Natural Selection and Variation in Populations Chapter 4 – from Stebbin’s 1950 Variation and in “Natural Selection”

¥ Cornerstone of evolution Ð 1860-1900 “Natural Selection”

¥ Cornerstone of evolution Ð 1860-1900 ¥ “ theory” supplants n.s. Ð 1900-1920s

Wilhelm Johannsen

Hugo DeVries The early observed an act of while studying the evening primrose . The original species, lamarckiana, had 14 , while the new species had 28. The new species was unable to breed with , and thus he named it Oenothera gigas (De Vires, 1905) “Natural Selection”

¥ Cornerstone of evolution Ð 1860-1900 ¥ “Mutation theory” supplants n.s. Ð 1900-1920s ¥ Resurgence of natural selection (NeoDarwinism) 1930s- Decline of Natural Selection

¥ Mutation theory of DeVries Ð evolution comes about with sudden new with large effects rare; most mutations have small effects

¥ Artificial selection ineffective only in choice of plants studied Resurgence of Natural Selection

We can no longer think of mutation as the primary source of directive tendencies in evolution and of selection in the purely negative role of eliminating unfavorable tendencies. On the contrary, the direction of evolution is determined largely by selection acting on the fund already present in the population, the component of which represent mutations that have occurred many generations ago. New mutations are important chiefly as a means of replenishing the store of variability which is continuously being depleted by selection.

Resurgence of Natural Selection

¥ Mutations with large effects rare; most mutations have small effects

but . . .

Goldschmidt, Richard. 1940. The Material Basis of Evolution. Yale Univ. Press.

"biologists seem inclined to think that because they have not themselves seen a 'large' mutation, such a thing cannot be possible. But such a mutation need only be an event of the most extraordinary rarity to provide the world with the important material for evolution" Resurgence of Natural Selection

¥ Mutations with large effects rare; most mutations have small effects

but . . .

Gottlieb LD. 1984. and morphological evolution in plants. Am. Nat. 123: 681–709 Resurgence of Natural Selection

¥ Mutations with large effects rare; most mutations have small effects

but . . .

Theissen, G. 2006. The proper place of hopeful monsters in evolutionary . Theory Biosci 124: 349-369.

Theissen, G. 2010. Homeosis of the angiosperm : Studies on three candidate cases of saltational evolution. Palaeodiversity 3, Supplement: 131-139. Resurgence of Natural Selection

¥ Mutations with large effects rare; most mutations have small effects

¥ Pure homozygous individuals rare in nature

¥ Differences among populations/races are not simple Mendelian but polygenic

¥ Analogy between breeders (artificial selection) and nature (natural selection) Ð heritability

Need for Experimental Evidence for Natural Selection (esp. outcrossers)

¥ Trifolium repens

¥ Potentilla glandulosa

¥ Taraxacum

¥ Hordeum vulgare Need for Experimental Evidence for Natural Selection (esp. outcrossers)

H. V. Harlan Plant Breeding Symposium: Who will train plant breeders? H.V. Harlan (1957)

"The field of plant breeding actually suffered in a way from the greater knowledge we had acquired. Mendel's work was quickly accepted as an enormous advantage in plant science. It was a definite, tangible thing that seemed to take plant breeding from the arts and place it as a science overnight. It captured the imagination of all workers, and genetics at once became a field offering prestige that both soothed and satisfied."

"A genetic paper gave new dignity to the author. We boys began to get our hair cut and our shoes shined. The effect on plant breeding was calamitous. Good varieties were still produced, but explorations in the field of practical plant breeding were wholly neglected."

"A few of us eventually realized that there would come a day when the world would recognize the difference between a good geneticist and a poor one, so we went back to thinking about plant breeding. We have undoubtedly lost the resources of many good minds from this field for a time, but they will be back." Need for Historical Evidence for Natural Selection

¥ Many animal studies, especially Drosophila

¥ Pasture grasses and forbs in Maryland (Kemp, 1937)

Fast forward 2015 Ð what plant or animal examples usually cited now? Adaptive Value of Character?

“the determination of the adaptive character of many types of differences between organisms is one of the most difficult problems in biology” Adaptive Value of Character?

Achillea:

adaptive non-adaptive

¥ Plant height ¥ Ligule size ¥ texture ¥ Flower color ¥ Head size ¥ Leaf cut ¥ Floret number ¥ Branching patter Adaptive Value of Character?

“the determination of the adaptive character of many types of differences between organisms is one of the most difficult problems in biology”

Other ways to claim “adaptive” nature of a character Ð not really mentioned by Stebbins

1. – “unity of type” 2. Convergence 3. Phylogenetic Adaptive Value of Character? - convergence

Foquieria Ð Foquieriaceae Allauidia Ð Didieriaceae western Madagascar Adaptive Value of Character? - phylogenetic

“the determination of the adaptive character of many types of differences between organisms is one of the most difficult problems in biology” adaptationism Adaptive Value of Character? - phylogenetic Adaptive Value of Character? - phylogenetic

1. Adaptation 2. Exaptation 3. Disaptation 4. Nonaptation Indirect Action of Natural Selection

1. Developmental correlation (Darwin)

2. Adaptive compensation (C.K.H.)

3. Selective correlation

“Developmental correlation brings about adaptive compensation which results in selective correlation” NATURE COMMUNICATIONS | DOI: 10.1038/ncomms4706 ARTICLE

a Sc8

Sc7

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Sc4 Arabidopsis lyrata Arabidopsis

Sc3

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ARTICLE

Received 6 Jan 2014 | Sc1Accepted 21 Mar 2014 | Published 23 Apr 2014 DOI: 10.1038/ncomms4706 OPEN The emerging biofuel crop Camelina sativa retains a

highly undifferentiatedCsa1 Csa2 Csa3 Csa4 hexaploidCsa5 Csa6 Csa7 genomeCsa8 Csa9 structure Csa10 Csa11 Csa12 Csa13 Csa14 Csa15 Csa16 Csa17 Csa18Csa19 Csa20 Sateesh Kagale1,2, Chushin Koh2, John Nixon1, Venkatesh Bollina1, Wayne E. Clarke1, Reetu TutejaCamelina3, sativa Charles Spillane3, Stephen J. Robinson1, Matthew G. Links1, Carling Clarke2, Erin E. Higgins1, Terry Huebert1, Andrew G. Sharpebcd2 & Isobel A.P. Parkin1

A A Camelina sativa is an oilseed with desirable agronomic and oil-quality attributes for a viable industrial oil platform crop. Here we generate the first -scale high-quality J A A F F reference sequence for C. sativa andA annotated 89,418 protein-codingJ genes, O F R O K representing a whole-genome triplication event relativeN to the crucifer model ArabidopsisF K thaliana. C. sativa represents the first crop species to be sequenced from lineage I of the B B I S S O U I G L P V Brassicaceae. The well-preservedN hexaploidU genomeJ structure of C. sativa surprisingly mirrors O D L P V D R F U G those of economically importantK amphidiploid BrassicaI crop species from lineage III as well as J K P R wheat and cotton. TheB three of C. sativa show no evidence of fractionation bias Q T D U T E H M and limited expression-levelI bias, both characteristics commonlyK associatedB withD polyploid M Q C W B G C H W evolution. The highly undifferentiated polyploid genomeE of C. sativa presentsB significant E L Q Q P J I N D D L U X consequences for breeding and geneticQ manipulation of thisL industrialV oil crop. C H N X R G C T U E T G T R C D D G O I D M M H M P P W 6 C S S E AK1 AK2 AK3 AK4 AK5 AK AK7 AK8 AK1 AK3 AK5 AK6 AK7 AK8 H W Csa01 V S AK2/4 E H C E C N O O S N Csa03 D Csa10 N N D D D Csa15 W I Csa13 Csa19 R Csa12 I I Csa20 E V Csa05 Csa14 X D E J E I E X Reciprocal I E E Pericentric Csa17 Csa08 Csa18 translocation I J U inversion E D I E Paracentric Csa02 Consecutive E D Csa07 J inversion I paracentric and I D W pericentric I AK2 I Csa16 Csa04 I I Csa06 inversions

E 1 Saskatoon Research Centre, Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, Saskatchewan, Canada S7N 0X2. 2 National Research Council J J J Canada, 110 Gymnasium Place, Saskatoon, Saskatchewan, Canada S7N 0W9. 3 Plant and AgriBiosciencesD Centre (PABC), School of NaturalJ Sciences, J National University of Ireland Galway, Galway, Ireland. CorrespondenceAK1 AK2 AK3AK4 andAK5 requestsAK6 AK7 AK8 for materials should be addressed to A.G.S. (email: andrew.sharpe@nrc- X Csa09 cnrc.gc.ca) or to I.A.P.P. (email: [email protected]).

NATURE COMMUNICATIONSCs-G1| 5:3706 | DOI: 10.1038/ncomms4706Csa11 Cs-G2 | www.nature.com/naturecommunicationsCs-G3 1 & 2014 Macmillan Publishers Limited. All rights reserved. AK4 AK4 AK2/4 AK2/4 AK2/4 Figure 3 | Comparative analysis and evolution of the C. sativa genome. (a) MUMer plot comparing the C. sativa and A. lyrata genomes. Syntenic and collinear regions making the three complete sub-genomes in C. sativa are circled in red, blue and green. (b) Reconstruction of the three sub-genomes of C. sativa. Chromosome and ancestral genomic-block-level organization of the sub-genomes in C. sativa is shown. Based on synteny and collinearity between C. sativa and Arabidopsis species, and GB contiguity in the ancestral karyotype, pseudochromosomes were assigned to three sub-genomes in C. sativa. Each pseudochromosome was subdivided among ancestral genomic blocks (A–X), which are coloured based on their occurrence in the ACK. (c) ACK consisting of the 24 conserved genomic blocks (A–X). (d) The ancestral diploid karyotype (derivative of ACK) of C. sativa.(e) The presumed origin and reconstruction of the fusion chromosome (AK2/4) of the dACK. of chromosome number and rearrangement of ancestral respect to A. thaliana and A. lyrata stands in contrast to these chromosomal blocks. This structure is also mirrored in observations but could reflect a more highly conserved nature of Australian Brassicaceae species, including Stenopetalum and these species within the Camelineae tribe. The three sub-genomes Ballantinia species that diverged B5.9 Mya (ref. 22). The within C. sativa, although showing some differentiation at the relatively unarranged nature of the C. sativa sub-genomes with -level (2–2.5% sequence variation across the coding

NATURE COMMUNICATIONS | 5:3706 | DOI: 10.1038/ncomms4706 | www.nature.com/naturecommunications 5 & 2014 Macmillan Publishers Limited. All rights reserved. Indirect Action of Natural Selection

Selective correlation Ð Plantago maritima Indirect Action of Natural Selection

Selective correlation Ð fleshy fruits in closed forest

Smith, J. 2001. High species diversity in fleshy-fruited tropical understory plants. American Naturalist 157: 646-53 Indirect Action of Natural Selection

Selective correlation Ð fleshy fruits in closed forest

Givnish et al. 2005. Repeated evolution of net venation and fleshy fruits among monocots in shaded habitats confirms a priori predictions: evidence from an ndhF phylogeny. Proceedings of the Royal Society of London, Biological Sciences 272: 1481-1490 Indirect Action of Natural Selection

Selective correlation Ð Asteraceae and Poaceae in California Summary Action of Natural Selection

1. Works immediately via adaptive value of the visible changes

2. Works on non-adaptive traits developmentally correlated with adaptive traits

3. Traits not directly adaptive may acquire selective value due to compensatory system of adaptation

4. Non-adaptive characters may become fixed due to chance Random or Drift Evolution

1. Gives three examples: Papaver, Hutchinsia, Linanthus Modern Research on Natural Selection and Drift in Plants?

1. Anderson JT, Willis JH, Mitchell-Olds T. 2011. Evolutionary genetics of plant adaptation. Trends Genet. 27: 258-66.

2. Savolainen O, Lascoux M, Merilä J. 2013. Ecological of local adaptation. Nat Rev Genet. 14: 807-20.

3. Others? Arabidopsis, Mimulus, Populus, Eucalyptus, island plant lineages, Cakile