Construction Of Gene Trees Research Articles

GATC: a genetic algorithm for gene tree construction under the Duplication-Transfer-Loss model of evolution

BackgroundSeveral methods have been developed for the accurate reconstruction of gene trees. Some of them use reconciliation with a species tree to correct, a posteriori, errors in gene trees inferred from multiple sequence alignments. Unfortunately the best fit to sequence information can be lost during this process.ResultsWe describe GATC, a new algorithm for reconstructing a binary gene tree with branch length. GATC returns optimal solutions according to a measure combining both tree likelihood (according to sequence evolution) and a reconciliation score under the Duplication-Transfer-Loss (DTL) model. It can either be used to construct a gene tree from scratch or to correct trees infered by existing reconstruction method, making it highly flexible to various input data types. The method is based on a genetic algorithm acting on a population of trees at each step. It substantially increases the efficiency of the phylogeny space exploration, reducing the risk of falling into local minima, at a reasonable computational time. We have applied GATC to a dataset of simulated cyanobacterial phylogenies, as well as to an empirical dataset of three reference gene families, and showed that it is able to improve gene tree reconstructions compared with current state-of-the-art algorithms.ConclusionThe proposed algorithm is able to accurately reconstruct gene trees and is highly suitable for the construction of reference trees. Our results also highlight the efficiency of multi-objective optimization algorithms for the gene tree reconstruction problem. GATC is available on Github at: https://github.com/UdeM-LBIT/GATC.

Gene Tree Construction and Correction Using SuperTree and Reconciliation.

The supertree problem asking for a tree displaying a set of consistent input trees has been largely considered for the reconstruction of species trees. Here, we rather explore this framework for the sake of reconstructing a gene tree from a set of input gene trees on partial data. In this perspective, the phylogenetic tree for the species containing the genes of interest can be used to choose among the many possible compatible "supergenetrees", the most natural criteria being to minimize a reconciliation cost. We develop a variety of algorithmic solutions for the construction and correction of gene trees using the supertree framework. A dynamic programming supertree algorithm for constructing or correcting gene trees, exponential in the number of input trees, is first developed for the less constrained version of the problem. It is then adapted to gene trees with nodes labeled as duplication or speciation, the additional constraint being to preserve the orthology and paralogy relations between genes. Then, a quadratic time algorithm is developed for efficiently correcting an initial gene tree while preserving a set of "trusted" subtrees, as well as the relative phylogenetic distance between them, in both cases of labeled or unlabeled input trees. By applying these algorithms to the set of Ensembl gene trees, we show that this new correction framework is particularly useful to correct weakly-supported duplication nodes. The C++ source code for the algorithms and simulations described in the paper are available at https://github.com/UdeM-LBIT/SuGeT.

Transcriptome-Wide Identification, Classification, and Characterization of AP2/ERF Family Genes in the Desert Moss Syntrichia caninervis.

APETALA2/Ethylene Responsive Factor (AP2/ERF) is a large family of plant transcription factors which play important roles in the control of plant metabolism and development as well as responses to various biotic and abiotic stresses. The desert moss Syntrichia caninervis, due to its robust and comprehensive stress tolerance, is a promising organism for the identification of stress-related genes. Using S. caninervis transcriptome data, 80 AP2/ERF unigenes were identified by HMM modeling and BLASTP searching. Based on the number of AP2 domains, multiple sequence alignment, motif analysis, and gene tree construction, ScAP2/ERF genes were classified into three main subfamilies (including 5 AP2 gene members, 72 ERF gene members, and 1 RAV member) and two Soloist members. We found that the ratio for each subfamily was constant between S. caninervis and the model moss Physcomitrella patens, however, as compared to the angiosperm Arabidopsis, the percentage of ERF subfamily members in both moss species were greatly expanded, while the members of the AP2 and RAV subfamilies were reduced accordingly. The amino acid composition of the AP2 domain of ScAP2/ERFs was conserved as compared with Arabidopsis. Interestingly, most of the identified DREB genes in S. caninervis belonged to the A-5 group which play important roles in stress responses and are rarely reported in the literature. Expression profile analysis of ScDREB genes showed different gene expression patterns under dehydration and rehydration; the majority of ScDREB genes demonstrated a stronger response to dehydration relative to rehydration indicating that ScDREB may play an important role in dehydrated moss tissues. To our knowledge, this is the first study to detail the identification and characterization of the AP2/ERF gene family in a desert moss. Further, this study will lay the foundation for further functional analysis of these genes, provide greater insight to the stress tolerance mechanisms in S. caninervis and provide a reference for AP2/ERF gene family classification in other moss species.

Gene tree correction guided by orthology

BackgroundReconciled gene trees yield orthology and paralogy relationships between genes. This information may however contradict other information on orthology and paralogy provided by other footprints of evolution, such as conserved synteny.ResultsWe explore a way to include external information on orthology in the process of gene tree construction. Given an initial gene tree and a set of orthology constraints on pairs of genes or on clades, we give polynomial-time algorithms for producing a modified gene tree satisfying the set of constraints, that is as close as possible to the original one according to the Robinson-Foulds distance. We assess the validity of the modifications we propose by computing the likelihood ratio between initial and modified trees according to sequence alignments on Ensembl trees, showing that often the two trees are statistically equivalent.AvailabilitySoftware and data available upon request to the corresponding author.

Biome specificity of distinct genetic lineages within the four-striped mouse Rhabdomys pumilio (Rodentia: Muridae) from southern Africa with implications for taxonomy

Within southern Africa, a link between past climatic changes and faunal diversification has been hypothesized for a diversity of taxa. To test the hypothesis that evolutionary divergences may be correlated to vegetation changes (induced by changes in climate), we selected the widely distributed four-striped mouse, Rhabdomys, as a model. Two species are currently recognized, the mesic-adapted R. dilectus and arid-adapted R. pumilio. However, the morphology-based taxonomy and the distribution boundaries of previously described subspecies remain poorly defined. The current study, which spans seven biomes, focuses on the spatial genetic structure of the arid-adapted R. pumilio (521 specimens from 31 localities), but also includes limited sampling of the mesic-adapted R. dilectus (33 specimens from 10 localities) to act as a reference for interspecific variation within the genus. The mitochondrial COI gene and four nuclear introns (Eef1a1, MGF, SPTBN1, Bfib7) were used for the construction of gene trees. Mitochondrial DNA analyses indicate that Rhabdomys consists of four reciprocally monophyletic, geographically structured clades, with three distinct lineages present within the arid-adapted R. pumilio. These monophyletic lineages differ by at least 7.9% (±0.3) and these results are partly confirmed by a multilocus network of the combined nuclear intron dataset. Ecological niche modeling in MaxEnt supports a strong correlation between regional biomes and the distribution of distinct evolutionary lineages of Rhabdomys. A Bayesian relaxed molecular clock suggests that the geographic clades diverged between 3.09 and 4.30Ma, supporting the hypothesis that the radiation within the genus coincides with paleoclimatic changes (and the establishment of the biomes) characterizing the Miocene-Pliocene boundary. Marked genetic divergence at the mitochondrial DNA level, coupled with strong nuclear and mtDNA signals of non-monophyly of R. pumilio, support the notion that a taxonomic revision of the genus is needed.

COMPARATIVE STUDY OF CYTOPLASMIC ACTIN DNA SEQUENCES FROM SIX SPECIES OF PLANORBIDAE (GASTROPODA: BASOMMATOPHORA)

Full-length actin-encoding sequences were PCR-amplified from genomic DNA of six planorbid species; Biomphalaria glabrata (Say; M-line strain), B. alexandrina (Ehrenberg), B. pfeifferi (Krauss), B. tenagophila (Orbigny), B. obstructa (Morelet) and Helisoma trivolvis (Say), using primers designed from a previously reported B. glabrata cytoplasmic (� ) actin cDNA. The amplified sequences contained two conserved exons (126 nt and 1005 nt, respectively), separated by an intron that varied in size between snail species (ranging from 671 to 794 nt). Sequence similarities occurred between the introns of the actin genes from B. glabrata, B. alexandrina and B. pfeifferi and between those from B. tenagophila and B. obstructa, yet considerable differences were evident between these two groups and the intron derived from H. trivolvis. Analysis of exons for sequence similarities, the presence of conserved residues (deduced amino acids), and construction of gene trees indicated that these planorbid genes encode cytoplasmic (� ) actins rather than muscular (� ) actins. Southern blotting and hybridisation experiments suggested that B. glabrata and H. trivolvis may have multiple (up to 5) actin genes, and it can not be ruled out that actin sequences obtained from different planorbid species were derived from paralogous genes. Interestingly however, the gene trees resolved actins derived from gastropod, cephalopod and bivalve molluscs. The sequences presented add to the growing body of information on the molecular biology of planorbid snails.

Phylogenetic Utility of Histone H3 Intron Sequences in the Perennial Relatives of Soybean (Glycine:Leguminosae)

Histone H3 loci form a large multigene family in most plant species. InGlycine,some of these loci possess introns, whose sequences can provide characters for assessing phylogenetic relationships among species of the genus. Phylogenetic analyses of two closely related H3-B loci revealed a complex evolutionary pattern, producing trees from which species relationships could not be inferred readily. The single H3-D locus, in contrast, provided data suitable for the construction of gene trees whose topologies were sufficiently similar to other hypotheses of relationships within the subgenusGlycineto give confidence that evolution at this locus is tracking species phylogenies. H3-D topologies identified several of the same groupings found in previous phylogenetic studies using the chloroplast genome. However, histone H3-D and chloroplast genome data sets were in other respects incongruent, as revealed by both topological differences and numerical measures of congruence. The principal difference involvedGlycine falcata,whose chloroplast genome belongs to one of the three strongly supported clades in the subgenus, but whose histone H3-D allele was sister to those of the remaining members of the subgenus. The H3-D topology is more in keeping with the morphologically, ecologically, and genetically divergent nature of this species. The H3-D locus appears to be a useful source of phylogenetic characters for interspecific studies inGlycine,providing resolution among taxa whose relationships were unresolved in previous studies.

Using allele frequencies and geographic subdivision to reconstruct gene trees within a species: molecular variance parsimony.

We formalize the use of allele frequency and geographic information for the construction of gene trees at the intraspecific level and extend the concept of evolutionary parsimony to molecular variance parsimony. The central principle is to consider a particular gene tree as a variable to be optimized in the estimation of a given population statistic. We propose three population statistics that are related to variance components and that are explicit functions of phylogenetic information. The methodology is applied in the context of minimum spanning trees (MSTs) and human mitochondrial DNA restriction data, but could be extended to accommodate other tree-making procedures, as well as other data types. We pursue optimal trees by heuristic optimization over a search space of more than 1.29 billion MSTs. This very large number of equally parsimonious trees underlines the lack of resolution of conventional parsimony procedures. This lack of resolution is highlighted by the observation that equally parsimonious trees yield very different estimates of population genetic diversity and genetic structure, as shown by null distributions of the population statistics, obtained by evaluation of 10,000 random MSTs. We propose a non-parametric test for the similarity between any two trees, based on the distribution of a weighted coevolutionary correlation. The ability to test for tree relatedness leads to the definition of a class of solutions instead of a single solution. Members of the class share virtually all of the critical internal structure of the tree but differ in the placement of singleton branch tips.