Search results for "phylogenetic tree"

2015

Songs in passerine birds are important for territory defense and mating. Speciation rates in oscine passerines are so high, due to cultural evolution, that this bird lineage makes up half of the extant bird species. Leaf warblers are a speciose Old-World passerine family of limited morphological differentiation, so that songs are even more important for species delimitation. We took 16 sonographic traits from song recordings of 80 leaf warbler taxa and correlated them with 15 potentially explanatory variables, pairwise, and in linear models. Based on a well-resolved molecular phylogeny of the same taxa, all pairwise correlations were corrected for relatedness with phylogenetically independe…

Reappraisal of some species of the giant galericine Deinogalerix (Mammalia, Eulipotyphla, Erinaceomorpha, Erinaceidae) from the Miocene of south-east…

2019

A revision of the remains of Deinogalerix from the Terre Rosse of Gargano, stored at the Department of Earth Sciences of Florence, improved our knowledge of the genus. The goals of this study are to clear the taxonomic status of the specimens and to tackle several issues connected with the evolutionary relationships of the different species. The sample of dental remains of Deinogalerix freudenthali provides new information, which confirms that this species belongs to the most primitive members of the genus, alongside D. masinii. It is now clear that D. freudenthali is very close to the hypothetical ancestor of all other Gargano species, except D. masinii. Nonetheless, the oldest fissures of…

On the origin of European sheep as revealed by the diversity of the Balkan breeds and by optimizing population-genetic analysis tools

2020

Background In the Neolithic, domestic sheep migrated into Europe and subsequently spread in westerly and northwesterly directions. Reconstruction of these migrations and subsequent genetic events requires a more detailed characterization of the current phylogeographic differentiation. Results We collected 50 K single nucleotide polymorphism (SNP) profiles of Balkan sheep that are currently found near the major Neolithic point of entry into Europe, and combined these data with published genotypes from southwest-Asian, Mediterranean, central-European and north-European sheep and from Asian and European mouflons. We detected clines, ancestral components and admixture by using variants of commo…

How challenging RADseq data turned out to favor coalescent-based species tree inference. A case study in Aichryson (Crassulaceae)

2022

Analysing multiple genomic regions while incorporating detection and qualification of discordance among regions has become standard for understanding phylogenetic relationships. In plants, which usually have comparatively large genomes, this is feasible by the combination of reduced-representation library (RRL) methods and high-throughput sequencing enabling the cost effective acquisition of genomic data for thousands of loci from hundreds of samples. One popular RRL method is RADseq. A major disadvantage of established RADseq approaches is the rather short fragment and sequencing range, leading to loci of little individual phylogenetic information. This issue hampers the application of coa…

Molecular Structure of a Gypsy Element of Drosophila Subobscura (Gypsyds) Constituting a Degenerate Form of Insect Retroviruses

1996

We have determined the nucleotide sequence of a 7.5 kb full-size gypsy element from Drosophila subobscura strain H-271. Comparative analyses were carried out on the sequence and molecular structure of gypsy elements of D.subobscura (gypsyDs), D.melanogaster (gypsyDm) and D.virilis (gypsyDv). The three elements show a structure that maintains a common mechanism of expression. ORF1 and ORF2 show typical motifs of gag and pol genes respectively in the three gypsy elements and could encode functional proteins necessary for intracellular expansion. In the three ORF1 proteins an arginine-rich region was found which could constitute a RNA binding motif. The main differences among the gypsy element…

Sampling and repeatability in the evaluation of hepatitis C virus genetic variability.

2003

Among the experimental techniques available to study the genetic variability of RNA virus populations, the most informative involve reverse transcription (RT), amplification, cloning and sequencing. The effects of several aspects of these techniques on the estimation of genetic variability in a virus population were analysed. Hepatitis C virus populations from four patients were examined. For each patient, ten series of data derived from independent PCR amplifications of a single RT reaction were obtained. The sample size of each data set was 10 sequences (in nine series) and 100 sequences (in one series). An additional data set derived from an independent RT reaction (about 10 sequences) p…

Widespread vertical transmission and associated host sex–ratio distortion within the eukaryotic phylum Microspora

2004

Vertical transmission (VT) and associated manipulation of host reproduction are widely reported among prokaryotic endosymbionts. Here, we present evidence for widespread use of VT and associated sex-ratio distortion in a eukaryotic phylum. The Microspora are an unusual and diverse group of eukaryotic parasites that infect all animal phyla. Following our initial description of a microsporidian that feminizes its crustacean host, we survey the diversity and distribution of VT within the Microspora. We find that vertically transmitted microsporidia are ubiquitous in the amphipod hosts sampled and that they are also diverse, with 11 species of microsporidia detected within 16 host species. We f…

Molecular characterisation of the species of the genus Zygosaccharomyces.

2003

The restriction fragments polymorphisms of the mitochondrial DNA and the PCR fragment that comprised the internal transcribes spacers and the 5.8S rRNA gene, together with the electrophoretic karyotypes of 40 strains from the 10 species of the genus Zygosaccharomyces, including the new species Z. lentus were examined. The RFLP's of the ITS-5.8S region showed a specific restriction pattern for each species, including the new species Z. lentus. The only exception were the species Z. cidri and Z. fermentati that produced identical restriction profiles. The electrophoretic chromosome patterns confirmed the differences between the species of this genus, including the phylogenetic closest species…

Isolation and characterization of two T-box genes from sponges, the phylogenetically oldest metazoan taxon

2003

It is now well established that all metazoan phyla derived from one common ancestor, the hypothetical Urmetazoa. Due to the basal position of Porifera (Demospongiae) in the phylogenetic tree of Metazoa, studies on the mechanisms controlling the development of these animals can provide clues on the understanding of the origin of multicellular animals and on how the first organization of the body plan evolved. In this report we describe the isolation and genomic characterization of two T-box genes from the siliceous sponge Suberites domuncula. The phylogenetic analysis classifies one into the subfamily of Brachyury, Sd-Bra, and the second into the Tbx2 subfamily, Sd-Tbx2. Analyses of the Sd-B…

Global functional variation in alpine vegetation

2021

International audience; Questions. What are the functional trade-offs of vascular plant species in global alpine ecosystems? How is functional variation related to vegetation zones, climatic groups and biogeographic realms? What is the relative contribution of macroclimate and evolutionary history in shaping the functional variation of alpine plant communities? Location. Global. Methods. We compiled a data set of alpine vegetation with 5,532 geo-referenced plots, 1,933 species and six plant functional traits. We used principal component analysis to quantify functional trade-offs among species and trait probability density to assess the functional dissimilarity of alpine vegetation in differ…