Number Of Well-supported Clades Research Articles

Phylogenomic relationship and evolutionary insights of sweet potato viruses from the western highlands of Kenya.

Sweet potato is a major food security crop within sub-Saharan Africa where 90% of Africa production occurs. One of the major limitations of sweet potato production are viral infections. In this study, we used a combination of whole genome sequences from a field isolate obtained from Kenya and those available in GenBank. Sequences of four sweet potato viruses: Sweet potato feathery mottle virus (SPFMV), Sweet potato virus C (SPVC), Sweet potato chlorotic stunt virus (SPCSV), Sweet potato chlorotic fleck virus (SPCFV) were obtained from the Kenyan sample. SPFMV sequences both from this study and from GenBank were found to be recombinant. Recombination breakpoints were found within the Nla-Pro, coat protein and P1 genes. The SPCSV, SPVC, and SPCFV viruses from this study were non-recombinant. Bayesian phylogenomic relationships across whole genome trees showed variation in the number of well-supported clades; within SPCSV (RNA1 and RNA2) and SPFMV two well-supported clades (I and II) were resolved. The SPCFV tree resolved three well-supported clades (I–III) while four well-supported clades were resolved in SPVC (I–IV). Similar clades were resolved within the coalescent species trees. However, there were disagreements between the clades resolved in the gene trees compared to those from the whole genome tree and coalescent species trees. However the coat protein gene tree of SPCSV and SPCFV resolved similar clades to the genome and coalescent species tree while this was not the case in SPFMV and SPVC. In addition, we report variation in selective pressure within sites of individual genes across all four viruses; overall all viruses were under purifying selection. We report the first complete genomes of SPFMV, SPVC, SPCFV, and a partial SPCSV from Kenya as a mixed infection in one sample. Our findings provide a snap shot on the evolutionary relationship of sweet potato viruses (SPFMV, SPVC, SPCFV, and SPCSV) from Kenya as well as assessing whether selection pressure has an effect on their evolution.

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.

A Molecular Phylogenetic Study of Arnica (Asteraceae): Low Chloroplast DNA Variation and Problematic Subgeneric Classification

DNA sequences from five chloroplast DNA regions (the rpl16 and rps16 introns and the psbA-trnH, ycf4-cemA, and trnT-L spacers), and the nuclear ribosomal internal and external transcribed spacer (ITS and ETS) regions, were analyzed using maximum parsimony and Bayesian methods to explore the putatively complicated history of the mainly North American genus Arnica. The chloroplast regions were found to contain minimal variation in Arnica. Of 3710 nucleotides, only 119 were variable and 45 informative. However, combined with the ribosomal DNA data, the analysis yielded a number of well-supported clades. Strong support for the monophyly of Arnica was found in both the separate and combined analyses but none of the five currently recognized subgenera was resolved as monophyletic in any of the analyses. Arnica (Whitneya) dealbata and A. mallotopus (Mallotopus japonicus), two species that were previously placed outside Arnica, were confidently confirmed as members of the genus. The analyses revealed that A. nevadensis (subg. Austromontana) is most closely related to A. dealbata and that A. mallotopus forms a strongly supported clade with A. unalaschcensis (subg. Andropurpurea). Earlier biogeographical hypotheses that suggested an arctic origin and southward spread of the genus are not supported by our analyses. Hybridization, homoplasy, and rapid evolution are possible explanations for conflicts between the chloroplast and nuclear ribosomal data sets and for low support of the deeper nodes.

Relationships within Myrtaceae sensu lato based on a matK phylogeny

Parsimony analysis of matK sequence data from 81 taxa representing 68 genera of Myrtaceae sensu lato, and a representative of each of three related families as outgroups, produced an estimate of the phylogeny of the family with little basal resolution but a number of well-supported clades containing most of the genera. Monophyly of Myrtaceae sensu stricto has moderate support but a broader circumscription, including the small genera Psiloxylon and Heteropyxis that are frequently placed in monogeneric families, is more strongly supported. Analysis of matK plus available sequences for the 5′ spacer region for a subset of 56 taxa resolved 14 major clades that received strong jackknife support. Relationships between these were, for the most part, incompletely resolved or poorly supported. A new infrafamilial classification is proposed which recognises two subfamilies (Myrtoideae, Psiloxyloideae) and 17 tribes (Backhousieae stat. nov., Chamelaucieae, Eucalypteae stat. nov., Heteropyxideae, Kanieae, Leptospermeae, Lindsayomyrteae trib. nov., Lophostemoneae trib. nov., Melaleuceae, Metrosidereae stat. nov., Myrteae, Osbornieae trib. nov., Psiloxyleae, Syncarpieae trib. nov., Syzygieae trib. nov., Tristanieae trib. nov., Xanthostemoneae trib. nov.).

Potential phylogenetic utility of the nuclear FLORICAULA/LEAFY second intron: comparison with three chloroplast DNA regions in Amorphophallus (Araceae)

FLORICAULA/LEAFY ( FLO/LFY) is a single-copy nuclear-encoded homeotic gene containing two introns. We have investigated the utility of the second intron of FLO/LFY ( FLint2) as a tool for phylogeny reconstruction at lower taxonomic levels. As an example, the phylogeny of 46 Amorphophallus, two Pseudodracontium, and four outgroup species is reconstructed using maximum parsimony and maximum likelihood analyses of FLint2 sequences. We designed new primers based on conserved sequences of the second and third exon for use in a range of Aroid taxa to amplify and sequence the second intron. In Amorphophallus FLint2 proved to be rather short (143–222 bp), highly variable and unsaturated. In all but two species a single amplification product was found. Results from phylogenetic analysis of FLint2 are largely congruent with results using the chloroplast regions rbcL, matK, and trnL, and compare favorably in percentage of informative characters, overall homoplasy levels, number of well-supported clades in consensus trees and resolution of ingroup relationships within Amorphophallus. When amplification products are not too large, alignment is relatively straightforward, and sequences are used in combination with other fast evolving markers, the Flint2 intron may be a valuable new tool for phylogenetic studies at lower taxonomic levels.

Elucidating Deep-Level Phylogenetic Relationships in Saxifragaceae Using Sequences for Six Chloroplastic and Nuclear DNA Regions

To elucidate relationships at deep levels within Saxifragaceae we analyzed phylogenetically a data set of sequences for six DNA regions, four representing the chloroplast genome (rbcL, matK, trnL-trnF, psbA-trnH) and two from the nuclear genome (ITS and expansion segments of the 26S rDNA). A total of 6676 bp was aligned per taxon, 4559 bp and 1878 bp from the chloroplast and nuclear genomes, respectively. Chloroplast and nuclear trees agreed closely, prompting analysis of a combined, six-gene data set. Application of both parsimony and maximum likelihood methods yielded similar topologies. The use of different ITS alignments and the exclusion of hard-to-align ITS regions had little impact on either the final nuclear-based topology, or the shortest trees from the analysis of six genes. The affinities of two monotypic genera (Saxifragella and Saxifragodes) endemic to Tierra del Fuego were elucidated. Saxifragella is an early branching member of the North Temperate genus Saxifraga s. str.; Saxifragodes is sister to Cascadia, a genus endemic to Oregon and Washington. Long-distance dispersal from east Asia or western North America to South America may have played an important role in forming these and other similar disjunctions in the family. A number of well-supported clades are present, including Saxifraga s. str., Micranthes, Saxifragopsis/Astilbe, Chrysosplenium/Peltoboykinia, and the Boykinia and Heuchera groups. The use of additional characters has provided greatly increased resolution and internal support at deep levels. Saxifragaceae comprise two major lineages: Saxifraga s. str. (including Saxifragella) and all other genera of the family (the heucheroids). This major split is accompanied by general biogeographical and morpihological differences. Whereas Saxifraga s. str. is largely arctic to alpine in occurrence, the heucheroid clade is largely temperate in distribution, Saxifraga s. str. has a relatively uniform floral morphology (generally actinomorphic; 5 sepals, 5 petals, 10 stamens, 2 carpels), whereas the heucheroid clade encompasses actinomorphic and zygomorphic forms, as well as variation in the number of sepals, petals, stamens, and carpels. Deep-level relationships within both Saxifraga s. str. and the heucheroid clade are well resolved and supported. A phylogenetic classification of the family is provided.