You can make a phylogenetic tree, which visualizes the evolutionary relationships between species or genes, primarily by analyzing genetic or morphological data. In the current era of abundant genome data, a common and robust method involves comparing the DNA or protein sequences of multiple shared genes across different organisms.
Constructing a Phylogenetic Tree: The Modern Approach
As referenced, in an era of genome data availability, the most common way to make a phylogenetic species tree is by using multiple protein-coding genes, conserved in multiple species. This approach provides a more reliable view of species evolution than relying on a single gene.
This methodology is composed of several key steps:
1. Orthology Inference
Before comparing sequences, you need to identify genes that are truly comparable across species. These are called orthologs. Orthologs are genes in different species that evolved from a common ancestral gene by speciation. They typically retain the same function. Identifying orthologs is crucial because comparing non-orthologous genes (like paralogs, which arise from gene duplication within a genome) would lead to an inaccurate evolutionary history.
- Why it's important: Ensures you are comparing apples to apples when looking at different species' genomes.
- Practical Insight: This step often involves using specialized bioinformatics tools and databases.
2. Multiple Sequence Alignment
Once orthologous genes are identified for your chosen species, the sequences of these genes (either DNA or the protein sequence they encode) are aligned. Multiple Sequence Alignment (MSA) lines up sequences to identify regions of similarity and difference. Gaps are introduced in the alignment to account for insertions or deletions that have occurred over evolutionary time.
- Goal: To make homologous positions (those that evolved from the same position in the ancestor) comparable across all sequences.
- Tools Used: Software like MUSCLE, CLUSTAL Omega, or MAFFT.
3. Inference of the Phylogeny
With the aligned sequences, the next step is to build the tree itself. This involves using dedicated computational tools and algorithms to analyze the patterns of variation (substitutions, insertions, deletions) in the alignment. Different methods exist, broadly categorized as:
- Distance Methods (e.g., Neighbor Joining): These calculate an overall 'distance' or difference between each pair of sequences and then build a tree that minimizes the total distance.
- Character-Based Methods (e.g., Maximum Parsimony, Maximum Likelihood, Bayesian Inference): These methods analyze each position (or 'character') in the alignment.
- Maximum Parsimony: Seeks the tree that requires the fewest evolutionary changes (mutations) to explain the observed differences.
- Maximum Likelihood & Bayesian Inference: Use statistical models of sequence evolution to find the tree that is most probable given the data and the model. These are often preferred for their robustness and ability to incorporate complex evolutionary models.
The result is a branching tree diagram where branch lengths often represent evolutionary time or the amount of genetic change, and nodes represent inferred common ancestors.
- Dedicated Tools: Software packages like RAxML, IQ-TREE, BEAST, or MEGA are commonly used for phylogenetic inference.
- Output: A phylogenetic tree file (e.g., in Newick format) and associated information about branch support (confidence levels for the branching patterns).
Why Use Multiple Genes?
Using multiple conserved protein-coding genes provides a more robust signal for species-level relationships compared to using just one gene. Different genes can have different evolutionary histories (e.g., due to gene duplication and loss, or varying rates of evolution), and combining data from many genes helps to average out gene-specific noise and reveal the underlying species phylogeny. This is particularly important for resolving difficult or rapid evolutionary divergences.
Alternative Data and Methods
While sequence data from multiple genes is a standard modern approach, phylogenetic trees can also be constructed using:
- Single Genes: Useful for studying the evolutionary history of the gene itself or when only one gene is available.
- Non-coding DNA: Like ribosomal RNA (rRNA) or intergenic regions.
- Morphological Data: Anatomical or physiological characteristics (historically significant, still used, especially for fossils). PRESENCE/ABSENCE of traits.
The choice of data and method depends on the research question, the organisms being studied, and the available resources.
In summary, making a phylogenetic tree in the genome era involves selecting relevant genetic data (often multiple conserved genes), aligning the sequences, and applying sophisticated computational tools to infer the most likely evolutionary history.
