Search results for "tree"
showing 10 items of 1841 documents
The genus Cyclops (Copepoda, Cyclopoida) in Europe
2016
16 páginas, 23 figuras, 1 tabla, información suplementaria.
Genetic variation of naturally growing olive trees in Israel: from abandoned groves to feral and wild?
2016
Background Naturally growing populations of olive trees are found in the Mediterranean garrigue and maquis in Israel. Here, we used the Simple Sequence Repeat (SSR) genetic marker technique to investigate whether these represent wild var. sylvestris. Leaf samples were collected from a total of 205 trees at six sites of naturally growing olive populations in Israel. The genetic analysis included a multi-locus lineage (MLL) analysis, Rousset’s genetic distances, Fst values, private alleles, other diversity values and a Structure analysis. The analyses also included scions and suckers of old cultivated olive trees, for which the dominance of one clone in scions (MLL1) and a second in suckers (…
Propagule pressure increase and phylogenetic diversity decrease community’s susceptibility to invasion
2017
Background Invasions pose a large threat to native species, but the question of why some species are more invasive, and some communities more prone to invasions than others, is far from solved. Using 10 different three-species bacterial communities, we tested experimentally if the phylogenetic relationships between an invader and a resident community and the propagule pressure affect invasion probability. Results We found that greater diversity in phylogenetic distances between the members of resident community and the invader lowered invasion success, and higher propagule pressure increased invasion success whereas phylogenetic distance had no clear effect. In the later stages of invasion,…
paco: implementing Procrustean Approach to Cophylogeny in R
2017
Summary The concordance of evolutionary histories and extant species interactions provides a useful metric for addressing questions of how the structure of ecological communities is influenced by macro-evolutionary processes. We introduce paco (v0.3.1), an R package to perform Procrustean Approach to Cophylogeny. This method assesses the phylogenetic congruence, or evolutionary dependence, of two groups of interacting species using both ecological interaction networks and their phylogenetic history. We demonstrate the functionality of paco through its application to empirical host-parasite and plant-pollinator communities. Although the package is intended to assess the phylogenetic congruen…
Underestimated regional species diversity in the Cape Floristic Region revealed by phylogenetic analysis of the Erica abietina/E. viscaria clade (Eri…
2017
New insight to the role of microbes in the methane exchange in trees: evidence from metagenomic sequencing
2021
Methane (CH4) exchange in tree stems and canopies and the processes involved are among the least understood components of the global CH4 cycle. Recent studies have focused on quantifying tree stems as sources of CH4 and understanding abiotic CH4 emissions in plant canopies, with the role of microbial in situ CH4 formation receiving less attention. Moreover, despite initial reports revealing CH4 consumption, studies have not adequately evaluated the potential of microbial CH4 oxidation within trees. In this paper, we discuss the current level of understanding on these processes. Further, we demonstrate the potential of novel metagenomic tools in revealing the involvement of microbes in the C…
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…
Evolving by deleting: patterns of molecular evolution of Apple stem pitting virus isolates from Poland
2019
In this study, 267 coat protein gene (CP) sequences from 48 Polish isolates of Apple stem pitting virus (ASPV) were determined. The genetic structure of the virus population was analysed and possible mechanisms of molecular evolution explored. We found evidence of recombination within the ASPV population and the presence of 17 ASPV molecular variants that differ in the length, number and arrangement of deletions in the CP. Population genetic analyses showed significant variation among isolates from pear and apple trees, between isolates from the same host species and, more interestingly, within isolates, supporting the existence of significant levels of variability within individual hosts, …
The effect of RNA substitution models on viroid and RNA virus phylogenies.
2018
Abstract Many viroids and RNA viruses have genomes that exhibit secondary structure, with paired nucleotides forming stems and loops. Such structures violate a key assumption of most methods of phylogenetic reconstruction, that sequence change is independent among sites. However, phylogenetic analyses of these transmissible agents rarely use evolutionary models that account for RNA secondary structure. Here, we assess the effect of using RNA-specific nucleotide substitution models on the phylogenetic inference of viroids and RNA viruses. We obtained data sets comprising full-genome nucleotide sequences from six viroid and ten single-stranded RNA virus species. For each alignment, we inferre…
Molecular phylogeny and forms of photosynthesis in tribe Salsoleae (Chenopodiaceae).
2016
Evolution of C3–C4 intermediate and C4 lineages are resolved in Salsoleae (Chenopodiaceae), and a model for structural and biochemical changes for the evolution of the Salsoloid form of C4 is considered.