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CHP4.SEvsCH

PCAdapt: SE - choose the number of Ks

screen shot 2017-10-04 at 10 16 08

p-value distributions

screen shot 2017-10-04 at 10 20 44

CH.LFMM.Figs

Figures for LFMM.CH data

CHN.hist

screen shot 2017-03-10 at 22 14 24

CHN.Venn
screen shot 2017-03-10 at 22 15 55

CHS.hist
screen shot 2017-03-10 at 22 52 38

CHS.Venn
screen shot 2017-03-10 at 23 00 36

CHS.VS.hist
screen shot 2017-03-10 at 23 12 29

CHS.VS.Venn
screen shot 2017-03-10 at 23 16 10

CHS.TI.hist

screen shot 2017-03-10 at 23 34 47

CHS.TI.Venn
screen shot 2017-03-10 at 23 38 27

CZ.hist
screen shot 2017-03-10 at 23 52 57

CZ.Venn
screen shot 2017-03-10 at 23 59 26

CHP2:NEW Data: filtered for MAC

CHN p-value distribution

screen shot 2017-10-03 at 11 36 11

CHN.Venn diagram
screen shot 2017-10-03 at 11 37 36

CHS.p-values

screen shot 2017-10-03 at 11 21 07

CHS.Venn

screen shot 2017-10-03 at 11 22 48

CHS.VS p-value

screen shot 2017-10-03 at 11 29 45

CHS.VS venn

screen shot 2017-10-03 at 11 31 15

CHS.TI p-values
screen shot 2017-10-03 at 11 42 30

CHS.TI.Venn diagram

screen shot 2017-10-03 at 11 44 35

CZ. p-value distribution

screen shot 2017-10-03 at 11 50 23

CZ.Venn
screen shot 2017-10-03 at 11 52 26

Chp2_env.variables

  1. distribution of residuals for m1 CHS.VS.TI

screen shot 2017-09-25 at 10 38 00

CHall.day10cm m1 and then m2
screen shot 2017-09-25 at 11 26 26

CHall.shadow.days m1 and then m2
screen shot 2017-09-25 at 11 25 52

CHall.pcpt.60d m1 and then m2

screen shot 2017-09-25 at 11 25 21

CHall.temp.laying.date m1 and then m2
screen shot 2017-09-25 at 11 24 50

CHall.sol.rad m1 and then m2
screen shot 2017-09-25 at 11 24 17

CHall.residuals for all m1 models
screen shot 2017-09-25 at 11 22 38

CHall.residuals for all m2 models

screen shot 2017-09-25 at 11 21 35

CHS.VS.TI

m2 hist of residuals

screen shot 2017-09-25 at 13 38 25

sol.rad. comparing models

screen shot 2017-09-25 at 13 41 31

temp.laying.date comparison of models

screen shot 2017-09-25 at 13 46 08

pcpt.60d comparison of models

screen shot 2017-09-25 at 13 48 05

shadow.days comparison of models
screen shot 2017-09-25 at 13 49 30

day10cm comparison of models
screen shot 2017-09-25 at 13 50 59

5_CH_landscapeGenomics

CHall missingness

screen shot 2016-09-26 at 17 50 55

CHsubset.0.8

screen shot 2016-09-26 at 20 43 02

TESS3 cross entropy

screen shot 2016-10-05 at 17 25 37

fastStucture_CHall. K2-5

screen shot 2016-10-05 at 18 45 13

screen shot 2016-10-05 at 18 45 26

screen shot 2016-10-05 at 18 45 37

screen shot 2016-10-05 at 18 45 44

TESS3_CHall_K2

screen shot 2016-10-05 at 18 27 19

screen shot 2016-10-05 at 18 29 32

screen shot 2016-10-05 at 18 36 06

screen shot 2016-10-05 at 18 50 45

screen shot 2016-10-05 at 18 51 36

screen shot 2016-10-05 at 18 56 53

PCadapt_CHall.992.1838

screen shot 2016-10-06 at 12 06 05

PCA

screen shot 2016-10-06 at 12 47 25

CorrelationPlot_ENVVariables

screen shot 2016-10-07 at 17 55 50

screen shot 2016-10-07 at 17 56 53

LFMM: choosing K using snmf

CHN: K=4
screen shot 2016-10-11 at 10 37 44

CHS:K10
screen shot 2016-10-11 at 10 55 22

CHS.TI_K6
screen shot 2016-10-11 at 10 45 45

CHS.VS_K4
screen shot 2016-10-11 at 10 42 10

CHall
screen shot 2016-10-11 at 11 03 39

CZ_K9
screen shot 2016-10-11 at 11 04 10

SummStats.1

screen shot 2016-10-17 at 10 59 02

SummStats.2
screen shot 2016-10-17 at 11 04 57

SummStats.3
screen shot 2016-10-14 at 16 33 04

screen shot 2016-10-17 at 10 14 41

screen shot 2016-10-17 at 10 56 29

HsvsElev
screen shot 2016-10-17 at 12 42 24

Hs.deg.layingdate
screen shot 2016-10-17 at 12 42 54

Hs.degdays
screen shot 2016-10-17 at 12 53 10

Fst:
screen shot 2016-10-17 at 14 48 00

IBD1
screen shot 2016-10-17 at 22 27 08

IBD2
screen shot 2016-10-24 at 17 36 42

screen shot 2016-10-25 at 16 35 54
screen shot 2016-10-25 at 16 50 59
screen shot 2016-10-25 at 17 03 30
screen shot 2016-10-25 at 16 52 06
screen shot 2016-10-25 at 16 53 30
screen shot 2016-10-25 at 16 49 11

screen shot 2016-10-28 at 12 28 57

screen shot 2016-10-28 at 13 34 14

screen shot 2016-10-28 at 13 33 19

screen shot 2016-10-28 at 13 41 33

5.SE_Dec2016

screen shot 2016-11-30 at 14 39 41

screen shot 2017-02-17 at 15 03 12

screen shot 2016-11-30 at 15 29 48

screen shot 2016-11-30 at 17 09 26

screen shot 2016-11-30 at 17 54 00

screen shot 2016-11-30 at 18 00 21

screen shot 2016-12-01 at 10 43 19

screen shot 2016-12-01 at 11 23 46

screen shot 2016-12-01 at 16 13 03

screen shot 2016-12-01 at 16 42 05

screen shot 2016-12-01 at 17 55 02

screen shot 2016-12-01 at 17 56 32

screen shot 2016-12-01 at 22 29 26

screen shot 2016-12-01 at 22 37 39

screen shot 2016-12-01 at 23 11 35

screen shot 2016-12-01 at 23 11 49

screen shot 2016-12-01 at 23 15 33

screen shot 2016-12-01 at 23 16 00

screen shot 2016-12-01 at 23 20 04

screen shot 2016-12-01 at 23 21 01

screen shot 2016-12-01 at 23 22 24

PCAdapt
screen shot 2016-12-01 at 23 38 30

screen shot 2016-12-01 at 23 44 33

screen shot 2016-12-01 at 23 44 49

screen shot 2016-12-02 at 11 22 29

screen shot 2016-12-02 at 12 33 53

RDA
RDA.SEfull

screen shot 2016-12-02 at 14 59 38

pRDA.geog
screen shot 2016-12-02 at 14 38 55

pRDA.climate
screen shot 2016-12-02 at 14 42 38

Fst per locus between individuals:

screen shot 2016-12-02 at 17 04 56

screen shot 2016-12-05 at 11 03 52

screen shot 2016-12-05 at 11 07 29

RawData renanalysis
screen shot 2016-12-05 at 11 35 06

screen shot 2016-12-05 at 11 46 02

screen shot 2016-12-05 at 11 50 11

screen shot 2016-12-05 at 11 51 18

screen shot 2016-12-05 at 11 52 06

screen shot 2016-12-05 at 12 05 35

screen shot 2016-12-05 at 12 06 54

screen shot 2016-12-05 at 12 07 48

screen shot 2016-12-05 at 12 12 41

screen shot 2016-12-05 at 12 20 18

screen shot 2016-12-05 at 12 47 36

screen shot 2016-12-05 at 12 52 04

screen shot 2016-12-05 at 12 53 00

pcadapt
screen shot 2016-12-05 at 13 09 39

screen shot 2016-12-05 at 13 18 01

screen shot 2016-12-05 at 13 20 30

Fst
screen shot 2016-12-05 at 13 24 13

screen shot 2016-12-05 at 13 28 51

screen shot 2016-12-05 at 13 37 01

screen shot 2016-12-05 at 13 51 43

screen shot 2016-12-05 at 13 52 00

screen shot 2016-12-05 at 13 59 48

screen shot 2016-12-05 at 14 00 08
screen shot 2016-12-05 at 14 01 43

screen shot 2016-12-05 at 14 03 32
screen shot 2016-12-05 at 14 04 04

screen shot 2016-12-05 at 14 15 52

screen shot 2016-12-05 at 14 21 20

screen shot 2016-12-05 at 14 24 46

screen shot 2016-12-05 at 14 44 47

screen shot 2016-12-05 at 14 47 25

screen shot 2016-12-07 at 15 06 41

screen shot 2016-12-07 at 15 06 41

screen shot 2016-12-07 at 21 09 14

screen shot 2016-12-07 at 21 10 20

screen shot 2016-12-07 at 21 39 03

screen shot 2016-12-07 at 22 02 32

screen shot 2016-12-07 at 22 12 17

screen shot 2016-12-07 at 22 19 27

screen shot 2016-12-14 at 14 08 11

screen shot 2016-12-14 at 14 36 51

screen shot 2016-12-14 at 15 34 42

screen shot 2016-12-14 at 15 44 57

screen shot 2016-12-14 at 17 11 28

LFMM adjusted p-value distributions
screen shot 2017-01-31 at 10 00 51

screen shot 2017-02-02 at 13 09 59

Bayenv.Fig1

screen shot 2017-02-09 at 09 58 19

BayEnv.Fig2

screen shot 2017-02-09 at 10 08 03

AvgHet.Final

screen shot 2017-02-15 at 23 40 57

corrplot.trees for bayenv covariance matrices

screen shot 2017-02-20 at 15 05 39

Venn.LFMM

screen shot 2017-02-20 at 15 52 46

Venn.BayEnv2

screen shot 2017-02-20 at 15 52 59

Venn.FSToutliers
screen shot 2017-02-20 at 16 06 11

Venn.EAA
screen shot 2017-02-20 at 16 13 34

VennEAAvsFst
screen shot 2017-02-20 at 16 23 30

Fstplot.all

screen shot 2017-02-20 at 17 42 03

screen shot 2017-05-31 at 16 31 08
screen shot 2017-05-31 at 17 15 03

screen shot 2017-05-31 at 17 22 25
screen shot 2017-05-31 at 17 25 19

CH.RDA

CH940.full model

screen shot 2017-03-08 at 22 05 24

CH940.full model with elev

screen shot 2017-03-10 at 15 24 37

CH940 pRDA.geog

screen shot 2017-03-08 at 22 15 06

CH940 pRDA.geog.elev

screen shot 2017-03-10 at 15 29 32

pRDA.CH940.climate
screen shot 2017-03-08 at 22 22 36

pRDA.CH940.climate.elev
screen shot 2017-03-10 at 15 34 25

RDA.CHNfull
screen shot 2017-03-08 at 22 32 00

RDA.CHNfull.elev

screen shot 2017-03-10 at 16 15 00

pRDA.CHN.geog

screen shot 2017-03-08 at 22 36 06

pRDA.CHN.geog.elev
screen shot 2017-03-10 at 16 18 00

pRDA.CHN.climate

screen shot 2017-03-08 at 22 40 55

pRDA.CHN.climate.elev
screen shot 2017-03-10 at 16 37 35

RDA.CHSfull.elev
screen shot 2017-03-10 at 16 52 45

pRDA.CHS.geog.elev
screen shot 2017-03-10 at 16 55 43

pRDA.CHS.climate.elev
screen shot 2017-03-10 at 16 59 06

RDA.CHS.VSfull

screen shot 2017-03-08 at 22 49 00

RDA.CHS.VSfull.elev
screen shot 2017-03-10 at 17 03 40

pRDA.CHS.VS.geog
screen shot 2017-03-08 at 22 52 17

pRDA.CHS.VS.geog.elev
screen shot 2017-03-10 at 17 06 55

pRDA.CHS.VS.climate
screen shot 2017-03-08 at 22 54 55

pRDA.CHS.VS.climate.elev
screen shot 2017-03-10 at 17 09 28

RDA.CHS.TIfull
screen shot 2017-03-08 at 22 59 10

RDA.CHS.TIfull.elev
screen shot 2017-03-10 at 17 16 42

pRDA.CHS.TI.geog
screen shot 2017-03-08 at 23 02 05

pRDA.CHS.TI.geog.elev
screen shot 2017-03-10 at 17 19 12

pRDA.CHS.TI.climate
screen shot 2017-03-08 at 23 05 02

pRDA.CHS.TI.climate.elev
screen shot 2017-03-10 at 17 21 31

RDA.CZ.Full
screen shot 2017-03-10 at 17 29 20

pRDA.CZ.geog

screen shot 2017-03-10 at 17 36 17

pRDA.CZ.climate

screen shot 2017-03-10 at 17 39 31

CH.Fst.Figs

#CHall data: Fst distributions

March 2017

CHall.Neutral Fst
screen shot 2017-03-11 at 12 00 14

CHN.Neutral.Fst
screen shot 2017-03-11 at 13 17 02

CHS.Neutral.Fst
screen shot 2017-03-11 at 12 51 05

CHS.TI.Neutral.Fst
screen shot 2017-03-11 at 13 07 34

CHS.VS.Neutral.Fst
screen shot 2017-03-11 at 13 16 21

CZ.Neutral.Fst
screen shot 2017-03-11 at 13 27 07

screen shot 2017-03-11 at 13 36 40

Methods.ContactZone

screen shot 2016-07-27 at 10 29 57

screen shot 2016-07-27 at 10 34 46

TESS3 min-entropy graph

screen shot 2016-07-27 at 13 18 57

TESS3
K2
screen shot 2016-07-27 at 18 39 30

K3
screen shot 2016-07-27 at 18 39 55

Assessing BGC TestRun 1

screen shot 2016-08-17 at 09 34 27

screen shot 2016-08-17 at 09 35 52

screen shot 2016-08-17 at 10 17 12

Run2
screen shot 2016-08-25 at 09 36 35

Run3
screen shot 2016-08-25 at 09 35 50

Run4_alpha
screen shot 2016-08-29 at 11 00 42

screen shot 2016-08-29 at 11 11 31

Run4_beta
screen shot 2016-08-29 at 11 00 32

screen shot 2016-08-29 at 11 11 19

Run4_LnL
screen shot 2016-08-29 at 11 00 19

screen shot 2016-08-29 at 11 04 26

Samples in contact zone Low, mid, and high elevation

screen shot 2016-09-15 at 11 53 34

screen shot 2016-09-15 at 11 47 52
screen shot 2016-09-15 at 11 47 28
screen shot 2016-09-15 at 11 47 09

PCAdapt plots

High-Low :
Screeplot
screen shot 2016-09-15 at 12 27 09

PCplot
screen shot 2016-09-15 at 13 59 21

High-Mid
Screeplot
screen shot 2016-09-15 at 14 03 42

PCplot
screen shot 2016-09-15 at 14 04 03

Low-Mid
Screeplot
screen shot 2016-09-15 at 14 06 55

PCplot
screen shot 2016-09-15 at 14 07 26

PCadaptPlots

screen shot 2016-09-15 at 15 14 43
screen shot 2016-09-15 at 15 14 04

screen shot 2016-09-15 at 15 10 47
screen shot 2016-09-15 at 15 09 51

screen shot 2016-09-15 at 15 00 46

screen shot 2016-09-15 at 14 55 51
screen shot 2016-09-15 at 14 55 03

screen shot 2016-09-15 at 14 51 31
screen shot 2016-09-15 at 14 50 59

screen shot 2016-09-15 at 14 47 11
screen shot 2016-09-15 at 14 45 53

Elev.vsTemp

screen shot 2016-09-15 at 16 20 22

SE_MS1

screen shot 2016-08-15 at 16 59 00

screen shot 2016-08-15 at 17 13 48

screen shot 2016-08-16 at 11 27 32

screen shot 2016-08-17 at 07 18 21

screen shot 2016-08-17 at 07 18 45

Map of Bio2:

screen shot 2016-08-17 at 17 34 23

screen shot 2016-08-17 at 18 07 41

Sample Info

screen shot 2016-08-17 at 18 54 59

screen shot 2016-10-07 at 17 46 19

screen shot 2016-10-07 at 17 46 42

screen shot 2016-11-07 at 17 45 18

screen shot 2016-11-07 at 18 35 23

screen shot 2016-11-11 at 14 55 51

########
SE_Nov2016

screen shot 2016-11-14 at 17 31 36

screen shot 2016-11-15 at 17 55 11

screen shot 2016-11-15 at 18 30 57

screen shot 2016-11-16 at 16 42 23

screen shot 2016-11-16 at 16 38 28

screen shot 2016-11-16 at 18 20 52

screen shot 2016-11-17 at 11 00 00

screen shot 2016-11-17 at 08 37 56

MAF across all pops

Fig1
screen shot 2016-11-17 at 12 32 51

Fig2
screen shot 2016-11-17 at 13 14 12

Variable loci count
screen shot 2016-11-17 at 13 47 24

ClusterLevel
screen shot 2016-11-17 at 15 30 43

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