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1 Denisova cave h,ps://

2 Gene tree- species tree conflict can result from introgression or incomplete lineage sorcng Sous & Hey 2013 DisCnguishing incomplete lineage sorcng from introgression (ABBA- BABA stacscc) Under incomplete lineage sorcng & no introgression Number of ABBA loci =Number of BABA loci D = (#(ABBA) #(BABA))/C, C= #(ABBA) + #(BABA) Green et al 2010, Nature

3 H2, H1, Neanderthal, Chimp H2, H1, Neanderthal, Chimp Under incomplete lineage sorcng & no introgression Number of ABBA loci =Number of BABA loci D = (#(ABBA) #(BABA))/C; C= #(ABBA) + #(BABA) 2,H 2,Denisova,chim Table 1 Sharing of derived alleles aybetween and archaic present-day homininsand archaic hominins Sample H 1 Sample H 2 Source D(H 1,H of 2 data,neanderthal,chimpanzee) D(H 1,H,Neanderthal,chimpanzee) D(H 1,H 2,Denisova,chimpanzee) D(H 1 for H 1 and H 2 Cambodian Mongolian n BABA n This ABBA study D (%) n BABA s.e. (%) 2,811 n ABBA Z-score D (%) n 2, BABA s.e. (%) 1.4 n ABBA Z-score D (%) n 0.1 BABA s.e. (%) 4,442 n ABBA Z-score 4,342 D (%) 1.1 Eurasian/Eurasian African/African* San Yoruba 23,690Ref. 23, , , , , , , Eurasian/African* Melanesian/Melanesian French San 25,242Ref. 22, , ,9827.6{ 4.739, , { , , { 1.7 French Yoruba 21,794Ref. 19, , ,8906.9{ 4.634, , { , , { 1.8 Han San 25,081Ref. 22, , ,4708.5{ 5.538, , { , , { 1.8 Han Yoruba 21,741Ref. 19, , ,4127.9{ 5.733, , { , , Mongolian Karitiana Mbuti 3,077 1,577 This2,765 1,473 study ,077 1, ,765 1, { ,514 2, ,505 2, { ,514 2, ,505 2, Eurasian/Melanesian* French Papuan1 15,523Ref. 15, , , , , , , { 24.0 Han Mongolian Papuan1 Bougainville 15,059Ref. This 14,677 8study 1.315,059 2, ,677 3, , , ,262 4, ,198 4, { Melanesian/African* Karitiana Papuan2 1,522This 1,658 study , , , , , , { 29.1 Papuan1 San 21,985Ref. 20, , ,3665.1{ 3.835, , { , , { 4.5 Papuan1 Yoruba 19,107Ref. 17, , ,6464.9{ 4.030, , { , , { 4.7 Papuan2 Mbuti 3,832This 3,324 study 7.1 3, ,3245.4{ 7.1 6, , { 7.86, , { 7.8

4 Under incomplete lineage sorcng D = (#(ABBA) #(BABA))/C D=0.037 ± (two- tailed D = 0, P = ) Genomic posicon

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6 Phenotypic Resemblance between Covariance relacves CorrelaCon Slope of linear regression

7 Francis Galton Phenotypic variacon with a populacon is usually concnuous, o`en has a normal distribucon. Inheritance is the blending together of parental phenotypes. Regression towards mediocrity (the mean) Galton, F. (1885).

8 Resemblance between relacves Gregor Mendel And the Mendelians e.g.bateson Galton And the Biometricians e.g. Pearson and Weldone

9 R.A. Fisher (1918) The correlations between relatives on the supposition of Mendelian inheritance Reconciled these two views by showing that the mendelian inheritance of many alleles, each of small effect, gave rise to: - - Resemblance between relacves. - - regression towards the mean. The apparent blending of traits is due to inheritance ½ alleles from Mum and ½ from Dad.

10 To what extent is my weight genecc? My height ~6 foot My weight ~160 pounds My BMI 21.7 Histogram from Barra, et al 2007 Phenotypes are always due to the interaccon of genes and environments.

11 My BMI is 22.4 Top 6 Alleles associated with BMI: SNP name My Genotype Avg. Effect on BMI* rs GT 0.33 for each T rs AA 0.2 for each G rs CC 0.19 for each T rs GG 0.15 for each A rs AA 0.07 for each G rs CT 0.1 for each C There are likely to be hundreds more genefc variants contribufng to BMI. Histogram from Barra, et al 2007 *Calculated by 23&Me. The heritability BMI (h 2 ) in Europeans is between 0.5 and 0.70

12 Resemblance between relacves in A trait with L loci QuanCtaCve traits Each segregacng an allele A 1 at freq. p l Each copy of the A 1 allele at a locus increasing our phenotype by a l, i.e. addicvely, around mean. Our genotype at locus l is 0,1,2 w.p. p l2,2p l (1- p l ), (1- p l ) 2 An individual s phenotype, X p, is made up of X P = X A + X E

13 Two alleles at a single locus controlling height. Frequency Short allele Tall allele Genotype Phenotype

14 Frequency bialleic loci. Phenotype Genotype

15 Frequency loci with equal addicve effect Trait distribucon follows Normal (Gaussian) DistribuCon. This is an example of the central limit theory, i.e. the sum of many small, independent random effects has a Normal distribucon Phenotype Genotype

16 163 loci Mean addicve effect on height at a locus: 0.24cm Mean allele frequency: 52% in French populacon Number of Individuals Frequency Number height increasing alleles Genetic effect on height, cm

17 An individual s phenotype, X p, is made up of X P = X A + X E X A GeneCc contribucon to phenotype has a normal distribucon N(0,V A ) - - Follows from the Central Limit Theory Assume that X E has a normal distribucon N(µ E,V E ) Thus X P has a normal distribucon N(µ A + µ E,V P ) V P =V E +V A *Heritability = h 2 = V A /V P *NARROW SENSE

18 Resemblance between relacves in QuanCtaCve traits Individual 1 s phenotype = X 1 Individual 2 s phenotype =X 2 Want to know the cov(x 1,X 2 ) = Cov((X 1M +X 1P +X 1E ), (X 2M +X 2P +X 2E ))

19 Heritability is escmated from mid- parent- offspring analysis as the slope of the regression line Slope=Cov(X,Y)/Var(X) =(V A /2) /(V P /2) = h 2 Offspring height Offspring s phenotype predicted by parental mean When mid- parental values does not influence offspring phenotype.

20 Offspring s Height Slope = 0.9

21 the effect of shared environment Need to eliminate the covariance of relacves due to shared environment. This is hard but doable through careful experiments. E.g. cross fostering, or common garden experiments Or by use of other pairings of relacves.