The value of scattered trees for wildlife: Contrasting effects of landscape context and tree size

Aim

The biodiversity value of scattered trees in modified landscapes is often overlooked in planning and conservation decisions. We conducted a multitaxa study to determine how wildlife abundance, species richness and community composition at individual trees are affected by (1) the landscape context in which trees are located; and (2) the size of trees.

Location

Canberra, south‐eastern Australia.

Methods

Trunk arthropod, bat and bird surveys were undertaken over 3 years (2012–2014) at 72 trees of three sizes (small (20–50 cm DBH), medium (51–80 cm), large (≥80 cm)) located in four landscape contexts (reserves, pasture, urban parklands, urban built‐up areas).

Results

Landscape context affected all taxa surveyed. Trunk arthropod communities differed between trees in urban built‐up areas and reserves. Bat activity and richness were significantly reduced at trees in urban built‐up areas suggesting that echolocating bats may be disturbed by high levels of urbanization. Bird abundance and richness were highest at trees located in modified landscapes, highlighting the value of scattered trees for birds. Bird communities also differed between non‐urban and urban trees. Tree size had a significant effect on birds but did not affect trunk arthropods and bats. Large trees supported higher bird abundance, richness and more unique species compared to medium and small trees.

Main conclusions

Scattered trees support a diversity of wildlife. However, landscape context and tree size affected wildlife in contrasting ways. Land management strategies are needed to collectively account for responses exhibited by multiple taxa at varying spatial scales. We recommend that the retention and perpetuation of scattered trees in modified landscapes should be prioritized, hereby providing crucial habitat benefits to a multitude of taxa.     

Rooted triple consensus and anomalous gene trees

Background  

Anomalous gene trees (AGTs) are gene trees with a topology different from a species tree that are more probable to observe than congruent gene trees. In this paper we propose a rooted triple approach to finding the correct species tree in the presence of AGTs.     

Automated group assignment in large phylogenetic trees using GRUNT: GRouping,Ungrouping, Naming Tool

Background  

Accurate taxonomy is best maintained if species are arranged as hierarchical groups in phylogenetic trees. This is especially important as trees grow larger as a consequence of a rapidly expanding sequence database. Hierarchical group names are typically manually assigned in trees, an approach that becomes unfeasible for very large topologies.     

PhyloPattern: regular expressions to identify complex patterns in phylogenetic trees

Background  

To effectively apply evolutionary concepts in genome-scale studies, large numbers of phylogenetic trees have to be automatically analysed, at a level approaching human expertise. Complex architectures must be recognized within the trees, so that associated information can be extracted.     

Robinson-Foulds Supertrees

Background  

Supertree methods synthesize collections of small phylogenetic trees with incomplete taxon overlap into comprehensive trees, or supertrees, that include all taxa found in the input trees. Supertree methods based on the well established Robinson-Foulds (RF) distance have the potential to build supertrees that retain much information from the input trees. Specifically, the RF supertree problem seeks a binary supertree that minimizes the sum of the RF distances from the supertree to the input trees. Thus, an RF supertree is a supertree that is consistent with the largest number of clusters (or clades) from the input trees.     

Fast calculation of the quartet distance between trees of arbitrary degrees

Background  

A number of algorithms have been developed for calculating the quartet distance between two evolutionary trees on the same set of species. The quartet distance is the number of quartets – sub-trees induced by four leaves – that differs between the trees. Mostly, these algorithms are restricted to work on binary trees, but recently we have developed algorithms that work on trees of arbitrary degree.     

Basal jawed vertebrate phylogeny inferred from multiple nuclear DNA-coded genes

Background  

Phylogenetic analyses of jawed vertebrates based on mitochondrial sequences often result in confusing inferences which are obviously inconsistent with generally accepted trees. In particular, in a hypothesis by Rasmussen and Arnason based on mitochondrial trees, cartilaginous fishes have a terminal position in a paraphyletic cluster of bony fishes. No previous analysis based on nuclear DNA-coded genes could significantly reject the mitochondrial trees of jawed vertebrates.     

Phylogenetic identification of lateral genetic transfer events

Background  

Lateral genetic transfer can lead to disagreements among phylogenetic trees comprising sequences from the same set of taxa. Where topological discordance is thought to have arisen through genetic transfer events, tree comparisons can be used to identify the lineages that may have shared genetic information. An 'edit path' of one or more transfer events can be represented with a series of subtree prune and regraft (SPR) operations, but finding the optimal such set of operations is NP-hard for comparisons between rooted trees, and may be so for unrooted trees as well.     

Visualising very large phylogenetic trees in three dimensional hyperbolic space

Background  

Common existing phylogenetic tree visualisation tools are not able to display readable trees with more than a few thousand nodes. These existing methodologies are based in two dimensional space.     

Three-Dimensional Phylogeny Explorer: Distinguishing paralogs,lateral transfer,and violation of "molecular clock" assumption with 3D visualization

Background  

Construction and interpretation of phylogenetic trees has been a major research topic for understanding the evolution of genes. Increases in sequence data and complexity are creating a need for more powerful and insightful tree visualization tools.     

A maximum pseudo-likelihood approach for estimating species trees under the coalescent model

Background  

Several phylogenetic approaches have been developed to estimate species trees from collections of gene trees. However, maximum likelihood approaches for estimating species trees under the coalescent model are limited. Although the likelihood of a species tree under the multispecies coalescent model has already been derived by Rannala and Yang, it can be shown that the maximum likelihood estimate (MLE) of the species tree (topology, branch lengths, and population sizes) from gene trees under this formula does not exist. In this paper, we develop a pseudo-likelihood function of the species tree to obtain maximum pseudo-likelihood estimates (MPE) of species trees, with branch lengths of the species tree in coalescent units.     

Transcriptional analysis of <Emphasis Type="Italic">Pinus sylvestris</Emphasis> roots challenged with the ectomycorrhizal fungus <Emphasis Type="Italic">Laccaria bicolor</Emphasis>

Background  

Symbiotic ectomycorrhizal associations of fungi with forest trees play important and economically significant roles in the nutrition, growth and health of boreal forest trees, as well as in nutrient cycling. The ecology and physiology of ectomycorrhizal associations with Pinus sp are very well documented but very little is known about the molecular mechanisms behind these mutualistic interactions with gymnosperms as compared to angiosperms.     

Factors affecting the concordance between orthologous gene trees and species tree in bacteria

Background  

As originally defined, orthologous genes implied a reflection of the history of the species. In recent years, many studies have examined the concordance between orthologous gene trees and species trees in bacteria. These studies have produced contradictory results that may have been influenced by orthologous gene misidentification and artefactual phylogenetic reconstructions. Here, using a method that allows the detection and exclusion of false positives during identification of orthologous genes, we address the question of whether putative orthologous genes within bacteria really reflect the history of the species.     

SPRIT: Identifying horizontal gene transfer in rooted phylogenetic trees

Background  

Phylogenetic trees based on sequences from a set of taxa can be incongruent due to horizontal gene transfer (HGT). By identifying the HGT events, we can reconcile the gene trees and derive a taxon tree that adequately represents the species' evolutionary history. One HGT can be represented by a rooted Subtree Prune and Regraft (RSPR) operation and the number of RSPRs separating two trees corresponds to the minimum number of HGT events. Identifying the minimum number of RSPRs separating two trees is NP-hard, but the problem can be reduced to fixed parameter tractable. A number of heuristic and two exact approaches to identifying the minimum number of RSPRs have been proposed. This is the first implementation delivering an exact solution as well as the intermediate trees connecting the input trees.     

Simplifying gene trees for easier comprehension

Background  

In the genomic age, gene trees may contain large amounts of data making them hard to read and understand. Therefore, an automated simplification is important.     

Metabolic pathways variability and sequence/networks comparisons

Background  

In this work a simple method for the computation of relative similarities between homologous metabolic network modules is presented. The method is similar to classical sequence alignment and allows for the generation of phenotypic trees amenable to be compared with correspondent sequence based trees. The procedure can be applied to both single metabolic modules and whole metabolic network data without the need of any specific assumption.     

Identification of genes differentially expressed during interaction of Mexican lime tree infected with " Candidatus Phytoplasma aurantifolia"

Background  

"Candidatus Phytoplasma aurantifolia", is the causative agent of witches' broom disease in Mexican lime trees (Citrus aurantifolia L.), and is responsible for major losses of Mexican lime trees in Southern Iran and Oman. The pathogen is strictly biotrophic, and thus is completely dependent on living host cells for its survival. The molecular basis of compatibility and disease development in this system is poorly understood. Therefore, we have applied a cDNA- amplified fragment length polymorphism (AFLP) approach to analyze gene expression in Mexican lime trees infected by " Ca. Phytoplasma aurantifolia".     

A statistical score for assessing the quality of multiple sequence alignments

Background  

Multiple sequence alignment is the foundation of many important applications in bioinformatics that aim at detecting functionally important regions, predicting protein structures, building phylogenetic trees etc. Although the automatic construction of a multiple sequence alignment for a set of remotely related sequences cause a very challenging and error-prone task, many downstream analyses still rely heavily on the accuracy of the alignments.