Genome BLAST distance phylogenies inferred from whole plastid and whole mitochondrion genome sequences

BACKGROUND: Phylogenetic methods which do not rely on multiple sequence alignments are important tools in inferring trees directly from completely sequenced genomes. Here, we extend the recently described Genome BLAST Distance Phylogeny (GBDP) strategy to compute phylogenetic trees from all completely sequenced plastid genomes currently available and from a selection of mitochondrial genomes representing the major eukaryotic lineages. BLASTN, TBLASTX, or combinations of both are used to locate high-scoring segment pairs (HSPs) between two sequences from which pairwise similarities and distances are computed in different ways resulting in a total of 96 GBDP variants. The suitability of these distance formulae for phylogeny reconstruction is directly estimated by computing a recently described measure of "treelikeness", the so-called δ value, from the respective distance matrices. Additionally, we compare the trees inferred from these matrices using UPGMA, NJ, BIONJ, FastME, or STC, respectively, with the NCBI taxonomy tree of the taxa under study. RESULTS: Our results indicate that, at this taxonomic level, plastid genomes are much more valuable for inferring phylogenies than are mitochondrial genomes, and that distances based on breakpoints are of little use. Distances based on the proportion of "matched" HSP length to average genome length were best for tree estimation. Additionally we found that using TBLASTX instead of BLASTN and, particularly, combining TBLASTX and BLASTN leads to a small but significant increase in accuracy. Other factors do not significantly affect the phylogenetic outcome. The BIONJ algorithm results in phylogenies most in accordance with the current NCBI taxonomy, with NJ and FastME performing insignificantly worse, and STC performing as well if applied to high quality distance matrices. δ values are found to be a reliable predictor of phylogenetic accuracy. CONCLUSION: Using the most treelike distance matrices, as judged by their δ values, distance methods are able to recover all major plant lineages, and are more in accordance with Apicomplexa organelles being derived from "green" plastids than from plastids of the "red" type. GBDP-like methods can be used to reliably infer phylogenies from different kinds of genomic data. A framework is established to further develop and improve such methods. δ values are a topology-independent tool of general use for the development and assessment of distance methods for phylogenetic inference

The dispersal of vascular plants in a forest mosaic by a guild of mammalian herbivores

Endozochorous seed dispersal by herbivores can affect plant spatial dynamics and macroecological patterns. We have investigated the number and species composition of viable seeds deposited in faeces of a full guild of macroherbivores (four deer and two lagomorph species) in a forest in eastern Britain. One hundred and one plant species germinated from faecal pellet material, 85 of which were among the 247 vascular plant species recorded in the forest. However, three species – Chenopodium album, Urtica dioica and Agrostis stolonifera – comprised 56% of the seedlings recorded. Of the species recorded in faecal samples, 36% had no recognised dispersal mechanism, while very few (7%) were adapted to endozoochorous dispersal (fleshy fruit or nut). The number of species dispersed by the herbivores was ranked Cervus elaphus and Dama dama (96) > Capreolus capreolus (40) > Muntiacus reevesi (31) > Oryctolagus cuniculus (21) > Lepus europaeus (19), with the other taxa dispersing subsets of those dispersed by C. elpahus and D. dama. The invasive M. reevesi deposited the fewest seeds per gram of faecal pellet material (0.4 g−1) and hence fewer seeds per unit area than other deer species despite their numerical dominance, while C. elaphus/D. dama deposited the most (0.43 seeds m−2 year−1). Due to differences in faecal seed density among habitats combined with the ranging behaviour of animals, more seeds were deposited in younger stands, enhancing the potential contribution of macroherbivores to population persistence by dispersal and colonisation in a successional mosaic