Search results for "Maximum parsimony"
showing 10 items of 19 documents
Reconstructing the Phylogeny of the Human Chromosome 4 Synteny using Comparative Karyology and Genomic Data Analysis
2010
Abstract This work focuses on the evolution of the architecture of human chromosome 4 (HSA4) through the analysis of chromosomal regions that have been conserved over time, and the comparison of regions that have been involved in different rearrangements in placental lineages. As with most elements of the human genome, HSA4 is considered to be evolutionarily stable. A more detailed analysis indicates that the syntenic association has been reshuffled by a series of rearrangements, yielding different chromosomes in various taxa. In its ancestral eutherian state, HSA4 has a syntenic association with HSA8p. We investigated the complex origin of this human chromosome using three different approa…
Molecular evidence for phylogenetic relationships among buntings and American sparrows (Emberizidae)
2001
To help clarify controversial phylogenetic relationships within the family Emberizidae, we sequenced 1238 bp of mitochondrial DNA from the cytochrome b gene and a flanking portion of ND5. Although the longspurs (Calcarius) and the snow buntings (Plectrophenax) have been grouped with the Old World buntings (Emberiza) in traditional classifications, our molecular phylogenies constructed with maximum likelihood and maximum parsimony place these general basal to a clade in which the Old World buntings and North American sparrows are sister groups. Contrary to the hypothesis that the radiation within Emberiza is recent following a westward expansion of emberizid stock into Eurasia from North Ame…
An 18S rDNA-Based Molecular Phylogeny of Aphidiinae (Hymenoptera: Braconidae)
2000
We have obtained a molecular phylogeny of the subfamily Aphidiinae (Hymenoptera: Braconidae) by sequencing the 18S rDNA in 37 aphidiine taxa. Approximately 1857 nucleotides were sequenced in each species. Evolutionary relationships were established by comparing the results of maximum-parsimony, maximum-likelihood, and distance analyses. The most variable region of this gene, V4 (approx 403 nucleotides), was employed to establish the basality of the tribe Ephedrini within this subfamily. All phylogenetic reconstructions yielded trees with very similar topologies that confirmed the existence of two of the four traditionally accepted tribes, Ephedrini and Praini, but questioned the existence o…
BythinellaMoquin-Tandon, 1856 (Gastropoda: Rissooidea: Bythinellidae) in Romania: species richness in a glacial refugium
2009
Mitochondrial cytochrome oxidase I (COI) and ribosomal internal transcribed spacer 1 (ITS-1) sequences were analysed in 12 Romanian Bythinella populations. Phylogenetic relationships were inferred using maximum parsimony, maximum likelihood and Bayesian techniques. For COI, the Kimura two-parameter (K2P) distances and haplotype networks were computed. Two sympatric and four allopatric groups were distinguished. The K2P distances are similar to those for congeneric rissooids, so each of the six groups represents a species. Two are identified as Bythinella molcsanyi H. Wagner, 1941, and Bythinella dacica Grossu, 1946. The other four groups cannot be ascribed to any known Bythinella. The occur…
Phylogenetics of Anthyllis (Leguminosae: Papilionoideae: Loteae): Partial incongruence between nuclear and plastid markers, a long branch problem and…
2010
Abstract Phylogenetic relationships in the genus Anthyllis (Leguminosae: Papilionoideae: Loteae) were investigated using data from the nuclear ribosomal internal transcribed spacer regions (ITS) and three plastid regions (psbA–trnH intergenic spacer, petB–petD region and rps16 intron). Bayesian and maximum parsimony (MP) analysis of a concatenated plastid dataset recovered well-resolved trees that are topologically similar, with many clades supported by unique indels. MP and Bayesian analyses of the ITS sequence data recovered trees that have several well-supported topological differences, both among analyses, and to trees inferred from the plastid data. The most substantial of these concer…
Phylogenetic relationship among genera of Polymorphidae (Acanthocephala), inferred from nuclear and mitochondrial gene sequences.
2013
Abstract Acanthocephalans of the family Polymorphidae Meyer, 1931 are obligate endoparasites with complex life cycles. These worms use vertebrates (marine mammals, fish-eating birds and waterfowl) as definitive hosts and invertebrates (amphipods, decapods and euphausiids) as intermediate hosts to complete their life cycle. Polymorphidae has a wordwide distribution, containing 12 genera, with approximately 127 species. The family is diagnosed by having a spinose trunk, bulbose proboscis, double-walled proboscis receptacle, and usually four to eight tubular cement glands. To conduct a phylogenetic analysis, in the current study sequences of the small (18S) and large-subunit (28S) ribosomal RN…
Molecular phylogeny of the families Campulidae and Nasitrematidae (Trematoda) based on mtDNA sequence comparison.
1998
Abstract Historically, the systematic arrangement of the genera within the family Campulidae, and its relationship with its allied family Nasitrematidae have been rather confused, particularly because only adult morphology has been available to classical taxonomic analysis. In this paper we provide a partial phylogeny of the genera of these families based on mtDNA from five campulid species: Campula oblonga, Zalophotrema atlanticum, Hadwenius tursionis, Oschmarinella rochebruni and ; and one nasitrematid, Nasitremaglobicephalae . Fasciola hepatica and Dicrocoelium dendriticum were used as outgroups. Maximum parsimony and neighbour-joining methods were applied. Both methods produced similar …
Simultaneous speciation in the European high mountain flowering plant genus Facchinia (Minuartia s.l., Caryophyllaceae) revealed by genotyping-by-seq…
2017
Understanding the relative importance of different mechanisms of speciation in a given lineage requires fully resolved interspecific relationships. Using Facchinia, a genus of seven species centred in the European Alps, we explore whether the polytomy found by Sanger sequencing analyses of standard nuclear (ITS) and plastid markers (trnQ-rps16) is a hard or soft polytomy by substantially increasing the amount of DNA sequence data, generated by genotyping-by-sequencing. In comparison to 142 phylogenetically informative sites in the Sanger sequences the GBS sequences yielded 3363 phylogenetically informative sites after exclusion of apparently oversaturated SNPs. Maximum parsimony, maximum li…
Phylogeny and the colourful history of jewel bugs (Insecta: Hemiptera: Scutelleridae)
2017
Members of the family Scutelleridae (Heteroptera: Pentatomomorpha: Pentatomoidea) are also called shield bugs because of the greatly enlarged scutellum, or jewel bugs because of the brilliant colours of many species. All scutellerids are phytophagous, feeding on various parts of their host plants. Due to lack of obvious synapomorphies and the failure to apply rigorous phylogenetic methods, the higher classification of Scutelleridae has been disputed for more than 150 years. Here we reconstructed a phylogeny of Scutelleridae based on complete sequences of 18S and 28S nuclear rDNAs and all 13 protein-coding genes of the mitochondrial genome, with the sampled taxa covering all of the currently…
A geographical pattern ofAntirrhinum(Scrophulariaceae) speciation since the Pliocene based on plastid and nuclear DNA polymorphisms
2009
Aim To infer phylogenetic relationships among Antirrhinum species and to reconstruct the historical distribution of observed sequence polymorphism through estimates of haplotype clades and lineage divergence. Location Antirrhinum is distributed primarily throughout the western Mediterranean, with 22 of 25 species in the Iberian Peninsula. Methods Plastid (83 trnS-trnG and 83 trnK-matK) and nuclear (87 ITS) sequences were obtained from 96 individuals representing 24 of the 25 Antirrhinum species. Sequences were analysed using maximum parsimony, Bayesian inference and statistical parsimony networking. Molecular clock estimates were obtained for plastid trnK-matK sequences using the penalized …