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1 Gene trees and species trees The lines of organismal descent that make up the tree of life serve as conduits for the passage of genetic material from generation to generation. Understanding how genes pass through lines of descent is therefore needed to fully understand how traits are transmitted down evolutionary lineages. Furthermore, with gene sequence data emerging as the main tool for reconstructing phylogenetic relationships, it is important to understand the structure of gene histories and how they relate to population histories. It will become clear that a set of organisms can have multiple true histories depending on what aspect of the organisms you choose to focus on. Therefore, before embarking upon the problem of inferring phylogenies, we need to ask ourselves, what kind of entities (genes, organisms, populations, species) do we wish to study? And, what aspects of their history do we want to reconstruct? We begin by clarifying the shape of gene trees as they relate to organismic pedigrees and population trees. We then lay out some of the issues to consider in integrating the concept of “species” into phylogenetic theory. Gene trees in asexual organisms Strictly asexual organisms have uniparental reproduction (one parent per offspring) and provide a simple starting point for thinking about the inheritance of the genetic information in DNA. A DNA strand has an order of nucleotides that gets copied, with some high degree of fidelity, during DNA replication. The figure depicts one parent DNA strand, its two children, and its four grandchildren. Each nucleotide position in a daughter sequence is copied from a particular position in its parent sequence. In this case, because there have been no insertion or deletion events, the first nucleotide positions in all four grandchildren are homologous, as are the second, the third, etc. A nucleotide position in an offspring is considered homologous to that in a parent if the former was copied from the latter during DNA replication. Homology of nucleotide positions is independent of the fact that copying is imperfect (sometimes a parent and offspring sequence will differ). For example, position number 7 is homologous in all the grandchildren despite the fact that two have A’s and two have T’s at this position. Pairing during DNA replication and the tendency for the daughter strand to match the parent strand, rather than the perfect identity of template and copy, is all that is needed for a positional homology. A nucleotide in a daughter strand is seen as being descended from a parental nucleotide even if there was an error in DNA replication that caused a change in nucleotide identity.2 Sequence evolution involves changes in the nucleotides occupying a particular position. As the underlined bases highlight, mutations have arisen (either during DNA replication or at another time in the life of the organisms) so that the four grandchildren have distinct sequences from one another and from the ancestral sequence. Just as we may draw a history of organisms and use it to summarize trait evolution in those organisms, we may also draw a history of a nucleotide position. Let us use the non-conventional but useful term position tree for the history of a single nucleotide position with the state of that position at each node shown. The small tree to the right shows the position tree for position number 7 in this sequence. We could draw position trees for all the other positions. Although the identity of the nucleotides occupying different parts of these trees will differ, each position tree has the same shape. This follows because each ancestral nucleotide has the same set of DNA molecules as its descendants. Each position tree is concordant with one another and with the organismic pedigree. In this example, we have dealt with a tiny stretch of DNA, but the principles scale up perfectly to the whole genome. Uniparental inheritance constrains all nucleotide positions in the genome to follow the same lines of inheritance. Consequently, so long as reproduction is strictly uniparental, all position trees in a genome are fully concordant. Gene trees in sexual populations Sexual populations are identical to asexual ones in the sense that all nucleotide positions have a tree-like history. A nucleotide position has only one parental position, so nucleotide positions have uniparental inheritance even when organisms show biparental inheritance. Nonetheless, sexual organisms differ in that each diploid genome has two A T A T T A A A A G C T A A G C C A T A A A G C T A T G C C A T A A A G C T A A G C T A T A A A G C T A T G C C A T A A A G C T A A G C T A T A G A G C T A A G C T A T A A A G C T A T G C G A T A3 copies of every nucleotide position. These two copies have passed through a different series of ancestral organisms before arriving in the mother’s or father’s genome. The two homologous positions in an individual may, thus, be distantly related tips on the underlying position tree. When a sexual organism undergoes meiosis, recombination builds a haploid genome that is a mixture of paternal and maternal copies of each position. Because these copies have different histories, the haploid genome will include positions with different histories. As a result, if we consider a set of sexual organisms, numerous, conflicting position trees coexist in the genome. Let us explore this in more detail. The figure to the right gives an example of a small sexual population. Each individual is indicated by two circles one representing the maternal copy of a particular nucleotide position (say the one on the left) and the other representing the paternal copy. For example, focus on the individual in the top left of the figure. Its mother (the source of the left hand circle) donated her paternal copy, whereas its father donated his maternal copy. There are four possible outcomes of each instance of sexual reproduction: the maternal or paternal copy of the mother could merge with the maternal or paternal copy of the father. With four possible outcomes per mating and, in this example 56 matings, there are a huge number of possible histories (9.8 million), of which just one set of events are shown here. Despite the fact that organismic inheritance is biparental, nucleotides show uniparental inheritance. Consequently, even though the organismic pedigree is net-like, the nucleotide history is tree like.


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UW-Madison BOTANY 563 - Gene trees and species trees

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