A large‐scale molecular phylogeny of flesh flies (Diptera: Sarcophagidae)

The available data for Sarcophagidae in GenBank were analysed in order to reconstruct the most comprehensive phylogeny to date. GenBank was explored for nine markers that are commonly used in various molecular and phylogenetic studies of flesh flies. We obtained data for 187 species and constructed an aligned dataset with 9241 characters. However, the matrix suffered from 74% missing data due to a low number of sequences for some markers and in most of the cases only short fragments of the analysed genes were available. The reconstructed tree was taxonomically biased towards the subfamilies Paramacronychiinae (12% of the described species) and Sarcophaginae (8.6% of the described species) and specifically the genus Sarcophaga. The third subfamily Miltogramminae was represented by only 0.7% of described species. Moreover, about half of the included species were of forensic importance, while the percentage of such species in the entire family was estimated at 7%. Many nodes had very low support, so in order to increase the support and thereby identify a ‘core topology’, we pruned ‘rogue’ taxa and applied different substitution models. Both strategies improved support considerably, although some nodes still were left unresolved. An analysis of the distribution of bootstrap values across chronograms showed that the weakest phylogenetic signal is restricted to that part of the tree which coincides with the onset of rapid radiations mainly within the genus Sarcophaga. Our study is concordant with phylogenies obtained by other authors, with the most noteworthy exception being the subfamily Paramacronychiinae emerging as paraphyletic with regard to the Miltogramminae, which is in strong conflict with morphological evidence. We discuss the new findings in the light of traditional taxonomical classifications of Sarcophagidae and recent molecular studies.     

Molecular phylogeny and habitat diversification of the genus Farfugium (Asteraceae) based on nuclear rDNA and plastid DNA

Background and Aims

Farfugium (Asteraceae) is a small genus that contains the two species F. japonicum and F. hiberniflorum and is distributed along a long archipelago in east Asia. The common taxon, F. japonicum, includes three varieties associated with a wide range of habitats, including forest understorey (sciophytes), coastal crag (heliophytes) and riverbed (rheophytes). Leaf shape is an important taxonomic character within this genus and is associated with the habitat.

Methods

Twenty populations that included all Farfugium taxa were collected throughout its range. Leaf morphology was measured to determine differences amongst the taxa. Phylogenetic analyses based on sequences of the internal transcribed spacer of nuclear rDNA and four plastid DNA regions (matK, trnL-trnF, trnH-psbA and rpl20-rps12) were conducted separately.

Key Results

Leaf morphology was significantly different amongst taxa, but morphological variations were partly explained by adaptation to certain environmental conditions that each population inhabited. Molecular phylogenies for the nDNA internal transcribed spacer and cpDNA were consistent in classifying F. hiberniflorum and the Taiwanese var. formosanum, whilst suggesting polyphyletic origins for the rheophyte, sciophyte and heliophyte taxa. All samples from the southern Ryukyus (Japan) and Taiwan clustered into a monophyletic group, which corroborates the land configuration theory involving Quaternary land-bridge formation and subsequent fragmentation into islands. The incongruence between the two DNA datasets may imply traces of introgressive hybridization and/or incomplete lineage sorting.

Conclusions

The occurrence of rheophyte, sciophyte and heliophyte plants within Farfugium may be attributable to their isolation on islands and subsequent adaptation to the riparian, coastal crag and forest understorey environments, following their migration over the Quaternary land-bridge formation along their distribution range. Nearly identical DNA sequences coupled with highly divergent morphologies amongst these taxa suggest that diversification was rapid.     

Molecular phylogeny of the genus Vitis (Vitaceae) based on plastid markers

? Premise of the study: This work represents the first molecular phylogeny of the economically important genus Vitis, an important genetic resource for breeding in grapevine, Vitis vinifera. ? Methods: A molecular phylogeny of Vitis using a combined data set of three noncoding regions of the plastid DNA genome was constructed from 47 accessions covering 30 species of Vitis. The data for the trnL-F marker were combined with previously published data across the Vitaceae. ? Key results: The molecular phylogeny demonstrated monophyly of the genus Vitis. Based on the combined analysis of three genes, Vitis is split into three clades that mirror the continental distribution of these accessions. The diversity is highest in the Asian clade, but the general genetic distances across taxa from different continents are relatively small. ? Conclusions: The findings support a relatively recent and intense gene flow between East Asia and North America and the possible impact of hybridization on the evolution of the genus Vitis. Taxon identity in important stock collections should be screened carefully because roughly 10% of the accessions analyzed in the present study had been misidentified.     

A global plastid phylogeny of the fern genus Asplenium (Aspleniaceae)

The infrageneric relationships and taxonomy of the largest fern genus, Asplenium (Aspleniaceae), have remained poorly understood. Previous studies have focused mainly on specific species complexes involving a few or dozens of species only, or have achieved a large taxon sampling but only one plastid marker was used. In the present study, DNA sequences from six plastid markers (atpB, rbcL, rps4, rps4-trnS, trnL and trnL-F) of 1030 accessions (616 of them newly sequenced here) representing c. 420 species of Asplenium (60% of estimated species diversity), 16 species of Hymenasplenium, three Diplaziopsidaceae, and four Rhachidosoraceae were used to produce the largest genus-level phylogeny yet for ferns. Our major results include: (i) Asplenium as broadly circumscribed is monophyletic based on our inclusion of representatives of 32 of 38 named segregate genera; (ii) 11 major clades in Asplenium are identified, and their relationships are mostly well-resolved and strongly supported; (iii) numerous species, unsampled in previous studies, suggest new relationships and numerous cryptic species and species complexes in Asplenium; and (iv) the accrued molecular evidence provides an essential foundation for further investigations of complex patterns of geographical diversification, speciation and reticulate evolution in this family.     

A plastid DNA phylogeny of the genus Acacia Miller (Acacieae, Leguminoseae)

Past classifications of the tribe Acacieae Rchb. are outlined and the confusion concerning the relationships of the three subgenera of Acacia Mill. are highlighted. A plastid DNA analysis of Acacieae shows that the genus Acacia is not monophyletic. Furthermore subgenera Acacia Vassal and Aculeiferum Vassal are sister taxa and neither appear closely related to subgenus Phyllodineae (DC.) Ser. Subgenera Acacia and Aculeiferum form a clade that is basal to a well-supported clade consisting of tribe Ingeae Benth. taxa, Faidherbia albida (Del.) A. Chev. and subgenus Phyllodineae. The series of relationships suggested by the cpDNA data contradicts previous investigations of the tribe. Possible explanations of this conflict are explored, and the taxonomic implications of the plastid DNA data set are considered.     

A molecular phylogeny of the Canidae based on six nuclear loci

We have reconstructed the phylogenetic relationships of 23 species in the dog family, Canidae, using DNA sequence data from six nuclear loci. Individual gene trees were generated with maximum parsimony (MP) and maximum likelihood (ML) analysis. In general, these individual gene trees were not well resolved, but several identical groupings were supported by more than one locus. Phylogenetic analysis with a data set combining the six nuclear loci using MP, ML, and Bayesian approaches produced a more resolved tree that agreed with previously published mitochondrial trees in finding three well-defined clades, including the red fox-like canids, the South American foxes, and the wolf-like canids. In addition, the nuclear data set provides novel indel support for several previously inferred clades. Differences between trees derived from the nuclear data and those from the mitochondrial data include the grouping of the bush dog and maned wolf into a clade with the South American foxes, the grouping of the side-striped jackal (Canis adustus) and black-backed jackal (Canis mesomelas) and the grouping of the bat-eared fox (Otocyon megalotis) with the raccoon dog (Nycteruetes procyonoides). We also analyzed the combined nuclear + mitochondrial tree. Many nodes that were strongly supported in the nuclear tree or the mitochondrial tree remained strongly supported in the nuclear + mitochondrial tree. Relationships within the clades containing the red fox-like canids and South American canids are well resolved, whereas the relationships among the wolf-like canids remain largely undetermined. The lack of resolution within the wolf-like canids may be due to their recent divergence and insufficient time for the accumulation of phylogenetically informative signal.     

Historical biogeography of the ancient lycophyte genus Selaginella: early adaptation to xeric habitats on Pangea

The ancient and cosmopolitan lycophyte genus Selaginella has living representatives around the world, but their historical biogeography has not been assessed with modern methods. We estimated a time‐calibrated phylogeny using DNA marker regions rbcL and ITS1‐5.8S‐ITS2 from 200 species. Node density analyses revealed that Selaginellaceae has significantly older median and mean node ages than other putative “ancient” families. We used statistical model comparison to assess different biogeographical models on our dated tree, and to estimate ancestral ranges. These revealed that Selaginella originated on Euramerica around 383 Ma in the Devonian period, while its peak diversification began with the formation of Pangea. The divergence of the two main species‐rich Selaginella lineages occurred approximately 318 Ma on the supercontinent. The major divergences within these main lineages of Selaginella took place in the Late Permian and Early Triassic, along with lineages highly adapted for xeric habitats on Pangea.     

Combined phylogeny of ray‐finned fishes (Actinopterygii) and the use of morphological characters in large‐scale analyses

This study evaluates the phylogeny of ray‐finned fishes (Actinopterygii) combining most available information (44 markers from nuclear and mitochondrial DNA and 274 morphological characters). The molecular partition of the dataset was produced through a pipeline (GB‐to‐TNT) that allows the fast building of large matrices from GenBank format. The analysed dataset has 8104 species, including representatives of all orders and 95% of the 475 families of Actinopterygii, making it the most diverse phylogenetic dataset analysed to date for this clade of fishes. Analysed morphological characters are features historically considered diagnostic for families or orders, which can be unequivocally coded from the literature. Analyses are by parsimony under several weighting schemes. General results agree with previous classifications, especially for groups with better gene sampling and those long thought (from morphological evidence) to be monophyletic. Many clades have low support and some orders are not recovered as monophyletic. Additional data and synthetic studies of homology are needed to obtain synapomorphies and diagnoses for most clades.     

A molecular phylogeny of the genus Gammarus (Crustacea: Amphipoda) based on mitochondrial and nuclear gene sequences

A phylogeny of the genus Gammarus Fabricius, 1775 was constructed using DNA sequence data from the mitochondrial genes COI and 16S, and the nuclear genes 18S and 28S. Both parsimony and Bayesian analyses were conducted on separate and combined data partitions. The Bayesian phylogeny from the combined analysis was selected as the preferred phylogenetic hypothesis. The hypothesis supports monophyly of the genus Gammarus, paraphyly of the European-North American Gammarus, and monophyly of the Asian Gammarus. The Asian clade was further split into a southeastern group and a northwestern group. The dramatic climate change following the uplift of the Tibetan Plateau was probably the most important factor in triggering the diversification of southeastern and northwestern groups. The genus Sinogammarus is invalid and should be part of the genus Gammarus.     

Molecular phylogeny of the genus Mus (Rodentia: Murinae) based on mitochondrial and nuclear data

The genus Mus encompasses at least 38 species divided into four subgenera: Mus , Pyromys , Nannomys and Coelomys . The subgenus Mus , which comprises the house mouse and related species, is by far the most extensively studied, although the subgenus Nannomys is the most speciose. Although the relationships within the subgenus Mus are rather well characterized, those between subgenera are still unclear. In the present study, phylogenetic analyses of the whole genus were performed using a larger species sample of Nannomys than in previous studies, and a nuclear gene (IRBP) in addition to mitochondrial data (cytochrome b and 12S rRNA). Members of the Acomyinae and Murinae were used as outgroups. Separate and combined analyses were performed with maximum parsimony, maximum likelihood and Bayesian methods, and divergence times were estimated. The results showed that the monophyly of the genus Mus and of each subgenus was strongly supported by the three genes and the combined analysis. The phylogenies derived from the three genes were on the whole congruent; however, several conflicting topologies were observed such as the relationships between the three Asian species of the subgenus Mus ( caroli , cervicolor and cookii ). Increasing the taxonomic sampling of Nannomys did not satisfactorily improve the resolution of relationships between the four subgenera. In addition, molecular calibrations indicate that the Mus and Nannomys radiation coincided with major environmental changes.  © 2005 The Linnean Society of London, Biological Journal of the Linnean Society , 2005, 84 , 417–427.     

Molecular phylogeny of Old WorldTrifolium (Fabaceae), based on plastid and nuclear markers

Phylogenies of Old WorldTrifolium species were constructed using nucleotide sequence data of the internal transcribed spacers (ITS) of nuclear ribosomal DNA and chloroplast DNA restriction site data from PCR-amplified genes and genic regions (rbcL,trnK, andrpoC1–C2). Biogeography, morphological evolution, and the existing classification forTrifolium were examined. The genusTrifolium is strongly supported as monophyletic, however, only one small section (Chronosemium) is monophyletic, although the data are in conflict regarding its placement. The two largest sections of the genus, Sects.Lotoidea andTrifolium, are not supported as monophyletic, as currently circumscribed. Many members of Sect.Lotoidea are basal within the genus, supporting previously-proposed hypotheses concerning plesiomorphic morphological characters and a Mediterranean-Mideast biogeographic origin of the genus.     

Molecular phylogeny of Gavilea (Chloraeinae: Orchidaceae) using plastid and nuclear markers

A phylogenetic analysis is provided for 70% of the representatives of genus Gavilea, as well as for several species of the remaining genera of subtribe Chloraeinae: Bipinnula, Chloraea and Geoblasta. Sequences from the plastid markers rpoC1, matK-trnK and atpB-rbcL and the nuclear marker ITS, were analyzed using Maximum Parsimony and Bayesian Inference. Monophyly of subtribe Chloraeinae was confirmed, as well as its position inside tribe Cranichideae. Neither Chloraea nor Bipinnula were recovered as monophyletic. Gavilea turned out polyphyletic, with Chloraeachica embedded in the genus while Gavilea supralabellata was related to Chloraea and might be a hybrid between both genera. None of the two sections of Gavilea were monophyletic, and the topologies obtained do not suggest a new division of the genus.     

A preliminary phylogeny of the scale insects (Hemiptera: Sternorrhyncha: Coccoidea) based on nuclear small-subunit ribosomal DNA

Scale insects (Hemiptera: Sternorrhyncha: Coccoidea) are a speciose and morphologically specialized group of plant-feeding bugs in which evolutionary relationships and thus higher classification are controversial. Sequences derived from nuclear small-subunit ribosomal DNA were used to generate a preliminary molecular phylogeny for the Coccoidea based on 39 species representing 14 putative families. Monophyly of the archaeococcoids (comprising Ortheziidae, Margarodidae sensu lato, and Phenacoleachia) was equivocal, whereas monophyly of the neococcoids was supported. Putoidae, represented by Puto yuccae, was found to be outside the remainder of the neococcoid clade. These data are consistent with a single origin (in the ancestor of the neococcoid clade) of a chromosome system involving paternal genome elimination in males. Pseudococcidae (mealybugs) appear to be sister to the rest of the neococcoids and there are indications that Coccidae (soft scales) and Kerriidae (lac scales) are sister taxa. The Eriococcidae (felt scales) was not recovered as a monophyletic group and the eriococcid genus Eriococcus sensu lato was polyphyletic.     

A large‐scale molecular survey of Clinostomum (Digenea,Clinostomidae)

Members of the genus Clinostomum Leidy, 1856 are parasites that mature in birds, with occasional reports in humans. Because morphological characters for reliable discrimination of species are lacking, the number of species considered valid has varied by an order of magnitude. In this study, sequences from the DNA barcode region of cytochrome c oxidase I (CO1) and/or internal transcribed spacer (ITS) from specimens from Mexico, Bolivia, Peru, Brazil, Kenya, China and Thailand were analysed together with published sequences from Europe, Africa, Indonesia and North America. Although ITS and CO1 distances among specimens were strongly correlated, distance‐based analysis of each marker yielded different groups. Putative species indicated by CO1 distances were consistent with available morphological identifications, while those indicated by ITS conflicted with morphological identifications in three cases. There was little overlap in sequence variation within and between species, particularly for CO1. Although ITS and CO1 distances tended to increase in specimens that were further apart geographically, this did not impair distance‐based species delineation. Phylogenetic analysis suggests a deep division between clades of Clinostomum inhabiting the New World and Old World, which parallels the distribution of their principal definitive hosts, the Ardeidae.     

A phylogeny of Anisophylleaceae based on six nuclear and plastid loci: ancient disjunctions and recent dispersal between South America, Africa, and Asia

The Anisophylleaceae comprise 29-34 species of shrubs and trees occurring in lowland forests and swamps in tropical Africa, Asia, and South America. These species are placed in four genera with disjunct geographic distributions; Anisophyllea has 25-30 species in South America, Africa, and Malesia; Combretocarpus has one species in Sumatra and Borneo; Poga one species in equatorial Africa; and Polygonanthus two in the Amazon Basin. Here we use a phylogeny based on six nuclear and plastid loci sequenced for 15 species representing the four genera to infer their relationships and the relative and absolute ages of the range disjunctions. Combretocarpus is sister to the other three genera, and Polygonanthus then sister to Poga and Anisophyllea. Ansiophyllea, represented by 12 species from all three continents, is monophyletic. A relaxed Bayesian clock calibrated with the oldest fossils from a relevant outgroup, Tetramelaceae, suggests that the disjunctions between Combretocarpus, Poga, and Polygonanthus date back to the Cretaceous, Mid-, and Upper Eocene, whereas the intercontinental disjunctions within Anisophyllea appear to date back only some 22-23 million years and thus probably result from long-distance dispersal.     

New species of Selaginella (Selaginellaceae) from the Guayana Highland of Venezuela

Three new species of Selaginella are described from the Guayana Highland of Venezuela: S. cardiophylla, S. hemicardia and S. pruskiana. They are illustrated and the relationships of each are discussed. Another species, provisionally determined as S. terezoana, is reported for the first time from Guyana.     

Molecular phylogeny and historical biogeography of Caltha (Ranunculaceae) based on analyses of multiple nuclear and plastid sequences

Caltha is a widely distributed genus in the buttercup family (Ranunculaceae) showing interesting distribution patterns in both hemispheres. Evolutionary history ofCaltha was examined by means of phylogenetic, molecular dating, and historical biogeographic analyses with a more comprehensive sampling than previous studies. The internal transcribed spacer from the nuclear genome and trnL-F and atpB-rbcL regions from the plastid genome were used and analyzed using parsimony and Bayesian methods. Divergence time was estimated using Bayesian dating analyses with multiple fossil calibrations. Historical biogeography was inferred using the Bayes-DIVA method implemented in RASP. We obtained a well-resolved and well-supported phylogeny within the Caltha lineage. Caltha natansPall. diverged first from the genus and the other species grouped into two clades. Our expanded sampling scheme revealed a complicated evolutionary pattern in theC. palustris complex. Caltha sinogracilis W. T. Wang was resolved to be a member of the C. palustris complex, rather than closely related to C. scaposa Hook. f. & Thomson. Caltha rubriflora B. L. Burtt & Lauener was also revealed to be not just a red-flower form of C. sinogracilis. The diversification of the genus began at 50.5 mya (95% high posterior density: 37.1–63.9 mya), and its ancestral range was very probably in the Northern Hemisphere. The South American species may derive from western North American ancestors that dispersed along the western American Cordillera during the Cenozoic era. The vicariance model of the Southern Hemisphere species proposed by a previous study was rejected in this study.