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Thread: Effective population size in open and isolated European populations

  1. #1
    Elite member Tomenable's Avatar
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    Ethnic group
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    Country: Poland



    Effective population size in open and isolated European populations

    From "Overcoming the dichotomy between open and isolated populations using genomic data from a large European dataset":


    http://www.nature.com/articles/srep41614


    Figure 4: Effective population size estimates based on 68,205 SNPs (16 chromosomes):








    "Effective population size in open and isolated European populations


    Among isolated populations, the estimated values of effective population size (Ne) range between 209 (Sauris, 208210; 95% confidence interval) and 3739 (Basque, 36073880; 95% confidence interval;Fig. 4,Supplementary Table S8). Regarding open populations, the values range between 2386 (Albania, 23422452; 95% confidence interval) and 8267 (Poland, 78508732; 95% confidence interval). Interestingly, seven open (Albania, Croatia, Greece, Aosta, Sicily, South Italy and Norway) and five isolated populations (Basques, Benetutti, Carloforte, North Sardinia, and Cimbrians) fall into the range of the alternative group. When repeating the estimates in the four populations for which SNP data at a higher resolution were available (HGDP panel; 647,789 SNPs) using an IBD sharing based method30, we obtained values that were different in absolute terms but highly correlated with those produced by GenoChip 2.0 (seeSupplementary Table S9)."
    There are words which carry the presage of defeat. Defence is such a word. What is the result of an even victorious defence? The next attempt of imposing it to that weaker, defender. The attacker, despite temporary setback, feels the master of situation:

    https://www.youtube.com/watch?v=Et1SkVldiHI

  2. #2
    Elite member Tomenable's Avatar
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    What conclusions about demographic history can we draw from this data? Why is Poland's effective population size larger than those of other analyzed populations?

  3. #3
    Elite member Tomenable's Avatar
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    In case if you are interested, here are Global25 coordinates for the Carloforte indviduals from that study:

    Carloforte_G25.txt

    ^^^
    You can check their distances to modern individuals (scaled) using tools from ExploreYourDNA website:

    https://www.exploreyourdna.com/calculateurs.aspx

    Code:
    Distance to:    Carloforte:Carloforte25
    0.02060687    Italian_Tuscany:MURLO114
    0.02203524    Italian_Tuscany:VO65
    0.02270215    French_Corsica:corsica29008
    0.02382759    Italian_Tuscany:Tuscany27
    0.02408773    Italian_Piedmont:ItalyPiedmont43
    
    Distance to:    Carloforte:Carloforte24
    0.03111992    French_Corsica:Corsica29708
    0.03178575    Italian_Lombardy:BGD301
    0.03242283    French_Corsica:corsica29008
    0.03393861    French_Corsica:CorsicaS10208
    0.03477982    French_Corsica:CorsicaS03308
    
    Distance to:    Carloforte:Carloforte23
    0.02502414    French_Corsica:CorsicaS04208
    0.02634923    French_Provence:S_34
    0.02678673    French_Corsica:Corsica14708
    0.02697060    Italian_Bergamo:HGDP01152
    0.02760781    Italian_Veneto:ALP116
    
    Distance to:    Carloforte:Carloforte22
    0.02754649    Italian_Piedmont:ItalyPiedmont119
    0.02915764    French_Corsica:Corsica24508
    0.02975085    Italian_Umbria:PG08
    0.03042940    Italian_Piedmont:Piedmont61
    0.03148665    Italian_Lombardy:ALP288
    
    Distance to:    Carloforte:Carloforte21
    0.02345935    French_Corsica:CorsicaS04208
    0.02741474    Italian_Tuscany:MURLO114
    0.02792962    French_Corsica:corsica29008
    0.02793493    Italian_Bergamo:HGDP01153
    0.02798926    Italian_Piedmont:ItalyPiedmont119
    
    Distance to:    Carloforte:Carloforte20
    0.02989832    Italian_Veneto:ALP322
    0.03005615    Italian_Tuscany:Tuscany74
    0.03059018    Italian_Piedmont:ItalyPiedmont136
    0.03115380    Italian_Lombardy:BGD31
    0.03157414    Italian_Tuscany:Tuscany38
    
    Distance to:    Carloforte:Carloforte19
    0.03326752    French_Corsica:Corsica24508
    0.03652852    Italian_Trentino-Alto-Adige:ALP114
    0.03714879    Italian_Veneto:ALP116
    0.03792314    Italian_Tuscany:NA20504
    0.03882890    French_Corsica:Corsica19508
    
    Distance to:    Carloforte:Carloforte18
    0.02826974    Italian_Lombardy:BGD301
    0.02905139    French_Corsica:Corsica29708
    0.03363338    Italian_Piedmont:ItalyPiedmont43
    0.03367496    French_Corsica:CorsicaS04208
    0.03414777    French_Corsica:CorsicaS10208
    
    Distance to:    Carloforte:Carloforte17
    0.02168102    Italian_Umbria:PG08
    0.02205581    Italian_Tuscany:VO65
    0.02300839    Italian_Tuscany:Tuscany27
    0.02377520    French_Corsica:CorsicaS04208
    0.02403134    French_Corsica:Corsica24508
    
    Distance to:    Carloforte:Carloforte16
    0.02689033    Italian_Tuscany:Tuscany98
    0.02837332    French_Corsica:Corsica29708
    0.02865747    Italian_Lombardy:BGD31
    0.02931224    Italian_Tuscany:MURLO114
    0.02960434    Italian_Tuscany:Tuscany38
    
    Distance to:    Carloforte:Carloforte15
    0.02658060    French_Corsica:Corsica24508
    0.02745413    Italian_Umbria:PG12
    0.02910978    Italian_Tuscany:NA20505
    0.02912615    Italian_Tuscany:MURLO114
    0.02922912    Italian_Umbria:PG04
    
    Distance to:    Carloforte:Carloforte14
    0.02874667    French_Corsica:CorsicaS10208
    0.03593885    French_Corsica:Corsica03708
    0.03603324    French_Corsica:CorsicaS03308
    0.03638609    French_Corsica:Corsica19508
    0.03756405    French_Corsica:CorsicaS29908
    
    Distance to:    Carloforte:Carloforte13
    0.02045407    French_Corsica:Corsica24508
    0.02467040    Italian_Tuscany:MURLO114
    0.02480578    French_Corsica:CorsicaS04208
    0.02506853    Italian_Tuscany:VO65
    0.02515156    Italian_Lombardy:ALP288
    
    Distance to:    Carloforte:Carloforte12
    0.02827321    French_Corsica:Corsica14708
    0.02834011    French_Corsica:Corsica24508
    0.03096742    French_Corsica:CorsicaS10208
    0.03267445    French_Corsica:CorsicaS04208
    0.03345236    French_Corsica:corsica29008
    
    Distance to:    Carloforte:Carloforte11
    0.02564571    Italian_Veneto:Alp401
    0.02610970    French_Provence:provance2708
    0.02643482    Italian_Veneto:KF1800751
    0.02731497    Italian_Lombardy:ALP288
    0.02752322    Swiss_Italian:Swiss_Italian2
    
    Distance to:    Carloforte:Carloforte10
    0.02600873    Italian_Piedmont:ItalyPiedmont43
    0.02645489    Italian_Lombardy:ALP288
    0.02806791    Italian_Piedmont:Piedmont154
    0.02821014    Italian_Tuscany:NA20502
    0.02827940    Italian_Tuscany:MURLO114
    
    Distance to:    Carloforte:Carloforte9
    0.01994032    Italian_Tuscany:NA20504
    0.02334022    Italian_Trentino-Alto-Adige:ALP114
    0.02377735    Italian_Piedmont:ItalyPiedmont149
    0.02466616    Italian_Veneto:ALP116
    0.02693919    Italian_Tuscany:Tuscany27
    
    Distance to:    Carloforte:Carloforte8
    0.03131110    Italian_Umbria:PG15
    0.03137646    Italian_Piedmont:ItalyPiedmont149
    0.03252576    Italian_Tuscany:NA20505
    0.03254824    Italian_Umbria:PG11
    0.03275238    Italian_Tuscany:VO65
    
    Distance to:    Carloforte:Carloforte7
    0.02328055    Italian_Bergamo:HGDP01155
    0.02448697    French_Corsica:corsica29008
    0.02540282    French_Corsica:CorsicaS04208
    0.02540591    French_Corsica:CorsicaS03308
    0.02660308    Italian_Bergamo:HGDP01153
    
    Distance to:    Carloforte:Carloforte6
    0.02752232    Italian_Veneto:ALP116
    0.02827306    Italian_Trentino-Alto-Adige:ALP114
    0.02980546    Swiss_Italian:Swiss_Italian3
    0.02982439    Italian_Veneto:KF1803151
    0.02983289    Italian_Veneto:KF1800751
    
    Distance to:    Carloforte:Carloforte5
    0.02308819    Italian_Lombardy:BGD103
    0.02356650    Italian_Tuscany:Tuscany98
    0.02421569    French_Provence:S_34
    0.02443298    Italian_Bergamo:HGDP01155
    0.02551748    Italian_Piedmont:ItalyPiedmont98
    
    Distance to:    Carloforte:Carloforte4
    0.02307707    Italian_Tuscany:Tuscany54
    0.02394105    Italian_Veneto:KF1800751
    0.02512910    Swiss_Italian:Swiss_Italian3
    0.02523581    Italian_Veneto:ALP209
    0.02530992    Italian_Piedmont:Piedmont61
    
    Distance to:    Carloforte:Carloforte3
    0.02198953    Italian_Veneto:ALP209
    0.02280479    Italian_Tuscany:Tuscany98
    0.02478209    Italian_Piedmont:ItalyPiedmont43
    0.02603310    Italian_Piedmont:ItalyPiedmont98
    0.02616689    Italian_Tuscany:Tuscany27
    
    Distance to:    Carloforte:Carloforte2
    0.02760839    French_Corsica:Corsica24508
    0.02985751    Italian_Veneto:ALP116
    0.03169578    Italian_Tuscany:VO65
    0.03234903    Italian_Tuscany:VO109
    0.03256628    French_Corsica:Corsica19508
    
    Distance to:    Carloforte:Carloforte1
    0.02171996    French_Corsica:Corsica14708
    0.02220513    French_Provence:provance2708
    0.02256662    Italian_Lombardy:ALP288
    0.02374905    Italian_Veneto:ALP116
    0.02415545    Swiss_Italian:Swiss_Italian2

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