Selection in Nature Ecological Interactions Constraints on Selection III. Back to the Neutral Theory!

III. Back to The Neutral Theory A. Neutral Variation - change in protein that does not affect fitness - ‘silent’ or ‘synonymous’ mutations are the prototype

III. Back to The Neutral Theory A. Neutral Variation - change in protein that does not affect fitness - ‘silent’ or ‘synonymous’ mutations are the prototype B. Predictions and Results 1. Rates of molecular evolution should vary in functional and non-functional regions

III. Back to The Neutral Theory A. Neutral Variation - change in protein that does not affect fitness - ‘silent’ or ‘synonymous’ mutations are the prototype B. Predictions and Results 1. Rates of molecular evolution should vary in functional and non-functional regions - Rates should vary in different codon positions. Variation at the third position should be higher, because these are usually silent mutations. Mutations at the second position change amino acids, and these changes are deleterious. PATTERN CONFIRMED. - Rates should vary in coding and non-coding regions. Variation in Introns should occur more rapidly than variation in exons, since introns are not transcribed and are also invisible to selection. PATTERN CONFIRMED - Rates should vary in functional and non-functional regions of proteins. PATTERN CONFIRMED

III. Back to The Neutral Theory A. Neutral Variation - change in protein that does not affect fitness - ‘silent’ or ‘synonymous’ mutations are the prototype B. Predictions and Results 1. Rates of molecular evolution should vary in functional and non-functional regions 2. Rates of replacement (substitution of one fixed allele by another that reaches fixation) should be constant over geologic time.

III. Back to The Neutral Theory A. Neutral Variation - change in protein that does not affect fitness - ‘silent’ or ‘synonymous’ mutations are the prototype B. Predictions and Results 1. Rates of molecular evolution should vary in functional and non-functional regions 2. Rates of replacement (substitution of one fixed allele by another that reaches fixation) should be constant over geologic time. - If changes are random and mutations occur at a given rate, then replacement should "tick" along like a clock. - Selection should speed rates when a new adaptive combination occurs, like in obviously adaptive morphological trait. Then inhibit further change unless it is adaptive or neutral - PATTERNS CONFIRMED (usually).

III. Back to The Neutral Theory A. Neutral Variation - change in protein that does not affect fitness - ‘silent’ or ‘synonymous’ mutations are the prototype B. Predictions and Results 1. Rates of molecular evolution should vary in functional and non-functional regions 2. Rates of replacement (substitution of one fixed allele by another that reaches fixation) should be constant over geologic time. 3. Rates of morphological change should be independent of the rate of molecular change.

III. Back to The Neutral Theory A. Neutral Variation - change in protein that does not affect fitness - ‘silent’ or ‘synonymous’ mutations are the prototype B. Predictions and Results 1. Rates of molecular evolution should vary in functional and non-functional regions 2. Rates of replacement (substitution of one fixed allele by another that reaches fixation) should be constant over geologic time. 3. Rates of morphological change should be independent of the rate of molecular change. - "Living Fossils" show extreme genetic change and variation, yet have remained morphologically unchanged for millennia. And, their rate of genetic change in this morphologically constant species is the same as in hominids, which have changed dramatically in morphology over a short period. PATTERN CONFIRMED

III. Back to The Neutral Theory A. Neutral Variation - change in protein that does not affect fitness - ‘silent’ or ‘synonymous’ mutations are the prototype B. Predictions and Results 1. Rates of molecular evolution should vary in functional and non-functional regions 2. Rates of replacement (substitution of one fixed allele by another that reaches fixation) should be constant over geologic time. 3. Rates of morphological change should be independent of the rate of molecular change. 4. A truly neutral clock should tick off mutations at a constant rate. But should this ticking occur per unit time, or per generation? (Selection will proceed faster in organisms with short generation times…)

III. Back to The Neutral Theory A. Neutral Variation - change in protein that does not affect fitness - ‘silent’ or ‘synonymous’ mutations are the prototype B. Predictions and Results 1. Rates of molecular evolution should vary in functional and non-functional regions 2. Rates of replacement (substitution of one fixed allele by another that reaches fixation) should be constant over geologic time. 3. Rates of morphological change should be independent of the rate of molecular change. 4. A truly neutral clock should tick off mutations at a constant rate. But should this ticking occur per unit time, or per generation? - Mutations occur during DNA replication of the DNA, so a truly neutral clock should tick at a rate dependent on the generation time of the organism. Species with rapid generation times should accumulate mutations at a faster rate than long-lived species with slower generation times. - This is true of non-coding DNA... but not true for proteins. Proteins accumulate mutations in absolute time, not generational time. THIS IS INCONSISTENT WITH THE NEUTRAL MODEL

Rate of evolution in proteins Clustering analysis based on amino acid similarity across seven proteins from 17 mammalian species.

Rate of evolution in proteins Now, we date the oldest mammalian fossil, which our evolution hypothesis dictates should be ancestral to all mammals, both the placentals (species 1-16) and the marsupial kangaroo. …. This dates to 120 million years 16

Rate of evolution in proteins And, through our protein analysis, we already know how many genetic differences (nitrogenous base substitutions) would be required to account for the differences we see in these proteins - 98. 16

Rate of evolution in proteins So now we can plot genetic change against time. 16

Rate of evolution in proteins Repeat for every node. How old is the putative common ancestor between rabbits and rodents (58 mya). How many substitutions required to explain the differences in AA sequence? (50).

Rate of evolution in proteins Just where genetic analysis of two different EXISTING species predicts. 16

Rate of evolution in proteins And all 16 nodes? Describes a straight line (constant mutation rate).

III. Back to The Neutral Theory A. Neutral Variation B. Predictions and Results C. Ohta’s “Nearly Neutral” Model

III. Back to The Neutral Theory A. Neutral Variation B. Predictions and Results C. Ohta’s “Nearly Neutral” Model - Included weak selection against slightly deleterious alleles. if s < 1/2Ne, then alleles are essentially neutral and become fixed as drift would predict. - In small populations, drift predominates unless selection is fairly strong (in a population of Ne = 5, drift will predominate unless s > 0.1). - In large populations, selection predominates, even if it is fairly weak (if Ne = 10,000, then selection will predominate if s > 0.00005).

SO. - We observe a constant AA substitution rate across species, even though we would expect that species with shorter generation times should have FASTER rates of substitution. Sub. Rate OBS. EXP. Short GEN TIME Long

SO. - We observe a constant AA substitution rate across species, even though we would expect that species with shorter generation times should have FASTER rates of substitution. - So, something must be 'slowing down' this rate of substitution in species with short gen. times. What's slowing it down is their large populations size, such that the effects of drift, alone, are reduced. LARGE POP. SIZE Sub. Rate OBS. EXP. Short GEN TIME Long

SO. - We observe a constant AA substitution rate across species, even though we would expect that species with shorter generation times should have FASTER rates of substitution. - So, something must be 'slowing down' this rate of substitution in species with short gen. times. What's slowing it down is their large populations size, such that the effects of drift, alone, are reduced. - Likewise, species with long generation times have small populations, and substitution by drift and fixation is more rapid than expected based on generation time, alone. SMALL POP. SIZE Sub. Rate OBS. EXP. Short GEN TIME Long

SO. - The constant rate of AA substitution across species is due to the balance between the effects of generation time and population size. SMALL POP. SIZE Sub. Rate OBS. EXP. Short GEN TIME Long

III. Back to The Neutral Theory A. Neutral Variation B. Predictions and Results C. Ohta’s “Nearly Neutral” Model III. Back to The Neutral Theory A. Neutral Variation B. Predictions and Results C. Ohta’s “Nearly Neutral” Model D. New Developments …. Some ‘synonymous’ substitutions are NOT neutral! - ‘synonymous’ mutations in exons may slow the rate of protein synthesis and cell growth. Patrick Goymer (2007) 'Genetic variation: Synonymous mutations break their silence', Nature Reviews Genetics 8, 92 (February 2007). Chamary, J. V. & Parmley, J. L. & Hurst, L. D. 'Hearing silence: non-neutral evolution at synonymous sites in mammals'. Nature Rev. Genet. 7, 98-108 (2006). Grzegorz Kudla et al (2009,Science 10 April 2009). Chamary and Hurst (2009) 'The price of silent mutations', Scientific American, June 2009, pp34-41. It appears that bases in protein coding exons can be also intron splicing recognition sites, and that a synonymous mutation can prevent intron splicing, resulting in mutated proteins

Patterns in Evolution I. Phylogenetic II. Morphological III. Historical (later) IV. Biogeographical

Patterns in Evolution I. Phylogenetic - Determining the genealogical, familial patterns among organisms, populations, species and higher taxa - "family trees"

Patterns in Evolution I. Phylogenetic A. Systematics: Taxonomy and Classification

Patterns in Evolution I. Phylogenetic A. Systematics: Taxonomy and Classification 1. Taxonomy - the naming of taxa (singular 'taxon")

Patterns in Evolution I. Phylogenetic A. Systematics: Taxonomy and Classification 1. Taxonomy - the naming of taxa (singular 'taxon") a. Rules for naming species: Latin binomen (Drosophila melanogaster) italicized or underlined author (Drosophila melanogaster Meigen, 1830) if a species is named twice, priority counts based on a 'holotype' or 'type' specimen 'paratypes' show range of variation 'species' is both singular and plural; genus (s.), genera (pl.)

Patterns in Evolution I. Phylogenetic A. Systematics: Taxonomy and Classification 1. Taxonomy - the naming of taxa (singular 'taxon") b. Rules for higher taxa Animal families end in "-idae" (Felidae) Animal sub-families end in "-inae" (Homininae) These are often derived from the same stem as the 'type genus' - the first genus described for the family. (Felis) Plant families end in "-aceae" (Betulaceae) Higher taxa are capitalized, but not italicized (as above) adjectives are not capitalized ("hominids")

Patterns in Evolution I. Phylogenetic A. Systematics: Taxonomy and Classification 1. Taxonomy - the naming of taxa (singular 'taxon") 2. Classification - determining the hierarchical position of each species within higher taxa. A Nested Hierarchy....

Patterns in Evolution I. Phylogenetic A. Systematics: Taxonomy and Classification 1. Taxonomy - the naming of taxa (singular 'taxon") 2. Classification - determining the hierarchical position of each species within higher taxa. 3. Phylogenetics

Patterns in Evolution I. Phylogenetic A. Systematics: Taxonomy and Classification 1. Taxonomy - the naming of taxa (singular 'taxon") 2. Classification - determining the hierarchical position of each species within higher taxa. 3. Phylogenetics Cladogenesis: you want the branching/"clade" pattern of taxa to reflect phylogenetic relationships, and you want your taxonomy to reflect phylogenetic relationships – “Archosaurs” for crocodilians and birds…

Patterns in Evolution I. Phylogenetic A. Systematics: Taxonomy and Classification 1. Taxonomy - the naming of taxa (singular 'taxon") 2. Classification - determining the hierarchical position of each species within higher taxa. 3. Phylogenetics Anagenesis: however, some evolutionary changes are so profound that we might honor the degree of difference ("Class: Aves”)

Terms: Monophyletic taxon: includes all (and only) the species descended from a common ancestor. Aves is good.

Terms: Monophyletic taxon: includes all (and only) the species descended from a common ancestor. Aves is good. Paraphyletic taxon: includes all descendants of a common ancestor, except for those placed in another taxon. So, “Reptilia” is a paraphyletic group, as it includes all amniotes EXCEPT mammals and birds (this gets the synapsids).

c. Terms: Monophyletic taxon: includes all (and only) the species descended from a common ancestor. Aves is good. Paraphyletic taxon: includes all descendants of a common ancestor, except for those placed in another taxon. So, “Reptilia” is a paraphyletic group, as it includes all diapsids and anapsids EXCEPT mammals and birds (this gets the synapsids). Polyphyletic taxon: includes organisms that do not share a common ancestor that is in the group. To be avoided. “Fliers” (Birds, Pterosaurs)

Linnaean Classification of Apes Pongidae Hylobatidae Hominidae Apes = primates (grasping hands, binocular vision) with no tails

Linnaean Classification of Apes Pongidae PARAPHYLETIC Hylobatidae

Linnaean Classification of Apes Hominidae Hylobatidae

Patterns in Evolution I. Phylogenetic A. Systematics: Taxonomy and Classification B. Reconstructing Phylogenies

Patterns in Evolution I. Phylogenetic A. Systematics: Taxonomy and Classification B. Reconstructing Phylogenies 1. Characters morphological behavioral cellular (structural or chemical) genetic - nitrogenous base sequence; amino acid sequence

Patterns in Evolution I. Phylogenetic A. Systematics: Taxonomy and Classification B. Reconstructing Phylogenies 1. Characters morphological behavioral cellular (structural or chemical) genetic - nitrogenous base sequence; amino acid sequence can be quantitative measurements, or qualitative "presence/absence“ or “A, C, T, G”

A B C D Trait 1 1 Trait 2 Trait 3 Trait 4 Trait 5 Patterns in Evolution I. Phylogenetic A. Systematics: Taxonomy and Classification B. Reconstructing Phylogenies 1. Characters 2. Trees a. Unrooted trees: show patterns among groups without specifying ancestral relationships A B C D Trait 1 1 Trait 2 Trait 3 Trait 4 Trait 5

A B C D Trait 1 1 Trait 2 Trait 3 Trait 4 Trait 5 Patterns in Evolution I. Phylogenetic A. Systematics: Taxonomy and Classification B. Reconstructing Phylogenies 1. Characters 2. Trees So, A and B share three traits that C and D don't have (1,2, 4) and are more similar to one another than they are to C and D. A B C D Trait 1 1 Trait 2 Trait 3 Trait 4 Trait 5

A B C D Trait 1 1 Trait 2 Trait 3 Trait 4 Trait 5 Patterns in Evolution I. Phylogenetic A. Systematics: Taxonomy and Classification B. Reconstructing Phylogenies 1. Characters 2. Trees Same for C and D. A B C D Trait 1 1 Trait 2 Trait 3 Trait 4 Trait 5

Patterns in Evolution I. Phylogenetic A. Systematics: Taxonomy and Classification B. Reconstructing Phylogenies 1. Characters 2. Trees So, A and B share three traits that C and D don't have (1,2, 4) and are more similar to one another than they are to C and D.

Patterns in Evolution I. Phylogenetic B C D Trait 1 1 Trait 2 Trait 3 Trait 4 Trait 5 Patterns in Evolution I. Phylogenetic A. Systematics: Taxonomy and Classification B. Reconstructing Phylogenies 1. Characters 2. Trees b. Rooted Trees: Hypothetical patterns of descent that could be produced with this pattern. You might suppose it would have to be this:

Patterns in Evolution I. Phylogenetic B C D Trait 1 1 Trait 2 Trait 3 Trait 4 Trait 5 Patterns in Evolution I. Phylogenetic A. Systematics: Taxonomy and Classification B. Reconstructing Phylogenies 1. Characters 2. Trees b. Rooted Trees: But it could easily be one of these, depending on whether the state ‘0’ or ‘1’ for traits 1 and 2 were ancestral. ‘1’ derived ‘0’ derived

Patterns in Evolution I. Phylogenetic A. Systematics: Taxonomy and Classification B. Reconstructing Phylogenies 1. Characters 2. Trees b. Rooted Trees: SO, in order to access ancestry, we need to compare the groups in question to an "outgroup". An outgroup is a sister taxon which should only share ancestral traits with the group in question. So reptiles would be the outgroup for comparisons among diverse mammals, for example; or a crocodile or dinosaur would be the outgroup to a comparison among diverse birds.

A B C D E (out) Trait 1 1 Trait 2 Trait 3 Trait 4 Trait 5 Now, we assume that spE expresses ANCESTRAL characters (plesiomorphies). Any different character state must have evolved FROM this ancestral state - and this evolved state is called DERIVED (apomorphy). A B C D E (out) Trait 1 1 Trait 2 Trait 3 Trait 4 Trait 5

A B C D E (out) Trait 1 1 Trait 2 Trait 3 Trait 4 Trait 5 Now, all species in a clade might share plesiomorphies, because they are all ultimately derived from the same ancestor. So shared ancestral traits tell us nothing about relationships within the group. But DERIVED traits will only be shared by species that share a more recent common ancestor... A B C D E (out) Trait 1 1 Trait 2 Trait 3 Trait 4 Trait 5

A B C D E (out) Trait 1 1 Trait 2 Trait 3 Trait 4 Trait 5 So, to reconstruct phylogenies and build a rooted tree, we don't just count shared traits... we count SHARED, DERIVED traits (synapomorphies) A B C D E (out) Trait 1 1 Trait 2 Trait 3 Trait 4 Trait 5

A B C 4 - 1 2 D Number of synapomorphies: So, A and B share 4 synapomorphies: 1, 2, 4, and 5 (they share these traits, and their state is different from the outgroup). B and C share 2 synapomorphy (3, 5). A B C D E (out) Trait 1 1 Trait 2 Trait 3 Trait 4 Trait 5 A B C 4 - 1 2 D Number of synapomorphies:

Now, there are a couple rooted trees that fit these data equally well: First, our assumed tree: A B C 4 - 1 2 D In this case, the shared trait between B and C must be interpreted as an instance of "convergent/parallel evolution (CE)", in which the trait evolved independently in both species (not inherited from ancestor). 3 A B C D E Trait 1 1 Trait 2 Trait 3 Trait 4 Trait 5 1, 2, and 4 5

Now, there are a couple rooted trees that fit these data equally well: But there is another: A B C 4 - 1 2 D In this case, the discrepancy between A, B, and C is explained as an evolutionary "reversal" in A, which has re-expressed the ancestral trait. 3 A B C D E Trait 1 1 Trait 2 Trait 3 Trait 4 Trait 5 1, 2, and 4 3 5

In both cases, species share traits for reasons OTHER than inheritance for an immediate common ancestor. These are called homoplasies, and they obviously can confound the reconstruction of phylogenies. Both trees require 6 evolutionary events, so they are equally "parsimonious" (simple). We could envision lots of other trees, but they would require more reversions and convergent events. We apply Occam's Razor - a philosophical dictum that we will accept (and subsequently test) the simplest trees that express "maximum parsimony". So these two trees are our phylogenetic hypotheses – to be tested by more data that explicitly addresses their differences.

We might combine what we know from both equally parsimonius trees into a “consensus tree”. Both trees have clade A-B, and E as the outgroup. Relationships of C and D to one another and to A-B is ambiguous, so a polytomy (“comb”) is used…. A B C D E

The only trait we did not define was an autapomorphy - this is a trait unique to a species. In our examples above, each trait has only two character states. But consider nucleotides, where each trait (position) has 4 possibilities. we can envision that a species might have a T whereas all other species in the tree have A, C, or G. This would be an autapomorphy, and obviously doesn't help us out in phylogeny reconstruction because it doesn't share this trait with anything else.