Phylogeny and systematics. Why are these disciplines important in evolutionary biology and how are they related to each other?

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1 Phylogeny and systematics Why are these disciplines important in evolutionary biology and how are they related to each other?

2 Phylogeny and systematics Phylogeny: the evolutionary history of a species or group of species Systematics: the study of the diversity and evolutionary relationships of organisms.

3 Homologies What are they? Why are they so important in determining the evolutionary relationships between taxa? Difference between homology and analogy? Why is this distinction so important?

4 Phylogenies reflect taxonomy and evolutionary history

5 Different types of phylogenetic trees

6 More phylogenetic trees

7 Even more

8 What they all have in common: The branching pattern reflects taxonomic hierarchy They all reflect evolutionary patterns They are all constructed based on shared, homologous characters

9 Cladistics vocabulary Clade: a group of species that includes an ancestral species and all its descendants

10 Cladistics vocabulary Monophyletic clade A clade that includes the common ancestor and all of its descendants the only evolutionarily meaningful group

11 A paraphyletic taxon contains its most recent common ancestor, but does not contain all the descendants of that ancestor. A polyphyletic taxon does not contain the most recent common ancestor of all its members.

12 Apomorphy vs Synapomorphy Apomorphy

13 More cladistics vocabulary Apomorphy: A character state that occurs only in later descendants Synapomorphy: a derived character state shared by two or more terminal groups (taxa included in a cladistic analysis as further indivisible units) and inherited from their most recent common ancestor.

14 More cladistics vocabulary Outgroup: a closely related group to the group of interest (called the ingroup) It is used to assess which traits are primitive and which are derived the outgroup branched from the parent group before the other groups branched from each other.

15 Molecular sequences used to construct phylogenetic trees Orthologous genes: any genes in different species, that originated from a common ancestor. Thus orthologs are separated by a speciation event Paralogous genes: a duplicated gene. Paralogs typically have the same or similar function, but sometimes one copy is free to mutate and acquire new functions.

16 Molecular Clock Hypothesis (MCH) The amount of molecular change between two species measures how long ago they shared a common ancestor. Based on the assumption that DNA replication rate was constant over time, across all species and every part of the genome.

17 Factors that invalidate the MCH Different generation times (A mutation generally becomes fixed only from one generation to another. The shorter this timespan is, the more mutations can become fixed) Population size (Apart from effects of small population size, genetic diversity will "bottom out" as populations become larger as the fitness advantage of any one mutation becomes smaller) Species-specific differences (due to differing metabolism, ecology, evolutionary history,...) Evolving functions of the encoded protein (can be ameliorated by utilizing non-coding DNA sequences or emphasizing silent mutations) Differences in the intensity of natural selection

18 Neutral theory of evolution Motoo Kimura pointed out that most mutations are neutral (not affected by natural selection) Neutral mutations occur when the change in nucleotide sequence does not affect the function of the translated product Kimura does not deny the existence of positive or negative selection, but sustains that most changes in DNA sequences have a neutral effect

19 Neutral mutations through time 1. Darwin recognized the existence of positive, negative, and neutral mutations 2. Neo-Darwinians neglected neutral changes 3. Kimura brought attention to neutral mutations and amplified their importance 4. The nearly neutral theory proposes that lots of changes have small effects on the phenotype 5. The neoselectionists point out that there are critical changes that are responsible for the transition between point mutations and regional changes

20 Tree of Life Formerly known as Prokaryotes Concept check: Was the former group Prokaryotes mono, poly, or paraphyletic?