How to interpret phylogenetc tree scale?4 answersInterpreting phylogenetic tree scale involves understanding the concept of phylogenetic scale, which has been formalized to provide insight into evolutionary biology, community ecology, biogeography, and macroecology. Phylogenetic scale encompasses phylogenetic grain, extent, scaling, and domains, influencing patterns and processes across the phylogeny. It aids in resolving controversies and enhancing understanding by considering the effects of scale on diversification rates, community structure, niche conservatism, and species-abundance distributions. Additionally, interpreting phylogenetic trees involves recognizing common misconceptions, understanding tree-building methods, and inferring relationships between organisms, traits, ecology, and genomic data. Time-scaling methods play a crucial role in accurately reconstructing temporal relationships in tree-based evolutionary analyses, with the "cal3" method being recommended for its fidelity in various simulation conditions.
How to construct phylogeny trees with DNA sequences?5 answersPhylogenetic trees can be constructed using DNA sequences through alignment-based or alignment-free methods. Alignment-based methods involve measuring the genetic distance between species based on pairwise sequence alignment. These methods are traditionally used but can be time-consuming for large datasets. Alignment-free methods, on the other hand, are gaining popularity due to their faster comparison capabilities. These methods utilize k-mer frequency, Average Common Substring (ACS), and ACS with position restrictions and mismatches to measure genetic similarity. Additionally, machine learning-based approaches can convert longer DNA sequences into k-mer forests, improving efficiency. Another approach is the hierarchical method, which constructs phylogenetic trees at multiple levels based on groups of isolates with similar similarity levels. These methods offer significant efficiency and accuracy compared to traditional methods. Overall, a combination of alignment-based and alignment-free methods can be used to construct phylogenetic trees using DNA sequences.
Does phylogeny tree help in explain how gene families evolve?5 answersPhylogenetic trees are frequently used to represent the evolution of gene families. Gene family evolution is usually represented within a species tree, but recent models also consider the evolution of protein domains within gene trees. Various simulation frameworks have been developed to validate the accuracy of phylogenetic reconciliation methods, such as the Duplication-Transfer-Loss (DTL) reconciliation algorithm. These frameworks simulate gene family evolution, including horizontal gene transfers and the evolution of domain families. The accuracy of DTL reconciliation has been evaluated on simulated datasets, showing its robustness to the presence of replacing transfers. Additionally, the construction of gene trees can be improved by considering dependencies between gene families, such as information from species trees, extant synteny, and ancestral synteny. RefineTree is a software package that corrects gene trees using these dependencies, resulting in more plausible trees. Phylogenetic trees and correction methods contribute to understanding how gene families evolve.
Does Phylogeny trees derived from transcriptome data are very helpful for investigations involving comparative genomics?5 answersPhylogeny trees derived from transcriptome data are indeed very helpful for investigations involving comparative genomics. Transcriptomes provide a cost-effective alternative to genome sequencing, allowing for the reconstruction of phylogenies using DNA sequences derived from transcriptomes. Studies comparing phylogenomic and phylotranscriptomic trees have shown that when a rigorous method for identifying orthologs is employed, the trees derived from transcriptome data are virtually identical to those derived from genome sequences. Additionally, curated databases of high-quality transcriptome assemblies, such as MATEdb, have been developed to facilitate comparative genomics analyses and accelerate research in animal phylogenomics. Furthermore, the quality of transcriptome assemblies has been shown to significantly impact the accuracy of phylogenomic inferences, with high-quality assemblies producing richer datasets with stronger phylogenetic signal. Overall, transcriptome data has proven to be a valuable resource for investigating phylogenetic relationships and conducting comparative genomics analyses.
Isit better to have more gene in phylogeentic study5 answersIt is generally better to have more genes in a phylogenetic study as it improves the accuracy of phylogenetic inference. Increased taxon sampling, which includes sampling more genes, has been shown to be highly beneficial for phylogenetic inference. Sampling a single individual for more loci has been found to outperform sampling multiple individuals for one locus in most cases. The number of independent loci, the total number of alleles sampled, and the total number of single nucleotide polymorphisms (SNPs) per data set have improved over time in phylogeographic studies. Uniparentally inherited organellar markers, such as animal mitochondrial and plant chloroplast DNA, continue to be important in phylogeographic data. Therefore, having more genes in a phylogenetic study can provide more accurate results and improve our understanding of organismal history.
Who introduced phylogenetic tree?2 answers