A multigenic perspective on phylogenetic relationships in the largest family of salamanders, the Plethodontidae

Despite several recent studies, the phylogeny of plethodontid salamanders is not yet fully resolved and the phylogenetic positions of several key genera, especially Aneides, Hemidactylium, Hydromantes and Karsenia, are contentious. Here we present a combined dataset of complete mitochondrial genomes and three nuclear loci for 20 species (16 genera) of plethodontids, representing all major clades in the family. The combined dataset without mitochondrial third codon positions provides a fully resolved, statistically well-supported tree. In this topology two major clades are recovered. A northern clade includes Aneides, Desmognathus, Ensatina, Hydromantes, Karsenia, Phaeognathus and Plethodon, with Plethodon being the sister taxon to the rest of the clade. Hydromantes and Karsenia are sister taxa, and Aneides is recovered as the sister taxon to Ensatina. Desmognathus+Phaeognathus form the sister taxon to Aneides+Ensatina. An eastern/southern clade comprises two subclades. One subclade, the spelerpines (Eurycea, Gyrinophilus, Pseudotriton, Stereochilus, Urspelerpes) is the sister taxon to a subclade comprising Hemidactylium, Batrachoseps and the tropical plethodontids (represented by Bolitoglossa, Nototriton and Thorius). In this topology Hemidactylium is well-supported as the sister taxon to Batrachoseps. Only when mitochondrial third codon positions are included using maximum likelihood analysis is Hemidactylium recovered as the sister taxon to Batrachoseps+tropical genera. Hypothesis testing of alternative topologies supports these conclusions. On the basis of these results we propose a conservative taxonomy for Plethodontidae.     

Phylogenetics of paniceae (poaceae)

Paniceae demonstrate unique variability of photosynthetic physiology and anatomy, including both non-Kranz and Kranz species and all subtypes of the latter. This variability suggests hypotheses of independent origin or reversals (e.g., from C(4) to C(3)). These hypotheses can be tested by phylogenetic analysis of independent molecular characters. The molecular phylogeny of 57 species of Paniceae was explored using sequences from the grass-specific insert found in the plastid locus rpoC2. Phylogenetic analyses confirmed some long-recognized alliances in Paniceae, some recent molecular phylogenetic results, and suggested new relationships. Broadly, Paniceae were found to be paraphyletic with Andropogoneae, Panicum was found to be polyphyletic, and Oplismenus hirtellus was resolved as the sister group to the remaining ingroup species. A particularly well-supported clade in the rpoC2 tree included four genera with non-Kranz species and three with distinctively keeled paleas. As previously suggested, the PCK (phosphoenol pyruvate carboxykinase) C(4) subtype arose once within Paniceae. All clades with non-Kranz species had Kranz ancestors or sister taxa suggesting repeated loss of the Kranz syndrome.     

Phylogeny of Oriental voles (Rodentia: Muridae: Arvicolinae): molecular and morphological evidence

The systematics of Oriental voles remains controversial despite numerous previous studies. In this study, we explore the systematics of all species of Oriental voles, except Eothenomys wardi, using a combination of DNA sequences and morphological data. Our molecular phylogeny, based on two mitochondrial genes (COI and cyt b), resolves the Oriental voles as a monophyletic group with strong support. Four distinct lineages are resolved: Eothenomys, Anteliomys, Caryomys, and the new subgenus Ermites. Based on morphology, we consider Caryomys and Eothenomys to be valid genera. Eothenomys, Anteliomys, and Ermites are subgenera of Eothenomys. The molecular phylogeny resolves subgenera Anteliomys and Ermites as sister taxa. Subgenus Eothenomys is sister to the clade Anteliomys + Ermites. Caryomys is the sister group to genus Eothenomys. Further, the subspecies E. custos hintoni and E. chinensis tarquinius do not cluster with E. custos custos and E. chinensis chinensis, respectively, and the former two taxa are elevated to species level and assigned to the new subgenus Ermites.     

Higher level phylogeny for the passion-vine butterflies (Nymphalidae, Heliconiinae) based on early stage and adult morphology

A higher level phylogeny for the passion-vine butterflies (Nymphalidae, Heliconiinae) was generated by cladistic analysis of 146 morphological characters from all life stages. The 24 species studied were selected representatives of the ten currently accepted genera of the sub-tribe Heliconiiti. Analyses of only characters from larvae and pupae did not produce well resolved trees. However, some characters of the immature stages provided critical support for the monophyly of two clades. Analysis of only adult characters yielded a tree that closely resembled that obtained from all data combined. The phylogeny here derived from the combined analysis of early stage and adult characters differed in topology from all previously proposed hypotheses, and supported the monophyly of all currently recognized genera. Characters supporting each clade are described and illustrated, and various hypotheses of phylogenetic relatedness of passion-vine butterfly taxa are discussed.     

Starting to unravel the toxoglossan knot: molecular phylogeny of the "turrids" (Neogastropoda: Conoidea)

The superfamily Conoidea is one of the most speciose groups of marine mollusks, with estimates of about 340 recent valid genera and subgenera, and 4000 named living species. Previous classifications were based on shell and anatomical characters, and clades and phylogenetic relationships are far from well assessed. Based on a dataset of ca. 100 terminal taxa belonging to 57 genera, information provided by fragments of one mitochondrial (COI) and three nuclear (28S, 18S and H3) genes is used to infer the first molecular phylogeny of this group. Analyses are performed on each gene independently as well as for a data matrix where all genes are concatenated, using Maximum Likelihood, Maximum Parsimony and Bayesian approaches. Several well-supported clades are defined and are only partly identifiable to currently recognized families and subfamilies. The nested sampling used in our study allows a discussion of the classification at various taxonomical levels, and several genera, subfamilies and families are found polyphyletic.     

Phylogeny of the Drosophila saltans species group based on combined analysis of nuclear and mitochondrial DNA sequences

Nucleotide sequences from two nuclear loci, alcohol dehydrogenase and internal transcribed spacer-1 of the nuclear ribosomal DNA repeats, and two mitochondrial genes, cytochrome oxidase I and cytochrome oxidase II, were determined from nine species in the Drosophila saltans species group. The partition homogeneity test and partitioned Bremer support were used to measure incongruence between phylogenetic hypotheses generated from individual partitions. Individual loci were generally congruent with each other and consistent with the previously proposed morphological hypothesis, although they differed in level of resolution. Since extreme conflict between partitions did not exist, the data were combined and analyzed simultaneously. The total evidence method gave a more resolved and highly supported phylogeny, as indicated by bootstrap proportions and decay indices, than did any of the individual analyses. The cordata and elliptica subgroups, considered to have diverged early in the history of the D. saltans group, were sister taxa to the remainder of the saltans group. The sturtevanti subgroup, represented by D. milleri and D. sturtevanti, occupies an intermediate position in this phylogeny. The saltans and parasaltans subgroups are sister clades and occupy the most recently derived portion of the phylogeny. As with previous morphological studies, phylogenetic relationships within the saltans subgroup were not satisfactorily resolved by the molecular data.      

Phylogenetic relationships and divergence times of Charadriiformes genera: multigene evidence for the Cretaceous origin of at least 14 clades of shorebirds

Comparative study of character evolution in the shorebirds is presently limited because the phylogenetic placement of some enigmatic genera remains unclear. We therefore used Bayesian methods to obtain a well-supported phylogeny of 90 recognized genera using 5 kb of mitochondrial and nuclear sequences. The tree comprised three major clades: Lari (gulls, auks and allies plus buttonquails) as sister to Scolopaci (sandpipers, jacanas and allies), and in turn sister to Charadrii (plovers, oystercatchers and allies), as in previous molecular studies. Plovers and noddies were not recovered as monophyletic assemblages, and the Egyptian plover Pluvianus is apparently not a plover. Molecular dating using multiple fossil constraints suggests that the three suborders originated in the late Cretaceous between 79 and 102 Mya, and at least 14 lineages of modern shorebirds survived the mass extinction at the K/T boundary. Previous difficulties in determining the phylogenetic relationships of enigmatic taxa reflect the fact that they are well-differentiated relicts of old, genus-poor lineages. We refrain from suggesting systematic revisions for shorebirds at this time because gene trees may fail to recover the species tree when long branches are connected to deep, shorter branches, as is the case for some of the enigmatic taxa.     

Phylogeny of Cyperaceae Based on DNA Sequence Data: Current Progress and Future Prospects

In the last decade, efforts to reconstruct suprageneric phylogeny of the Cyperaceae have intensified. We present an analysis of 262 taxa representing 93 genera in 15 tribes, sequenced for the plastid rbcL and trnL-F (intron and intergenic spacer). Cyperaceae are monophyletic and resolved into two clades, here recognised as Mapanioideae and Cyperoideae, and the overall topology is similar to results from previous studies. Within Cyperoideae, Trilepideae are sister to rest of taxa whereas Cryptangieae, Bisboeckelerieae and Sclerieae are resolved within Schoeneae. Cladium and Rhynchospora (and Pleurostachys) are resolved into clades sister to the rest of Schoeneae, lending support to the recognition of these taxa in separate tribes. However, we retain these taxa in Schoeneae pending broader sampling of the group. The phylogenetic position of 40 species in 21 genera is presented in this study for the first time, elucidating their position in Abildgaardieae (Trachystylis), Cryptangieae (Didymiandrum, Exochogyne), Cypereae (Androtrichum, Volkiella), Eleocharideae (Chillania), and Schoeneae (Calyptrocarya, Morelotia). More sampling effort (more taxa and the use of more rapidly evolving markers) is needed to resolve relationships in Fuireneae and Schoeneae.     

Molecular phylogeny of new world primates (Platyrrhini) based on beta2-microglobulin DNA sequences

Neotropical primates, traditionally grouped in the infraorder Platyrrhini, comprise 16 extant genera. Cladistic analyses based on morphological characteristics and molecular data resulted in topologic arrangements depicting disparate phylogenetic relationships, indicating that the evolution of gross morphological characteristics and molecular traits is not necessarily congruent. Here we present a phylogenetic arrangement for all neotropical primate genera obtained from DNA sequence analyses of the beta2-microglobulin gene. Parsimony, distance, and maximum likelihood analyses favored two families, Atelidae and Cebidae, each containing 8 genera. Atelids were resolved into atelines and pitheciines. The well-supported ateline clade branched into alouattine (Alouatta) and ateline (Ateles, Lagothrix, Brachyteles) clades. In turn, within the Ateline clade, Lagothrix and Brachyteles were well-supported sister groups. The pitheciines branched into well-supported callicebine (Callicebus) and pitheciine (Pithecia, Cacajao, Chiropotes) clades. In turn, within the pitheciine clade, Cacajao and Chiropotes were well-supported sister groups. The cebids branched into callitrichine (Saguinus, Leontopithecus, Callimico, Callithrix-Cebuella), cebine (Cebus, Saimiri), and aotine (Aotus) clades. While the callitrichine clade and the groupings of species and genera within this clade were all well supported, the cebine clade received only modest support, and the position of Aotus could not be clearly established. Cladistic analyses favored the proposition of 15 rather than 16 extant genera by including Cebuella pygmaea in the genus Callithrix as the sister group of the Callithrix argentata species group. These analyses also favored the sister grouping of Callimico with Callithrix and then of Leontopithecus with the Callithrix-Callimico clade.     

Toward understanding Anophelinae (Diptera,Culicidae) phylogeny: insights from nuclear single-copy genes and the weight of evidence

A phylogeny of the mosquito subfamily Anophelinae was inferred from fragments of two protein-coding nuclear genes, G6pd (462 bp) and white (801 bp), and from a combined data set (2,136 bp) that included a portion of the mitochondrial gene ND5 and the D2 region of the ribosomal 28S gene. Sixteen species from all three anopheline genera and six Anopheles subgenera were sampled, along with six species of other mosquitoes used as an outgroup. Each of four genes analyzed individually recovered the same well-supported clades; topological incongruence was limited to unsupported or poorly supported nodes. As assessed by the incongruence length difference test, most of the conflicting signal was contributed by third codon positions. Strong structural constraints, as observed in white and G6pd, apparently had little impact on phylogenetic inference. Compared with the other genes, white provided a superior source of phylogenetic information. However, white appears to have experienced accelerated rates of evolution in few lineages, the affinities of which are therefore suspect. In combined analyses, most of the inferred relationship were well-supported and in agreement with previous studies: monophyly of Anophelinae, basal position of Chagasia, monophyly of Anopheles subgenera, and subgenera Nyssorhynchus + Kerteszia as sister taxa. The results suggested also monophyletic origin of subgenera Cellia + Anopheles, and the white gene analysis supported genus Bironella as a sister taxon to Anopheles. The present data and other available evidence suggest a South American origin of Anophelinae, probably in the Mesozoic; a rapid diversification of Bironella and basal subgeneric lineages of Anopheles, potentially associated with the breakup of Gondwanaland; and a relatively recent and rapid dispersion of subgenus Anopheles.     

Molecular phylogenetics of Prescottiinae s.l. and their close allies (Orchidaceae, Cranichideae) inferred from plastid and nuclear ribosomal DNA sequences

The Andes are a cradle of orchid evolution, but most phylogenetic studies of Orchidaceae in this biodiversity hotspot have dealt with epiphytic epidendroid lineages. Here we present a study on neotropical, terrestrial, orchidoid taxa of Prescottiinae s.l. (8 genera, ～100 species), which are adapted to some of the highest elevation habitats on earth that support orchids. They are currently included within an expanded concept of Cranichidinae in the tribe Cranichideae, but DNA sequence data show that neither Prescottiinae s.l. nor Cranichidinae s.s. are monophyletic. Prescottiinae s.l. consist of two strongly supported lineages: the Altensteinia and Prescottia clades, which have closer affinities to Spiranthinae than to Cranichidinae. The Prescottia clade comprises two well-supported subclades, one including most sampled species of Prescottia and a second one with Pseudocranichis thysanochila sister to Prescottia tubulosa. As a group, they are sister to Spiranthinae. Sister to this pair is the Altensteinia clade comprised of six genera, whose intergeneric relationships are well resolved. Finally, Cranichidinae s.s. is sister to all three of these clades. Morphological and ecological features distinguishing the major groups are discussed, as are potential synapomorphies to define them. The reconstructed phylogeny indicates that the classification of Cranichideae needs to be reexamined.     

Phylogeny of Coreopsideae (Asteraceae) using ITS sequences suggests lability in reproductive characters

Relationships among the 21 genera within the tribe Coreopsideae (Asteraceae) remain poorly resolved despite phylogenetic studies using morphological and anatomical traits. Recent molecular phylogenies have also indicated that some Coreopsideae genera are not monophyletic. We used internal transcribed spacer (ITS) sequences from representatives of 19 genera, as well as all major lineages in those genera that are not monophyletic, to examine phylogenetic relationships within this group. To examine the affects of alignment and method of analysis on our conclusions, we obtained alignments using five different parameters and analyzed all five alignments with distance, parsimony, and Bayesian methods. The method of analysis had a larger impact on relationships than did alignments, although different analytical methods gave very similar results. Although not all relationships could be resolved, a number of well-supported lineages were found, some in conflict with earlier hypotheses. We did not find monophyly in Bidens, Coreopsis, and Coreocarpus, though other genera were monophyletic for the taxa we included. Morphological and anatomical traits which have been used previously to resolve phylogenetic relationships in this group were mapped onto the well-supported nodes of the ITS phylogeny. This analysis indicated that floral and fruit characters, which have been used extensively in phylogenetic studies in the Coreopsideae, show a higher degree of evolutionary lability in this group than the more highly conserved vegetative and photosynthetic traits.     

Molecular and morphological phylogeny of Diplazontinae (Hymenoptera,Ichneumonidae)

Klopfstein, S., Quicke, D. L. J., Kropf, C. & Frick, H. (2011) Molecular and morphological phylogeny of Diplazontinae (Hymenoptera, Ichneumonidae). —Zoologica Scripta, 40, 379–402. Parasitoid wasps are among the most species rich and at the same time most understudied of all metazoan taxa. To understand their diversification and test hypotheses about their evolution, we need robust phylogenetic hypotheses. Here, we reconstruct the phylogeny of the subfamily Diplazontinae using four genes and 66 morphological characters both in separate analyses and in a total evidence approach. The resulting phylogeny is highly resolved, with most clades supported by multiple independent data partitions. It contains three highly supported genus groups, for which we suggest morphological and behavioural synapomorphies. The placement of some of the genera, especially Xestopelta Dasch, is unexpected, but also supported by morphology. Most of the genera are retrieved as monophyletic, with the exception of the morphologically diverse genus Syrphoctonus Förster. We split this genus into three genera, including Fossatyloides gen. n., to restore the phylogeny–classification link. Conflict between the morphological and the molecular topology was mostly resolved in favour of the molecular partition in the total evidence approach. We discuss reasons for this finding, and suggest strategies for future taxon and character sampling in Diplazontinae.     

Combined nuclear and mitochondrial DNA sequences resolve generic relationships within the Cracidae (Galliformes,Aves)

The Cracidae is one of the most endangered and distinctive bird families in the Neotropics, yet the higher relationships among taxa remain uncertain. The molecular phylogeny of its 11 genera was inferred using 10,678 analyzable sites (5,412 from seven different mitochondrial segments and 5,266 sites from four nuclear genes). We performed combinability tests to check conflicts in phylogenetic signals of separate genes and genomes. Phylogenetic analysis showed that the unrooted tree of ((curassows, horned guan) (guans, chachalacas)) was favored by most data partitions and that different data partitions provided support for different parts of the tree. In particular, the concatenated mitochondrial DNA (mtDNA) genes resolved shallower nodes, whereas the combined nuclear sequences resolved the basal connections among the major clades of curassows, horned guan, chachalacas, and guans. Therefore, we decided that for the Cracidae all data should be combined for phylogenetic analysis. Maximum parsimony (MP), maximum likelihood (ML), and Bayesian analyses of this large data set produced similar trees. The MP tree indicated that guans are the sister group to (horned guan, (curassows, chachalacas)), whereas the ML and Bayesian analysis recovered a tree where the horned guan is a sister clade to curassows, and these two clades had the chachalacas as a sister group. Parametric bootstrapping showed that alternative trees previously proposed for the cracid genera are significantly less likely than our estimate of their relationships. A likelihood ratio test of the hypothesis of a molecular clock for cracid mtDNA sequences using the optimal ML topology did not reject rate constancy of substitutions through time. We estimated cracids to have originated between 64 and 90 million years ago (MYA), with a mean estimate of 76 MYA. Diversification of the genera occurred approximately 41-3 MYA, corresponding with periods of global climate change and other Earth history events that likely promoted divergences of higher level taxa.     

African Dacus (Diptera: Tephritidae: Molecular data and host plant associations do not corroborate morphology based classifications

The genus Dacus Fabricius includes economically important pest fruit flies distributed in the Afrotropical and Indo-Australian regions. Two recent revisions based on morphological characters proposed new and partially discordant classifications synonymizing/revalidating several subgeneric names and forming species groups. Regardless these efforts, the phylogenetic relationships among Dacus species remained largely unresolved mainly because of the difficulties in assigning homologous character states. Therefore we investigated the phylogeny of African Dacus by sequencing 71 representatives of 32 species at two mitochondrial (COI, 16S) and one nuclear (period) gene fragments. Phylogenetic relationships were inferred through Bayesian and Maximum Parsimony methods and hypotheses about the monophyly of Dacus subgenera were tested by Shimodaira–Hasegawa tests. The congruence tests and the analyses of the single gene fragments revealed that the nuclear gene supports similar conclusions as the two mitochondrial genes. Levels of intra- and inter-specific differentiation of Dacus species were highly variable and, in some cases, largely overlapping. The analyses of the concatenated dataset resolved two major bootstrap-supported groups as well as a number of well-supported clades and subclades that often comprised representatives of different subgenera. Additionally, specimens of Dacus humeralis from Eastern and Western African localities formed separate clades, suggesting cryptic differentiation within this taxon. The comparisons between the molecular phylogeny and the morphological classification revealed a number of discrepancies and, in the vast majority of cases, the molecular data were not compatible with the monophyly of the currently recognised subgenera. Conversely, the molecular data showed that Apocynaceae feeders are a monophyletic sister group of species feeding on both Cucurbitaceae and Passifloraceae (these latter being also monophyletic). These results show a clear association between the molecular phylogeny of African Dacus and the evolution of host plant choice and provide a basis towards a more congruent taxonomy of this genus.     

Cladistic Analysis of A Problematic Ammonite Group: the Hamitidae (Cretaceous, Albian–turonian) and Proposals for New Cladistic Terms

The Hamitidae are a family of mid–Cretaceous heteromorph ammonites including lineages leading to four other families. Problems are outlined in trying to describe the phylogeny of completely extinct groups such as these heteromorph ammonites using the existing cladistic terminology, which is largely concerned with extant taxa and their ancestors. To solve these problems, two new terms are proposed: †crown groups and †stem groups, which are equivalent to crown and stem groups in terms of the evolutionary history of a clade, but are not defined on the basis of extant taxa. Instead they are defined by the topology of the phylogenetic tree, the †crown group being a clade defined by synapomorphies but which gave rise to no descendants. A †stem group is a branch of a phylogenetic tree which comprises the immediate sister groups of a given †crown group but is not itself a clade. Examples of these terms are described here with reference to the phylogeny of the Hamitidae and their descendants. The Hamitidae are paraphyletic and form †stem groups to a number of †crown groups, namely the Anisoceratidae, Baculitidae, Scaphitidae, and Turrilitidae. The definitions of the genera and subgenera are refined with respect to the type species and the clades within which they occur, and four new genera are described: Eohamites , Helicohamites , Sziveshamites , and Planohamites .     

Molecular phylogeny of gill monogeneans (Platyhelminthes, Monogenea, Dactylogyridae) and colonization of Indo-West Pacific butterflyfish hosts (Perciformes, Chaetodontidae)

We investigated the phylogenetic relationships among monogenean parasites of the Chaetodontidae (butterflyfishes) from the Indo-West Pacific Ocean. Molecular phylogenies of selected taxa within the Dactylogyridae, including the ancyrocephaline parasites of butterflyfishes, based on two nuclear and one mitochondrial gene fragments (complete 18S rDNA, partial 28S rDNA (D1-D3), and partial 16S rDNA) were reconstructed using parsimony, maximum likelihood and Bayesian inference methods. Our results show the non-monophyletic nature of the monogenean fauna of butterflyfishes. The group is divided into two independent lineages. The first clade contains species of the genera Aliatrema and Euryhaliotrematoides , which parasitize Chaetodontidae exclusively. The second contains species of Haliotrema , a generalist group of parasites. The positions of several other species of the Ancyrocephalinae, including freshwater species, at the base of the two clades, provide strong evidence that the monogenean fauna did not result from a single colonization event, but rather that they have colonized their butterflyfish hosts independently at least twice.     

Molecular phylogenetics of the bee-eaters (Aves: Meropidae) based on nuclear and mitochondrial DNA sequence data

The bee-eaters (family Meropidae) comprise a group of brightly colored, but morphologically homogeneous, birds with a wide variety of life history characteristics. A phylogeny of bee-eaters was reconstructed using nuclear and mitochondrial DNA sequence data from 23 of the 25 named bee-eater species. Analysis of the combined data set provided a well-supported phylogenetic hypothesis for the family. Nyctiornis is the sister taxon to all other bee-eaters. Within the genus Merops, we recovered two well-supported clades that can be broadly separated into two groups along geographic and ecological lines, one clade with mostly African resident species and the other clade containing a mixture of African and Asian taxa that are mostly migratory species. The clade containing resident African species can be further split into two groups along ecological lines by habitat preference into lowland forest specialists and montane forest and forest edge species. Intraspecific sampling in several of the taxa revealed moderate to high (3.7-6.5%, ND2) levels of divergence in the resident taxa, whereas the lone migratory taxon showed negligible levels of intraspecific divergence. This robust molecular phylogeny provides the phylogenetic framework for future comparative tests of hypotheses about the evolution of plumage patterns, sociality, migration, and delayed breeding strategies.