Scientists select traits for constructing phylogenetic trees and cladograms based on several criteria. Primarily, the traits must be heritable, meaning they are passed down from ancestors to descendants. The chosen traits should also be informative, which means they provide clear insights into the evolutionary relationships among the organisms being studied. For example, a trait that is too common (found in almost all organisms) or too rare (found in only a few) might not be very informative. Scientists often look for traits that have evolved relatively recently, as these can be more helpful in distinguishing between closely related species. Morphological (physical) traits are commonly used, but molecular traits, such as DNA sequences, have become increasingly important because they often provide a more detailed and accurate picture of evolutionary relationships. The choice of traits is also influenced by the availability of data and the specific goals of the study. For instance, studies aiming to understand deep evolutionary relationships might rely more on molecular data, while those focusing on recent evolutionary events might use a combination of morphological and molecular traits.

Homologous traits are crucial in phylogenetic studies as they indicate evolutionary relationships stemming from a common ancestor. Unlike analogous traits, which arise due to convergent evolution and reflect similar functions rather than common ancestry, homologous traits are derived from the same structure in a common ancestor. For instance, the forelimbs of mammals, birds, reptiles, and amphibians, though they may serve different functions (like flying, swimming, or walking), all share a common structural origin. These similarities in structure, despite differences in function, provide evidence of common descent. In phylogenetic analysis, homologous traits help scientists reconstruct the evolutionary history of organisms. By tracing how these traits have been modified over time, scientists can infer the paths of evolutionary change and the relationships among different groups of organisms. Homologous traits are especially useful in distinguishing true evolutionary relationships from those that might appear similar due to convergent evolution but do not actually indicate a close genetic relationship.

Convergent evolution plays a significant role in the context of phylogenetic tree construction, primarily as a source of potential confusion. Convergent evolution occurs when unrelated organisms independently evolve similar traits as a result of having to adapt to similar environments or ecological niches. This can lead to the phenomenon of analogy, where traits appear similar but do not arise from a common ancestor. In phylogenetic tree construction, distinguishing between homologous traits (traits derived from a common ancestor) and analogous traits (traits resulting from convergent evolution) is crucial. If analogous traits are mistakenly interpreted as homologous, it could lead to incorrect inferences about evolutionary relationships, placing unrelated species closer together on the phylogenetic tree. Scientists must carefully analyze the traits being used in phylogenetic studies to ensure they reflect true evolutionary histories rather than similarities due to convergent evolution. Molecular data, which provides a more detailed genetic understanding, can be particularly helpful in resolving these issues.

Phylogenetic trees and cladograms can indeed change over time, and this is a fundamental aspect of their nature. As they are hypotheses based on the best available data, any new discoveries or advancements in technology can lead to revisions. New fossil discoveries can provide previously unavailable information about extinct species, potentially altering our understanding of how current species are related. Similarly, advancements in molecular biology, such as new techniques for DNA sequencing, can reveal more detailed genetic information, leading to a reevaluation of relationships depicted in existing phylogenetic trees and cladograms. Furthermore, as our understanding of evolutionary processes deepens, the methods and models used to construct these trees and cladograms may also evolve, leading to refinements in how we interpret and represent evolutionary relationships. In essence, phylogenetic trees and cladograms are dynamic, evolving with our expanding knowledge of biology and the natural world.

Phylogenetic trees and cladograms differ significantly in their representation of evolutionary time. A phylogenetic tree is a diagram that not only shows the relationships among various species but also incorporates an aspect of time, often depicted through the length of the branches. The branches in a phylogenetic tree can represent chronological time or genetic change, and they can be calibrated using various methods, such as molecular clocks or fossil records. This allows for an approximation of when certain evolutionary events, like divergences, occurred. On the other hand, cladograms focus strictly on the relationships between species without incorporating a time scale. In cladograms, the length of the branches does not convey time or the degree of change; rather, it illustrates the order of evolutionary branching or divergence. The primary purpose of a cladogram is to show patterns of shared ancestry among groups of organisms, but it does not provide direct information about when these divergences or evolutionary changes took place.