversial cases. This study also affirms that V. umbellata and V. angularis are the diploid progenitors of the only tetraploid species (V. glabrescens) known in the genus.     

Mitochondrial phylogeny of the endemic mouthbrooding lineages of cichlid fishes from Lake Tanganyika in eastern Africa

Of the three cichlid species flocks in eastern Africa, Lake Tanganyika harbors the oldest species assemblage, which is also the most diverse morphologically and behaviorally. For 12 species (20 individuals) of 12 genera of the tribe Ectodini, 852 bp from two segments (cytochrome b and control region) of the mitochondrial genome were sequenced. In addition, orthologous sequences were obtained from eight species (11 individuals) representing other mouthbrooding lineages from Lake Tanganyika. Comparisons of sequence divergences revealed that the single Tanganyikan tribe Ectodini appears to be approximately five times older than the whole Lake Malawi cichlid species flock, suggesting that the radiation of the Tanganyikan mouthbrooding lineages took place long before the species flocks of Lakes Malawi and Victoria evolved. Seven of nine surveyed tribes of Tanganyikan cichlids appear to be approximately equally divergent, and this seems to corroborate the hypothesis of a rapid simultaneous formation of lineages at an early stage in the history of the Lake Tanganyika species flock. The close genetic relationship between the endemic Tropheus lineage and a nonendemic "Haplochromine," Astatotilapia burtoni, indicates that members of the tribe Tropheini may be the sister group of the cichlid flocks of Lakes Malawi and Victoria. The phylogenetic analyses demonstrate the monophyly of the Ectodini and identify the Cyprichromini as their sister group among the Tanganyikan cichlids. Within the tribe Ectodini the molecular data suggest both a branching pattern different than that previously proposed and a subdivision of the Ectodini into four clades, instead of the two originally described. The previously postulated model of morphological transformations believed to be responsible for the drastically different types of ecological specialization found among the Ectodini might therefore be in need of reinterpretation. Characters immediately related to foraging and nutrition seem to be particularly prone to homoplasy, even among members of a single lineage of cichlid fishes.      

Mitochondrial phylogeny of the Lamprologini, the major substrate spawning lineage of cichild fishes from Lake Tanganyika in eastern Africa

Lake Tanganyika harbors the oldest, morphologically and behaviorally most diverse flock of cichlid species. While the cichlids in Lakes Malawi and Victoria breed their eggs exclusively by buccal incubation (termed "mouthbrooding"), the Tanganyikan cichlid fauna comprise mouthbrooding and substrate-spawning lineages (fish spawn on rocks, and never orally incubate eggs or wrigglers). The substrate-spawning tribe Lamprologini appears to occupy a key position that might allow one to elucidate the origin of the Tanganyika flock, because five riverine (therefore nonendemic) species from the Zaire River system have been assigned to this tribe, in addition to the lake's endemic species, which make up almost 50% of all 171 species known from this lake (Poll 1986). From 16 species (18 individuals) of the tribe Lamprologini, a 402-bp segment of the mitochondrial cytochrome b gene was sequenced, and, from 25 lamprologine species (35 individuals), sequences from the mitochondrial control region were obtained. To place the Lamprologini into a larger phylogenetic framework, orthologous sequences were obtained from eight nonlamprologine Tanganyikan cichlid species (13 individuals). The Lamprologini are monophyletic, and a clade of six Tanganyikan lineages of mouthbrooders, representing five tribes (Poll 1986), appears to be their sister group. Comparisons of sequence divergences of the control region indicate that the Lamprologini may be older than the endemic Tanganyikan tribe Ectodini, and short basal branches might suggest a rapid formation of lineages at an early stage of the Tanganyika radiation. It is interesting that three analyzed riverine members of the tribe form a monophyletic group; however, they are not the most ancestral branch of the Lamprologini. This might indicate that they are derived from an endemic lamprologine ancestor that left Lake Tanganyika by entering the Zaire River system. These riverine species may not have seeded the Tanganyikan radiation, as currently thought, but may have recently recolonized the river after a long period of isolation, as soon as the lake was connected to the Zaire River again about 2 Mya. Neolamprologus moorii, endemic to Lake Tanganyika, appears to represent the most basal clade of the Lamprologini. Complex breeding behavior, involving the usage of gastropod shells and associated with dwarfism, is likely to have evolved in parallel in several lineages among the Lamprologini. The tribe Lamprologini may be in need of revision, since several genera appear to be polyphyletic.      

Molecular phylogeny of Corynosoma Lühe, 1904 (Acanthocephala), based on 5.8S and internal transcribed spacer sequences

Species of Corynosoma (Acanthocephala) are distributed worldwide as parasites of marine mammals and sea birds. Species diagnosis is based on morphological characters, including the size and number of hooks in the proboscis and the number of spines in the dorsal and ventral regions of the body. We inferred the phylogenetic relationships of 10 nominal species of Corynosoma through analysis of internal transcribed spacers (ITS-1, ITS-2) and 5.8S ribosomal RNA sequences. Nucleotide distances between species of Corynosoma ranged from 0.4 to 11% for ITS sequences. Maximum parsimony and likelihood analyses indicated that species of Corynosoma that inhabit hosts in the marine environment form a monophyletic assemblage, but yielded conflicting hypotheses for the relationship of Corynosoma cetaceum to other members of the genus. However, parsimony and likelihood analyses were consistent for many Corynosoma sister species relationships of (e.g., C. australe plus C. bullosum, C. validum plus C. villosum, C. caspicum plus C. magdaleni, and C. enhydri plus C. strumosum). This phylogenetic framework was used to evaluate taxonomic controversies concerning C. cetaceum and C. caspicum.     

Evolution of the mimetic African swallowtail butterfly Papilio dardanus: molecular data confirm relationships with P. phorcas and P. constantinus

Sister group relationships of the African Mocker Swallowtail, Papilio dardanus, were determined using mitochondrial 16S rRNA and Cytochrome B sequences, and nuclear Elongation Factor EF-la and the ITS-1 region of the ribosomal RNA locus. All four data sets placed P. dardanus as the sister species of P. phorcas, with P. constantinus as the next closest relative, and quite distinct from other African Papilios such as P. nobilis. These data support earlier morphological studies indicating that the only two African Papilio species with multiple female colour forms have a common ancestor not shared with any other living species. This information is important for conclusions about the evolution of female-limited mimicry in swallowtail butterflies, and successful use of the ITS-1 gene opens up new possibilities for studying this phenomenon within P. dardanus.     

Affinities between Asian non-human Schistosoma species,the S. indicum group,and the African human schistosomes

Schistosoma species have traditionally been arranged in groups based on egg morphology, geographical origins, and the genus or family of snail intermediate host. One of these groups is the 'S. indicum group' comprising species from Asia that use pulmonate snails as intermediate hosts. DNA sequences were obtained from the four members of this group (S. indicum, S. spindale, S. nasale and S. incognitum) to provide information concerning their phylogenetic relationships with other Asian and African species and species groups. The sequences came from the second internal transcribed spacer (ITS2) of the ribosomal gene repeat, part of the 28S ribosomal RNA gene (28S), and part of the mitochondrial cytochrome c oxidase subunit 1 (CO1) gene. Tree analyses using both distance and parsimony methods showed the S. indicum group not to be monophyletic. Schistosoma indicum, S. spindale and S. nasale were clustered among African schistosomes, while S. incognitum was placed as sister to the African species (using ITS2 and 28S nucleotide sequences and CO1 amino acid sequences), or as sister to all other species of Schistosoma (CO1 nucleotide sequences). Based on the present molecular data, a scenario for the evolution of the S. indicum group is discussed.     

Nuclear markers reveal unexpected genetic variation and a Congolese-Nilotic origin of the Lake Victoria cichlid species flock

Phylogenetic analyses based on mitochondrial (mt) DNA have indicated that the cichlid species flock of the Lake Victoria region is derived from a single ancestral species found in East African rivers, closely related to the ancestor of the Lake Malawi cichlid species flock. The Lake Victoria flock contains ten times less mtDNA variation than the Lake Malawi radiation, consistent with current estimates of the ages of the lakes. We present results of a phylogenetic investigation using nuclear (amplified fragment length polymorphism) markers and a wider coverage of riverine haplochromines. We demonstrate that the Lake Victoria-Edward flock is derived from the morphologically and ecologically diverse cichlid genus Thoracochromis from the Congo and Nile, rather than from the phenotypically conservative East African Astatotilapia. This implies that the ability to express much of the morphological diversity found in the species flock may by far pre-date the origin of the flock. Our data indicate that the nuclear diversity of the Lake Victoria-Edward species flock is similar to that of the Lake Malawi flock, indicating that the genetic diversity is considerably older than the 15 000 years that have passed since the lake began to refill. Most of this variation is manifested in trans-species polymorphisms, indicating very recent cladogenesis from a genetically very diverse founder stock. Our data do not confirm strict monophyly of either of the species flocks, but raise the possibility that these flocks have arisen from hybrid swarms.     

Molecular evidence reveals a polyphyletic origin and chromosomal speciation of Lake Baikal's endemic asellid isopods

The six endemic isopod species of Lake Baikal have been regarded as a small species flock with uncertain affinities to related asellids. We provide evidence from 16S rRNA sequences for polyphyletic origins of Baikalian Asellidae. One clade of two species is related to the Eurasian genus Asellus. The other clade, Baicalasellus, shows affinities to North American asellids and may have a long evolutionary history within the lake basin. Some speciation events within Baicalasellus clearly have a chromosomal basis. In contrast with numerous taxa exhibiting monophyletic radiations in ancient lakes, the endemic Baikalian isopods arose by multiple invasions and chromosomal mechanisms.     

Molecular phylogenetic investigations of the Viviparidae (Gastropoda: Caenogastropoda) in the lakes of the Rift Valley area of Africa

The freshwater gastropod family Viviparidae is nearly cosmopolitan, but absent from South America. On the African continent, two genera are recognized; the widespread Bellamya and the monotypic Neothauma, which is confined to Lake Tanganyika. Most of the African Bellamya species are confined to the major lakes of the Rift Valley area in Africa, i.e. Lake Albert, Lake Malawi, Lake Mweru, and Lake Victoria. The phylogenetic analyses of mitochondrial (COI and 16S) and nuclear (H3, 18S and 28S) DNA inferred three major lake-clades; i.e. Lake Victoria/Kyoga/Albert, Lake Malawi and Lake Mweru/Bangweulu. The endemic B. rubicunda from Lake Albert and B. unicolor from Lake Kyoga were inferred to be part of the Lake Victoria clade. Bellamya capillata as identified by shell characters was polyphyletic in gene trees. The monophyletic Bellamya species radiation in Lake Malawi was most nearly related to the Lake Victoria/Kyoga/Albert-clade. Taxa from the Zambian lakes, Mweru and Bangweulu, were inferred together and placed ancestral to the other lakes. Neothauma tanganyicense was inferred as the sister-group to the Zambian Bellamya. Within the lake-clades the endemic radiations show very low genetic diversities (0–4.1% in COI), suggesting much faster morphological divergence than molecular divergence. Alternatively, Bellamya in Africa constitutes only a few species with several sub-species or eco-phenotypic morphs. The African viviparids were inferred to be the sister-group to a clade comprising Asian species, and the relatively low genetic diversity between the clades (12.6–15.5% in COI) makes a recent Miocene dispersal event from Asia to Africa much more likely than an ancient Gondwana vicarience distribution.     

A comprehensive molecular phylogeny of the starlings (Aves: Sturnidae) and mockingbirds (Aves: Mimidae): congruent mtDNA and nuclear trees for a cosmopolitan avian radiation

We generated a comprehensive phylogeny for the avian families Sturnidae (starlings, mynas, Rhabdornis, oxpeckers, and allies) and Mimidae (mockingbirds, thrashers, and allies) to explore patterns of morphological and behavioral diversification. Reconstructions were based on mitochondrial DNA sequences from five coding genes (4108 bp), and nuclear intron sequences from four loci (2974 bp), for most taxa, supplemented with NDII gene sequences (1041 bp) derived from museum skin specimens from additional taxa; together the 117 sampled taxa comprise 78% of the 151 species in these families and include representatives of all currently or recently recognized genera. Phylogenetic analyses consistently identified nine major clades. The basal lineage is comprised of the two Buphagus oxpeckers, which are presently confined to Africa where they are obligately associated with large mammals. Some species in nearly all of the other major clades also feed on or around large vertebrates, and this association may be an ancestral trait that fostered the world-wide dispersal of this group. The remaining taxa divide into sister clades representing the New-World Mimidae and Old-World Sturnidae. The Mimidae are divided into two subclades, a group of Central American and West Indian catbirds and thrashers, and a pan-American clade of mockingbirds and thrashers. The Sturnidae are subdivided into six clades. The Phillipine endemic Rhabdornis are the sister lineage to a larger and substantially more recent radiation of South Asian and Pacific island starlings and mynas. A clade of largely migratory or nomadic Eurasian starlings (within which the basal lineage is the model taxon Sturnus vulgaris) is allied to three groups of largely African species. These reconstructions confirm that Buphagus should not be included in the Sturnidae, and identify many genera that are not monophyletic. They also highlight the substantial diversity among the major Sturnidae subclades in rates of species accumulation, morphological differentiation, and behavioral variation.     

Evolution and biogeography of Alectryon (Sapindaceae).

Phylogenetic analysis of nucleotide sequences from four plastid loci (matK, partial trnK-matK introns, rps16 intron) and one nuclear locus (the internal transcribed spacer of rDNA; ITS-1) was conducted for 14 species of Alectryon and five related genera in Sapindaceae. Both matK and rps16 intron provide few informative characters within Alectryon, whereas ITS-1 provides the largest number of parsimony-informative characters and has the greatest sequence divergence between taxa. Support for branches in cladograms produced in PAUP increased markedly upon inclusion of ITS-1 data to matK and rps16 intron data. Analyses of each region alone or combined produced congruent results, suggesting that the regions are complementary. Phylogenetic analysis indicates that there are two main lineages within Alectryon, with A. subcinereus sister to the remaining sampled Alectryon taxa. Two morphological characters, presence/absence of petals and aril patterning, are congruent with the molecular phylogeny. One robustly supported clade is characterized by smooth arils and petals, in contrast to the taxa in the other major clade which have patterned arils and an absence of petals. These analyses also support a number of revised subgeneric groupings for Alectryon. The decision to submerge Heterodendrum in Alectryon is supported, although taxa belonging to Heterodendrum do not form a clade. The majority of the Australian Alectryon appear to belong to the tropical monsoonal/arid flora with species from both lineages being found in representative vine thickets across northern Australia. It appears that the seasonally dry rainforest communities comprise a number of elements that do not share common evolutionary histories within this genus.     

A new view of insect-crustacean relationships II. Inferences from expressed sequence tags and comparisons with neural cladistics

The enormous diversity of Arthropoda has complicated attempts by systematists to deduce the history of this group in terms of phylogenetic relationships and phenotypic change. Traditional hypotheses regarding the relationships of the major arthropod groups (Chelicerata, Myriapoda, Crustacea, and Hexapoda) focus on suites of morphological characters, whereas phylogenomics relies on large amounts of molecular sequence data to infer evolutionary relationships. The present discussion is based on expressed sequence tags (ESTs) that provide large numbers of short molecular sequences and so provide an abundant source of sequence data for phylogenetic inference. This study presents well-supported phylogenies of diverse arthropod and metazoan outgroup taxa obtained from publicly-available databases. An in-house bioinformatics pipeline has been used to compile and align conserved orthologs from each taxon for maximum likelihood inferences. This approach resolves many currently accepted hypotheses regarding internal relationships between the major groups of Arthropoda, including monophyletic Hexapoda, Tetraconata (Crustacea + Hexapoda), Myriapoda, and Chelicerata sensu lato (Pycnogonida + Euchelicerata). "Crustacea" is a paraphyletic group with some taxa more closely related to the monophyletic Hexapoda. These results support studies that have utilized more restricted EST data for phylogenetic inference, yet they differ in important regards from recently published phylogenies employing nuclear protein-coding sequences. The present results do not, however, depart from other phylogenies that resolve Branchiopoda as the crustacean sister group of Hexapoda. Like other molecular phylogenies, EST-derived phylogenies alone are unable to resolve morphological convergences or evolved reversals and thus omit what may be crucial events in the history of life. For example, molecular data are unable to resolve whether a Hexapod-Branchiopod sister relationship infers a branchiopod-like ancestry of the Hexapoda, or whether this assemblage originates from a malacostracan-like ancestor, with the morphologically simpler Branchiopoda being highly derived. Whereas this study supports many internal arthropod relationships obtained by other sources of molecular data, other approaches are required to resolve such evolutionary scenarios. The approach presented here turns out to be essential: integrating results of molecular phylogenetics and neural cladistics to infer that Branchiopoda evolved simplification from a more elaborate ancestor. Whereas the phenomenon of evolved simplification may be widespread, it is largely invisible to molecular techniques unless these are performed in conjunction with morphology-based strategies.     

Phylogenetic inferences in Antennaria (Asteraceae: Gnaphalieae: Cassiniinae) based on sequences from Nuclear Ribosomal DNA internal transcribed spacers (ITS)

The phylogenetic relationships among sexually reproducing species of Antennaria (Asteraceae) are poorly understood. An earlier cladistic analysis based on morphology did not fully resolve the phylogeny of these taxa and therefore a different approach using molecular data was explored. The internal transcribed spacer regions (ITS-1 and ITS-2) of nuclear ribosomal DNA were sequenced for 30 species of Antennaria and one species from each of the outgroup genera Anaphalis, Ewartia, Leontopodium, and Pseudognaphalium. The ITS-1 sequence in Antennaria ranged from 253 to 260 base pairs (bp) in length, and the proportion of nucleotide differences between pairs of species of Antennaria ranged from 1 to 14%. For ITS-2, the divergence between pairs of species of Antennaria ranged from 0 to 8%. ITS-2 is shorter than ITS-1, ranging from 213 to 219 bp. Phylogenetic analysis indicates that, relative to the outgroups included, Antennaria is a well-supported monophyletic group. Based on the genera surveyed, Leontopodium appears to be the sister genus of Antennaria. The general topology of the molecular trees agrees with that based on previous morphological analyses and indicates that Antennaria is composed of six clades of equal rank, corresponding to the traditionally recognized informal groups, the Geyeriae, Argenteae, Arcuatae, Dimorphae, Pulcherrimae, and Catipes. Sequence and morphological data indicate that the Alpinae and Dioicae are unnatural, polyphyletic units that should be abandoned and redefined as the monophyletic Catipes group. Phylogenetic analysis of ITS sequences also suggests the dissociation of A. stenophylla from the Dimorphae, where it is traditionally placed, and its affiliation with the Argenteae, as well as the placement of A. arcuata in its own group.     

Molecular phylogeny of Trichomonadidae family inferred from ITS-1, 5.8S rRNA and ITS-2 sequences

The Trichomonads have been the subject of several molecular studies that reported some discrepancies both at the lower and higher taxonomic levels. The purpose of this study was to make an extensive phylogenetic analysis of the Trichomonadidae using ITS-1/5.8S/ITS-2 sequences, to better understand its phylogeny and the usefulness of this marker. ITS-1/5.8S/ITS-2 sequences of 36 strains from 14 species belonging to Trichomonadidae and Monocercomonadidae were analysed, in which 20 were newly determined. Maximum likelihood, maximum parsimony, neighbour joining, and Bayesian phylogenetic methods were employed in order to reconstruct and compare the evolutionary history of this group. Tetratrichomonas gallinarum and four strains of Tetratrichomonas sp. isolated from bull genital organs were found closely related, confirming the classification of the latter, probably as a new species. The monophyly of Tritrichomonadinae and Trichomonadinae subfamilies were corroborated, with the exclusion of Trichomitus batrachorum from the latter since it grouped consistently with Hypotrichomonas acosta. Tritrichomonas foetus, Tritrichomonas suis and potentially also Tritrichomonas mobilensis seemed to correspond to the same species. Monocercomonas sp. and Ditrichomonas honigbergii emerged as independent lineages, with their phylogenetic positions undetermined. Neither Trichomonadidae nor Monocercomonadidae were supported as monophyletic groups. The ITS-1/5.8S/ITS-2 seems to be a reliable locus for phylogenetic studies in the Trichomonadida, mainly at lower taxonomic levels, and at least up to the family level.