The History in Our Genes

Explain how gene trees reconstruct the historical relationships among alleles within a population.
- Gene trees depict how alleles in a population have evolved from common ancestors over time.
Explain the term coalescence.
- Coalescence is defined as the process in which the genealogy of any pair of homologous alleles merges in a common ancestor.
Explain why gene trees do not always match species trees.
- There are instances where the evolutionary histories captured by gene trees diverge from those of the actual species due to factors like incomplete lineage sorting and introgression.
Explain incomplete lineage sorting and introgression.
- Incomplete lineage sorting occurs when descendant species inherit different subsets of ancestral alleles, leading to discrepancies in expected lineage relationships.
- Introgression involves the transfer of alleles from one species to another through hybridization, which can alter the apparent genetic relationships in gene trees.

Data Sources for Phylogenetic Analysis:
- Phylogenetic trees can be constructed from both morphological traits and DNA sequences to explore evolutionary relationships.
- Until the 1990s, morphological traits were the primary data type used for constructing phylogenies.
- Advances in computational technology now permit researchers to analyze molecular data (e.g., DNA sequences) for building gene trees.
Gene Trees Evidenced by DNA Sequence:
- The characters of a gene tree are based on the nucleotide sequences of genes.

Constructing Gene Trees:
- Gene trees can be studied at the allele level, which offers insights into genetic relationships over generations.
- Each circle in the representation corresponds to a BRCA1 allele.
- Subsequent columns represent BRCA1 alleles across generations, with connections illustrated by black lines highlighting descent from a single allele.
Illustration of Allelic Changes:
- Changes in allelic form are visually represented, for example, an orange line indicates the transition from G to T in a BRCA1 allele, which arose from mutation.
- The various colored circles indicate relationships based on shared ancestry; two orange circles share a common ancestor with a black circle.

Definitions of Gene Trees:
- Gene Tree: The branching path of descent with modification that describes the genealogy of a gene.
- A gene tree is defined as the branched genealogical lineage of homologous alleles that traces their evolution from an ancestral allele.
- Gene trees facilitate the reconstruction of the historical relationships among alleles in various populations and species.
- The change from G to T within an allele represents a genetic synapomorphy, a shared derived character state amongst related lineages.

Concept of Coalescence:
- Coalescence functions as a historical analysis—traveling backward on the gene tree to find a common ancestor.
- Time of Coalescence: This indicates the duration needed for two alleles to converge on their common ancestor.
- The time for coalescence is usually shorter for alleles that are closely related compared to those that are more distantly related.
Ancestral Population Dynamics:
- Although many individuals in an ancestral population may carry an ancestral allele, the extant alleles will coalesce onto one specific individual.
- The eventual fixation of a gene does not imply that the population was exclusively comprised of one individual with that allele; rather, it simply reflects that the allele from a specific individual later became predominant.

Mismatch between Gene Trees and Species Trees:
- Gene trees do not always align with species trees due to varying evolutionary events and lineage sorting.
- Dots in diagrams represent individual organisms, while colored lines correspond to different alleles.
Examples of Correspondence and Discrepancies:
- A matching example illustrates that the alleles in species 1 and species 2 diverged more recently than either did from the allele present in species 3, mirroring the same relationships as in the species tree.
- An example of a mismatch occurs when alleles in species 2 and 3 diverged more recently among themselves than from the allele in species 1, indicating discrepancies in evolutionary history as suggested by the species tree.

Reasons for Gene Tree and Species Tree Mismatches:
- Incomplete Lineage Sorting: Refers to a situation where descendant species inherit different subsets of ancestral alleles, often due to the coalescence of specific genes occurring before speciation events.
Introgression and Its Effects:
- Introgression: This phenomenon describes the movement of alleles between distinct species or populations through hybridization.
- Individuals from one species may interbreed withAnother species, producing hybrid offspring, which can later mate with individuals from the original species, resulting in intermingling of gene copies.
- If these new gene copies confer beneficial traits, they can be positively selected in the recipient species, complicating the gene trees.
- Gene trees reconstructed from certain regions may show closer relationships to donor species rather than the recipient's own relatives, altering the perceived mapping of species trees.

Approach to Constructing Accurate Species Phylogenies:
- Whole genome phylogenies provide a comprehensive evaluation of species' evolutionary histories, revealing the correct species tree of organisms like apes.
- Analyses based on segments of 1000 base pairs of genomes may lead to differing phylogenetic trees due to variable evolutionary paths for different genomic segments.