2016 09-16-fairdom
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Transcript of 2016 09-16-fairdom
A major transition in social evolution
& some data tidbits
[email protected] https://wurmlab.github.io
Avant
Workers staying outside die« preventive self-sacrifice »
Tofilski et al 2008
Forelius pusillus hides the nest entrance at night
Animal biomass (Brazilian rainforest)
from Fittkau & Klinge 1973
Other insects AmphibiansReptiles
Birds
Mammals
Earthworms
Spiders
Soil fauna excluding earthworms,
ants & termites
Ants & termites
www.sciencemag.org SCIENCE VOL 331 25 FEBRUARY 2011 1067
REPORTS
on
Mar
ch 1
2, 2
013
ww
w.s
cien
cem
ag.o
rgD
ownl
oade
d fro
m
Solenopsis invicta fire ants are a big problem!very well studied!
Ascunce et al 2011
Solenopsis invicta fire ant: two social forms
•1 large queen•Independent founding•Highly territorial•Many sizes of workers
•2-100 smaller queens•Dependent founding•No inter-colony aggression•All workers similar size
Single-queen form: Multiple-queen form:
Allozyme screen Social form associated to Gp-9 locus
Frequency of the most
common allele
Locus!
0.3!0.4!0.5!0.6!0.7!0.8!0.9!1.0!
Single queen!Multiple queen!
Est-6!Est-4!G3pdh-1!Ca-4!Pgm-4!Ddh-1!Pro-5!
Pgm-3!
Acoh-5!
acoh-1!
Acy-1!
Pgm-1!
Aat-2!
Gp-9!
Ken Ross and colleaguesLaurent Keller and colleagues
Single queen form Multiple queen form
Ken Ross and colleaguesLaurent Keller and colleagues
Social form completely associated to Gp-9 locus
bbbbBB BB Bb bb
Ken Ross and colleaguesLaurent Keller and colleagues
Single queen form Multiple queen form
Social form completely associated to Gp-9 locus
(>15% ) (< 5% )
bbBB BB Bb
x
Gp-9 bb females rareKen Ross and colleagues
Laurent Keller and colleagues
Single queen form Multiple queen form
Social form completely associated to Gp-9 locus
(>15% ) (< 5% )
BB BB Bb
Ken Ross and colleaguesLaurent Keller and colleagues
Single queen form Multiple queen form
Social form completely associated to Gp-9 locus
(>15% ) (< 5% )
BB BB Bb
xKen Ross and colleagues
Laurent Keller and colleagues
Single queen form Multiple queen form
Social form completely associated to Gp-9 locus
(>15% ) (< 5% )
BB BB Bb
x xKen Ross and colleagues
Laurent Keller and colleagues
Social form completely associated to Gp-9 locus
Single queen form Multiple queen form(>15% ) (< 5% )
BB BB Bb
x x xKen Ross and colleagues
Laurent Keller and colleagues
Single queen form Multiple queen form(>15% ) (< 5% )
Social form completely associated to Gp-9 locus
• Is this gene the single überregulator?
maybe 1/14th of the genome?
•Only 14 allozyme markers
Locus!
0.3!0.4!0.5!0.6!0.7!0.8!0.9!1.0!
Single queen!Multiple queen!
Est-6!Est-4!G3pdh-1!Ca-4!Pgm-4!Ddh-1!Pro-5!
Pgm-3!
Acoh-5!
acoh-1!
Acy-1!
Pgm-1!
Aat-2!
Gp-9!
Social form completely associated to Gp-9 locus
This changes everything.
Any lab can sequence anything!
http://genome.gov/sequencingcosts
Bb
unfertilised eggs
haploid ♂
Gp-9 B Gp-9 b Gp-9 B Gp-9 b Gp-9 b Gp-9 B
38 B♂ & 38 b♂
RAD genotyping
Identify polymorphismindividual x locus
genotype table
RAD genotyping: sequencing the same 0.01% of the genome in many individuals
A B C D E F
L1 A C A A C CL2 G G T - T GL3 - A G A - GL4 C - - G G CL5 T T C T C -L6 G A A - - G
2419
loci
38 B� & 38 b�
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20+
Amount of variance explained per principal component
Principal Component
% V
aria
nce
Exp
lain
ed
05
1015
2025
30
12.7%
6.1% 5.4% 4.8% 4.7% 3.9% 3.5% 3.2% 3.1% 2.9% 2.8% 2.6% 2.4% 2.3% 2.2% 2.0% 1.9% 1.7% 1.6%
30.2%
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20+
Amount of variance explained per principal component
Principal Component
% V
aria
nce
Exp
lain
ed
05
1015
2025
30
PCA: Principal Component Analysis
pc: 2 % variance: 6.073
pc: 3
%
var
ianc
e: 5
.441
-0.2
-0.1
0.0
0.1
0.2
-0.2 -0.1 0.0 0.1 0.2pc: 2 % variance: 6.073
pc: 3
%
var
ianc
e: 5
.441
-0.2
-0.1
0.0
0.1
0.2
-0.2 -0.1 0.0 0.1 0.2
Principal Components: PC2 vs PC3
Gp-9 B �Gp-9 b �
pc: 1 % variance: 12.666
pc: 2
%
var
ianc
e: 6
.073
-0.2
-0.1
0.0
0.1
0.2
-0.10 -0.05 0.00 0.05 0.10 0.15
Principal Components: PC1 vs PC2
pc: 1 % variance: 12.666
pc: 2
%
var
ianc
e: 6
.073
-0.2
-0.1
0.0
0.1
0.2
-0.10 -0.05 0.00 0.05 0.10 0.15
Gp-9 B ♂Gp-9 b ♂
brc_m013_0001..brc_m013_0005brc_m013_0006..brc_m013_0014brc_m013_0015..brc_m013_0017brc_m013_0018brc_m013_0019..brc_m013_0020brc_m013_0021..brc_m013_0029brc_m013_0030..brc_m013_0031brc_m013_0032..brc_m013_0034brc_m013_0035..brc_m013_0036brc_m013_0037..brc_m013_0038brc_m013_0039..brc_m013_0043brc_m013_0044brc_m013_0045brc_m013_0046..brc_m013_0048brc_m013_0049brc_m013_0050..brc_m013_0051brc_m013_0052..brc_m013_0056brc_m013_0057..brc_m013_0061
brc_m013_0062..brc_m013_0075brc_m013_0076..brc_m013_0078brc_m013_0079..brc_m013_0081
brc_m013_0082..brc_m013_0088
brc_m013_0089..brc_m013_0092
brc_m013_0093..brc_m013_0096brc_m013_0097brc_m013_0098..brc_m013_0113brc_m013_0114..brc_m013_0119brc_m013_0120..brc_m013_0130brc_m013_0131brc_m013_0132..brc_m013_0134brc_m013_0135..brc_m013_0136brc_m013_0137..brc_m013_0139brc_m013_0140..brc_m013_0142brc_m013_0143brc_m013_0144..brc_m013_0146brc_m013_0147..brc_m013_0154brc_m013_0155
brc_m013_0156brc_m013_0157..brc_m013_0180brc_m013_0181brc_m013_0182brc_m013_0183..brc_m013_0188brc_m013_0189..brc_m013_0208brc_m013_0209brc_m013_0210..brc_m013_0211brc_m013_0212..brc_m013_0215brc_m013_0216brc_m013_0217brc_m013_0218..brc_m013_0224brc_m013_0225..brc_m013_0228brc_m013_0229..brc_m013_0237brc_m013_0238..brc_m013_0245
brc_m013_0246..brc_m013_0270
brc_m013_0271..brc_m013_0274brc_m013_0275brc_m013_0276..brc_m013_0278
brc_m013_0279
brc_m013_0280
brc_m013_0281..brc_m013_0294
brc_m013_0295..brc_m013_0303brc_m013_0304brc_m013_0305..brc_m013_0307brc_m013_0308brc_m013_0309..brc_m013_0314brc_m013_0315..brc_m013_0317brc_m013_0318..brc_m013_0320brc_m013_0321..brc_m013_0326brc_m013_0327brc_m013_0328brc_m013_0329..brc_m013_0330brc_m013_0331..brc_m013_0333brc_m013_0334..brc_m013_0339brc_m013_0340brc_m013_0341..brc_m013_0343brc_m013_0344brc_m013_0345..brc_m013_0349brc_m013_0350
brc_m013_0351..brc_m013_0354brc_m013_0355brc_m013_0356brc_m013_0357..brc_m013_0361brc_m013_0362..brc_m013_0376brc_m013_0377..brc_m013_0390brc_m013_0391..brc_m013_0393brc_m013_0394..brc_m013_0400brc_m013_0401..brc_m013_0439brc_m013_0440..brc_m013_0478brc_m013_0479..brc_m013_0480
0
20
40
60
80
100
120
140
160
180
LG1brc_m013_0481brc_m013_0482..brc_m013_0484brc_m013_0485..brc_m013_0488brc_m013_0489..brc_m013_0502brc_m013_0503brc_m013_0504..brc_m013_0519brc_m013_0520..brc_m013_0532brc_m013_0533..brc_m013_0534brc_m013_0535..brc_m013_0537brc_m013_0538..brc_m013_0540brc_m013_0541..brc_m013_0543brc_m013_0544..brc_m013_0545brc_m013_0546..brc_m013_0549
brc_m013_0550..brc_m013_0554
brc_m013_0555..brc_m013_0560
brc_m013_0561..brc_m013_0562brc_m013_0563..brc_m013_0565
brc_m013_0566brc_m013_0567brc_m013_0568..brc_m013_0570brc_m013_0571..brc_m013_0573
brc_m013_0574..brc_m013_0575brc_m013_0576..brc_m013_0578brc_m013_0579..brc_m013_0580brc_m013_0581brc_m013_0582..brc_m013_0584brc_m013_0585brc_m013_0586brc_m013_0587brc_m013_0588..brc_m013_0591brc_m013_0592brc_m013_0593brc_m013_0594..brc_m013_0612brc_m013_0613..brc_m013_0614brc_m013_0615..brc_m013_0632brc_m013_0633brc_m013_0634..brc_m013_0648brc_m013_0649..brc_m013_0655brc_m013_0656brc_m013_0657..brc_m013_0694brc_m013_0695..brc_m013_0703brc_m013_0704brc_m013_0705brc_m013_0706..brc_m013_0707brc_m013_0708brc_m013_0709..brc_m013_0711brc_m013_0712..brc_m013_0715brc_m013_0716..brc_m013_0721brc_m013_0722brc_m013_0723brc_m013_0724..brc_m013_0728brc_m013_0729brc_m013_0730brc_m013_0731brc_m013_0732..brc_m013_0735brc_m013_0736..brc_m013_0769brc_m013_0770..brc_m013_0771brc_m013_0772..brc_m013_0773brc_m013_0774..brc_m013_0775brc_m013_0776..brc_m013_0782brc_m013_0783brc_m013_0784..brc_m013_0795brc_m013_0796..brc_m013_0798brc_m013_0799..brc_m013_0801brc_m013_0802..brc_m013_0805brc_m013_0806..brc_m013_0809brc_m013_0810..brc_m013_0811brc_m013_0812..brc_m013_0824brc_m013_0825..brc_m013_0826brc_m013_0827..brc_m013_0829brc_m013_0830..brc_m013_0831brc_m013_0832..brc_m013_0842brc_m013_0843..brc_m013_0854brc_m013_0855..brc_m013_0861brc_m013_0862brc_m013_0863..brc_m013_0864brc_m013_0865..brc_m013_0867brc_m013_0868..brc_m013_0883brc_m013_0884..brc_m013_0893brc_m013_0894brc_m013_0895..brc_m013_0897brc_m013_0898..brc_m013_0906brc_m013_0907..brc_m013_0910brc_m013_0911..brc_m013_0925brc_m013_0926..brc_m013_0928brc_m013_0929..brc_m013_0931
0
20
40
60
80
100
120
140
LG2brc_m013_0932..brc_m013_0941brc_m013_0942..brc_m013_0943brc_m013_0944..brc_m013_0945brc_m013_0946..brc_m013_0949brc_m013_0950..brc_m013_0952
brc_m013_0953..brc_m013_0975
brc_m013_0976..brc_m013_1019brc_m013_1020brc_m013_1021brc_m013_1022..brc_m013_1061brc_m013_1062brc_m013_1063
brc_m013_1064..brc_m013_1065
brc_m013_1066..brc_m013_1068brc_m013_1069brc_m013_1070
brc_m013_1071..brc_m013_1074
brc_m013_1075
brc_m013_1076..brc_m013_1081
brc_m013_1082..brc_m013_1086brc_m013_1087..brc_m013_1088brc_m013_1089..brc_m013_1098brc_m013_1099..brc_m013_1106brc_m013_1107..brc_m013_1116brc_m013_1117brc_m013_1118..brc_m013_1121brc_m013_1122..brc_m013_1127brc_m013_1128brc_m013_1129..brc_m013_1136brc_m013_1137..brc_m013_1138brc_m013_1139..brc_m013_1141brc_m013_1142..brc_m013_1144brc_m013_1145..brc_m013_1156brc_m013_1157brc_m013_1158..brc_m013_1170brc_m013_1171..brc_m013_1181brc_m013_1182..brc_m013_1185brc_m013_1186brc_m013_1187..brc_m013_1205brc_m013_1206..brc_m013_1218brc_m013_1219..brc_m013_1220brc_m013_1221..brc_m013_1224brc_m013_1225..brc_m013_1228brc_m013_1229brc_m013_1230..brc_m013_1236brc_m013_1237brc_m013_1238..brc_m013_1247brc_m013_1248..brc_m013_1251
brc_m013_1252brc_m013_1253..brc_m013_1268brc_m013_1269..brc_m013_1270brc_m013_1271..brc_m013_1273brc_m013_1274brc_m013_1275..brc_m013_1280brc_m013_1281
brc_m013_1282..brc_m013_1286brc_m013_1287..brc_m013_1298brc_m013_1299..brc_m013_1307brc_m013_1308brc_m013_1309..brc_m013_1313brc_m013_1314..brc_m013_1317brc_m013_1318..brc_m013_1319brc_m013_1320..brc_m013_1326brc_m013_1327..brc_m013_1340brc_m013_1341..brc_m013_1362brc_m013_1363..brc_m013_1385
0
20
40
60
80
100
120
140
LG3brc_m013_1386..brc_m013_1388brc_m013_1389..brc_m013_1398brc_m013_1399..brc_m013_1406brc_m013_1407..brc_m013_1411brc_m013_1412..brc_m013_1413brc_m013_1414..brc_m013_1416
brc_m013_1417brc_m013_1418..brc_m013_1420brc_m013_1421..brc_m013_1424brc_m013_1425..brc_m013_1432brc_m013_1433..brc_m013_1442brc_m013_1443brc_m013_1444..brc_m013_1450brc_m013_1451brc_m013_1452brc_m013_1453..brc_m013_1455brc_m013_1456..brc_m013_1467brc_m013_1468..brc_m013_1469brc_m013_1470brc_m013_1471..brc_m013_1474brc_m013_1475brc_m013_1476brc_m013_1477brc_m013_1478..brc_m013_1482brc_m013_1483
brc_m013_1484brc_m013_1485..brc_m013_1487brc_m013_1488..brc_m013_1490
brc_m013_1491brc_m013_1492..brc_m013_1494brc_m013_1495..brc_m013_1496
brc_m013_1497..brc_m013_1500brc_m013_1501brc_m013_1502..brc_m013_1513brc_m013_1514..brc_m013_1562brc_m013_1563..brc_m013_1565brc_m013_1566..brc_m013_1567
brc_m013_1568..brc_m013_1580brc_m013_1581..brc_m013_1587brc_m013_1588..brc_m013_1591brc_m013_1592..brc_m013_1593brc_m013_1594..brc_m013_1604brc_m013_1605..brc_m013_1607brc_m013_1608..brc_m013_1609brc_m013_1610..brc_m013_1611brc_m013_1612..brc_m013_1616brc_m013_1617..brc_m013_1618brc_m013_1619..brc_m013_1620brc_m013_1621..brc_m013_1629brc_m013_1630..brc_m013_1633brc_m013_1634..brc_m013_1638brc_m013_1639..brc_m013_1647brc_m013_1648..brc_m013_1649brc_m013_1650..brc_m013_1656brc_m013_1657..brc_m013_1665brc_m013_1666..brc_m013_1672brc_m013_1673..brc_m013_1674brc_m013_1675..brc_m013_1678brc_m013_1679..brc_m013_1682brc_m013_1683brc_m013_1684brc_m013_1685..brc_m013_1686brc_m013_1687..brc_m013_1700brc_m013_1701..brc_m013_1702brc_m013_1703brc_m013_1704..brc_m013_1707brc_m013_1708..brc_m013_1709brc_m013_1710..brc_m013_1714brc_m013_1715..brc_m013_1728brc_m013_1729..brc_m013_1742
0
20
40
60
80
100
120
140
LG4brc_m013_1743..brc_m013_1750
brc_m013_1751..brc_m013_1766brc_m013_1767brc_m013_1768
brc_m013_1769..brc_m013_1772
brc_m013_1773..brc_m013_1779brc_m013_1780brc_m013_1781brc_m013_1782..brc_m013_1783brc_m013_1784brc_m013_1785..brc_m013_1786
brc_m013_1787
brc_m013_1788brc_m013_1789..brc_m013_1790brc_m013_1791..brc_m013_1793brc_m013_1794..brc_m013_1797brc_m013_1798..brc_m013_1800brc_m013_1801..brc_m013_1804brc_m013_1805brc_m013_1806..brc_m013_1808brc_m013_1809brc_m013_1810..brc_m013_1813brc_m013_1814..brc_m013_1818brc_m013_1819..brc_m013_1820brc_m013_1821..brc_m013_1822brc_m013_1823..brc_m013_1824brc_m013_1825brc_m013_1826..brc_m013_1840brc_m013_1841..brc_m013_1842brc_m013_1843brc_m013_1844..brc_m013_1848brc_m013_1849brc_m013_1850brc_m013_1851..brc_m013_1853brc_m013_1854..brc_m013_1858brc_m013_1859..brc_m013_1866brc_m013_1867..brc_m013_1868brc_m013_1869brc_m013_1870..brc_m013_1874brc_m013_1875..brc_m013_1876brc_m013_1877..brc_m013_1878brc_m013_1879..brc_m013_1883brc_m013_1884brc_m013_1885brc_m013_1886..brc_m013_1888brc_m013_1889..brc_m013_1895brc_m013_1896..brc_m013_1899brc_m013_1900..brc_m013_1913brc_m013_1914brc_m013_1915..brc_m013_1922brc_m013_1923brc_m013_1924..brc_m013_1928brc_m013_1929..brc_m013_1942brc_m013_1943..brc_m013_1946brc_m013_1947..brc_m013_1948brc_m013_1949brc_m013_1950..brc_m013_1953brc_m013_1954..brc_m013_1955brc_m013_1956brc_m013_1957..brc_m013_1963brc_m013_1964..brc_m013_1966brc_m013_1967..brc_m013_1968brc_m013_1969..brc_m013_1970brc_m013_1971brc_m013_1972brc_m013_1973..brc_m013_1980brc_m013_1981..brc_m013_1983brc_m013_1984..brc_m013_1990brc_m013_1991..brc_m013_1993brc_m013_1994..brc_m013_1996brc_m013_1997..brc_m013_2009
0
20
40
60
80
100
120
LG5brc_m013_2010..brc_m013_2028
brc_m013_2029..brc_m013_2038brc_m013_2039
brc_m013_2040..brc_m013_2041brc_m013_2042..brc_m013_2047brc_m013_2048..brc_m013_2050brc_m013_2051..brc_m013_2053brc_m013_2054..brc_m013_2062brc_m013_2063brc_m013_2064..brc_m013_2065brc_m013_2066..brc_m013_2067brc_m013_2068brc_m013_2069..brc_m013_2071brc_m013_2072..brc_m013_2081brc_m013_2082
brc_m013_2083brc_m013_2084brc_m013_2085..brc_m013_2099brc_m013_2100brc_m013_2101..brc_m013_2102brc_m013_2103..brc_m013_2107brc_m013_2108brc_m013_2109..brc_m013_2112
brc_m013_2113..brc_m013_2114brc_m013_2115..brc_m013_2123brc_m013_2124..brc_m013_2131brc_m013_2132brc_m013_2133brc_m013_2134..brc_m013_2136
brc_m013_2137
brc_m013_2138..brc_m013_2139
brc_m013_2140..brc_m013_2142brc_m013_2143..brc_m013_2150brc_m013_2151..brc_m013_2152brc_m013_2153..brc_m013_2161brc_m013_2162..brc_m013_2163
brc_m013_2164..brc_m013_2165brc_m013_2166..brc_m013_2170brc_m013_2171..brc_m013_2172brc_m013_2173brc_m013_2174..brc_m013_2182brc_m013_2183..brc_m013_2186brc_m013_2187..brc_m013_2190brc_m013_2191..brc_m013_2193brc_m013_2194brc_m013_2195..brc_m013_2201brc_m013_2202..brc_m013_2203brc_m013_2204..brc_m013_2220brc_m013_2221..brc_m013_2232brc_m013_2233..brc_m013_2239brc_m013_2240..brc_m013_2261brc_m013_2262..brc_m013_2267brc_m013_2268..brc_m013_2269brc_m013_2270..brc_m013_2271brc_m013_2272..brc_m013_2282brc_m013_2283..brc_m013_2284brc_m013_2285..brc_m013_2299brc_m013_2300..brc_m013_2301brc_m013_2302..brc_m013_2305brc_m013_2306..brc_m013_2307brc_m013_2308..brc_m013_2330brc_m013_2331..brc_m013_2337brc_m013_2338..brc_m013_2352
0
20
40
60
80
100
120
LG6brc_m013_2353..brc_m013_2365brc_m013_2366..brc_m013_2369
brc_m013_2370..brc_m013_2372brc_m013_2373..brc_m013_2378brc_m013_2379..brc_m013_2386brc_m013_2387brc_m013_2388..brc_m013_2394brc_m013_2395..brc_m013_2397brc_m013_2398brc_m013_2399brc_m013_2400brc_m013_2401brc_m013_2402..brc_m013_2407brc_m013_2408..brc_m013_2411brc_m013_2412..brc_m013_2416brc_m013_2417brc_m013_2418brc_m013_2419..brc_m013_2436brc_m013_2437..brc_m013_2441brc_m013_2442brc_m013_2443..brc_m013_2444brc_m013_2445brc_m013_2446..brc_m013_2453brc_m013_2454brc_m013_2455..brc_m013_2460brc_m013_2461brc_m013_2462..brc_m013_2470brc_m013_2471..brc_m013_2474brc_m013_2475..brc_m013_2482brc_m013_2483brc_m013_2484..brc_m013_2487brc_m013_2488brc_m013_2489..brc_m013_2492brc_m013_2493..brc_m013_2496brc_m013_2497brc_m013_2498..brc_m013_2504brc_m013_2505brc_m013_2506..brc_m013_2510brc_m013_2511..brc_m013_2523brc_m013_2524..brc_m013_2531brc_m013_2532..brc_m013_2536brc_m013_2537..brc_m013_2555brc_m013_2556..brc_m013_2571brc_m013_2572..brc_m013_2573brc_m013_2574..brc_m013_2579brc_m013_2580..brc_m013_2581brc_m013_2582..brc_m013_2587brc_m013_2588brc_m013_2589..brc_m013_2594
brc_m013_2595
brc_m013_2596..brc_m013_2597brc_m013_2598..brc_m013_2604brc_m013_2605brc_m013_2606..brc_m013_2616brc_m013_2617..brc_m013_2619brc_m013_2620..brc_m013_2623
brc_m013_2624brc_m013_2625..brc_m013_2626brc_m013_2627..brc_m013_2628
brc_m013_2629..brc_m013_2630
0
20
40
60
80
100
LG7brc_m013_2631..brc_m013_2632brc_m013_2633brc_m013_2634..brc_m013_2635brc_m013_2636..brc_m013_2642brc_m013_2643..brc_m013_2657brc_m013_2658..brc_m013_2659brc_m013_2660..brc_m013_2661brc_m013_2662
brc_m013_2663
brc_m013_2664brc_m013_2665..brc_m013_2666
brc_m013_2667..brc_m013_2668brc_m013_2669..brc_m013_2670brc_m013_2671..brc_m013_2680brc_m013_2681..brc_m013_2682brc_m013_2683brc_m013_2684..brc_m013_2685brc_m013_2686..brc_m013_2694
brc_m013_2695..brc_m013_2698brc_m013_2699..brc_m013_2713
brc_m013_2714..brc_m013_2725brc_m013_2726..brc_m013_2727brc_m013_2728..brc_m013_2731brc_m013_2732brc_m013_2733..brc_m013_2753brc_m013_2754..brc_m013_2758brc_m013_2759..brc_m013_2763brc_m013_2764..brc_m013_2779brc_m013_2780brc_m013_2781brc_m013_2782..brc_m013_2784brc_m013_2785..brc_m013_2787brc_m013_2788..brc_m013_2791brc_m013_2792..brc_m013_2797brc_m013_2798..brc_m013_2799brc_m013_2800brc_m013_2801..brc_m013_2804brc_m013_2805..brc_m013_2809
brc_m013_2810..brc_m013_2811
brc_m013_2812..brc_m013_2813brc_m013_2814..brc_m013_2817brc_m013_2818..brc_m013_2827brc_m013_2828brc_m013_2829..brc_m013_2832brc_m013_2833brc_m013_2834..brc_m013_2840brc_m013_2841..brc_m013_2846brc_m013_2847brc_m013_2848..brc_m013_2852brc_m013_2853brc_m013_2854..brc_m013_2856brc_m013_2857..brc_m013_2862brc_m013_2863..brc_m013_2868brc_m013_2869..brc_m013_2874brc_m013_2875..brc_m013_2896
0
20
40
60
80
100
LG8
brc_m013_2897..brc_m013_2920brc_m013_2921..brc_m013_2928brc_m013_2929..brc_m013_2931brc_m013_2932
brc_m013_2933
brc_m013_2934..brc_m013_2935brc_m013_2936brc_m013_2937..brc_m013_2943brc_m013_2944brc_m013_2945..brc_m013_2946brc_m013_2947brc_m013_2948brc_m013_2949..brc_m013_2950brc_m013_2951..brc_m013_2957brc_m013_2958..brc_m013_2961brc_m013_2962..brc_m013_2970brc_m013_2971..brc_m013_2980brc_m013_2981..brc_m013_2992brc_m013_2993..brc_m013_2996brc_m013_2997..brc_m013_2998brc_m013_2999..brc_m013_3000brc_m013_3001brc_m013_3002..brc_m013_3003brc_m013_3004brc_m013_3005brc_m013_3006..brc_m013_3010brc_m013_3011..brc_m013_3014brc_m013_3015brc_m013_3016..brc_m013_3019brc_m013_3020brc_m013_3021..brc_m013_3030brc_m013_3031..brc_m013_3032brc_m013_3033..brc_m013_3034brc_m013_3035..brc_m013_3036brc_m013_3037..brc_m013_3045brc_m013_3046..brc_m013_3052brc_m013_3053brc_m013_3054..brc_m013_3061brc_m013_3062..brc_m013_3066brc_m013_3067..brc_m013_3068brc_m013_3069..brc_m013_3076brc_m013_3077..brc_m013_3084brc_m013_3085..brc_m013_3087brc_m013_3088..brc_m013_3089brc_m013_3090..brc_m013_3096brc_m013_3097..brc_m013_3100brc_m013_3101..brc_m013_3104brc_m013_3105brc_m013_3106..brc_m013_3112brc_m013_3113..brc_m013_3122brc_m013_3123..brc_m013_3124brc_m013_3125..brc_m013_3127brc_m013_3128..brc_m013_3145brc_m013_3146..brc_m013_3159brc_m013_3160..brc_m013_3172
0
20
40
60
80
100
LG9brc_m013_3173..brc_m013_3175brc_m013_3176..brc_m013_3180brc_m013_3181..brc_m013_3189brc_m013_3190..brc_m013_3198brc_m013_3199brc_m013_3200..brc_m013_3201brc_m013_3202..brc_m013_3203brc_m013_3204brc_m013_3205..brc_m013_3206brc_m013_3207..brc_m013_3211brc_m013_3212..brc_m013_3214brc_m013_3215..brc_m013_3227brc_m013_3228..brc_m013_3230brc_m013_3231..brc_m013_3235brc_m013_3236..brc_m013_3238brc_m013_3239..brc_m013_3242brc_m013_3243..brc_m013_3244brc_m013_3245brc_m013_3246..brc_m013_3247brc_m013_3248..brc_m013_3249brc_m013_3250..brc_m013_3252brc_m013_3253..brc_m013_3257brc_m013_3258brc_m013_3259brc_m013_3260..brc_m013_3261brc_m013_3262..brc_m013_3263brc_m013_3264brc_m013_3265..brc_m013_3269brc_m013_3270..brc_m013_3274brc_m013_3275..brc_m013_3276brc_m013_3277..brc_m013_3281brc_m013_3282..brc_m013_3284brc_m013_3285brc_m013_3286..brc_m013_3289brc_m013_3290..brc_m013_3296brc_m013_3297brc_m013_3298..brc_m013_3300brc_m013_3301..brc_m013_3302brc_m013_3303..brc_m013_3305brc_m013_3306..brc_m013_3308brc_m013_3309..brc_m013_3314brc_m013_3315..brc_m013_3317brc_m013_3318..brc_m013_3329brc_m013_3330..brc_m013_3331brc_m013_3332..brc_m013_3338brc_m013_3339..brc_m013_3340brc_m013_3341..brc_m013_3344brc_m013_3345..brc_m013_3349brc_m013_3350..brc_m013_3357brc_m013_3358..brc_m013_3359brc_m013_3360brc_m013_3361..brc_m013_3368brc_m013_3369..brc_m013_3372brc_m013_3373..brc_m013_3376brc_m013_3377brc_m013_3378..brc_m013_3386brc_m013_3387..brc_m013_3388brc_m013_3389..brc_m013_3395brc_m013_3396..brc_m013_3399
0
20
40
60
80
LG10brc_m013_3400..brc_m013_3411brc_m013_3412brc_m013_3413..brc_m013_3424brc_m013_3425brc_m013_3426brc_m013_3427..brc_m013_3429
brc_m013_3430
brc_m013_3431..brc_m013_3432brc_m013_3433..brc_m013_3435brc_m013_3436brc_m013_3437..brc_m013_3439
brc_m013_3440..brc_m013_3441brc_m013_3442
brc_m013_3443..brc_m013_3445brc_m013_3446..brc_m013_3447brc_m013_3448..brc_m013_3449brc_m013_3450..brc_m013_3454brc_m013_3455brc_m013_3456..brc_m013_3462brc_m013_3463..brc_m013_3464brc_m013_3465brc_m013_3466..brc_m013_3467brc_m013_3468..brc_m013_3472brc_m013_3473brc_m013_3474..brc_m013_3476brc_m013_3477..brc_m013_3487brc_m013_3488brc_m013_3489..brc_m013_3491brc_m013_3492..brc_m013_3500brc_m013_3501..brc_m013_3512brc_m013_3513..brc_m013_3514brc_m013_3515..brc_m013_3524brc_m013_3525..brc_m013_3527brc_m013_3528..brc_m013_3531brc_m013_3532..brc_m013_3547brc_m013_3548..brc_m013_3557brc_m013_3558..brc_m013_3566brc_m013_3567..brc_m013_3568brc_m013_3569..brc_m013_3570brc_m013_3571..brc_m013_3574brc_m013_3575..brc_m013_3582brc_m013_3583..brc_m013_3592brc_m013_3593..brc_m013_3605brc_m013_3606..brc_m013_3616brc_m013_3617..brc_m013_3618brc_m013_3619..brc_m013_3622brc_m013_3623..brc_m013_3624brc_m013_3625..brc_m013_3628brc_m013_3629..brc_m013_3635
0
20
40
60
80
LG11
brc_m013_3636..brc_m013_3661brc_m013_3662..brc_m013_3665
brc_m013_3666..brc_m013_3667brc_m013_3668brc_m013_3669..brc_m013_3671
brc_m013_3672
brc_m013_3673..brc_m013_3674brc_m013_3675..brc_m013_3682
brc_m013_3683..brc_m013_3685
brc_m013_3686..brc_m013_3688
brc_m013_3689..brc_m013_3693
brc_m013_3694..brc_m013_3698brc_m013_3699
brc_m013_3700brc_m013_3701..brc_m013_3702brc_m013_3703..brc_m013_3704brc_m013_3705..brc_m013_3712brc_m013_3713brc_m013_3714..brc_m013_3716brc_m013_3717..brc_m013_3724brc_m013_3725..brc_m013_3730brc_m013_3731..brc_m013_3752brc_m013_3753..brc_m013_3758brc_m013_3759..brc_m013_3789brc_m013_3790..brc_m013_3801brc_m013_3802..brc_m013_3814brc_m013_3815..brc_m013_3818brc_m013_3819..brc_m013_3822brc_m013_3823..brc_m013_3826brc_m013_3827..brc_m013_3832brc_m013_3833..brc_m013_3837brc_m013_3838brc_m013_3839..brc_m013_3841brc_m013_3842..brc_m013_3847
brc_m013_3848..brc_m013_3853brc_m013_3854..brc_m013_3858brc_m013_3859..brc_m013_3868brc_m013_3869..brc_m013_3871brc_m013_3872..brc_m013_3901brc_m013_3902brc_m013_3903..brc_m013_3909brc_m013_3910brc_m013_3911..brc_m013_3926brc_m013_3927..brc_m013_3931brc_m013_3932..brc_m013_3948
0
20
40
60
80
LG12
brc_m013_3949..brc_m013_3952brc_m013_3953..brc_m013_3958brc_m013_3959..brc_m013_3970brc_m013_3971
brc_m013_3972..brc_m013_3975brc_m013_3976
brc_m013_3977..brc_m013_3985
brc_m013_3986brc_m013_3987..brc_m013_3994brc_m013_3995..brc_m013_3997brc_m013_3998..brc_m013_4004
brc_m013_4005..brc_m013_4006brc_m013_4007..brc_m013_4008brc_m013_4009..brc_m013_4010brc_m013_4011..brc_m013_4013brc_m013_4014brc_m013_4015brc_m013_4016..brc_m013_4019brc_m013_4020..brc_m013_4021brc_m013_4022..brc_m013_4025brc_m013_4026..brc_m013_4032brc_m013_4033..brc_m013_4036brc_m013_4037..brc_m013_4041brc_m013_4042..brc_m013_4043
brc_m013_4044..brc_m013_4046brc_m013_4047..brc_m013_4056brc_m013_4057brc_m013_4058..brc_m013_4063brc_m013_4064..brc_m013_4071brc_m013_4072..brc_m013_4075brc_m013_4076brc_m013_4077brc_m013_4078..brc_m013_4085brc_m013_4086..brc_m013_4089brc_m013_4090..brc_m013_4091brc_m013_4092..brc_m013_4093brc_m013_4094..brc_m013_4095brc_m013_4096..brc_m013_4114brc_m013_4115..brc_m013_4117brc_m013_4118..brc_m013_4131brc_m013_4132..brc_m013_4133brc_m013_4134..brc_m013_4146
0
20
40
60
80
LG13
brc_m013_4147..brc_m013_4150brc_m013_4151..brc_m013_4167
brc_m013_4168brc_m013_4169
brc_m013_4170brc_m013_4171..brc_m013_4172brc_m013_4173..brc_m013_4175brc_m013_4176brc_m013_4177..brc_m013_4178brc_m013_4179..brc_m013_4183brc_m013_4184..brc_m013_4185brc_m013_4186..brc_m013_4187brc_m013_4188..brc_m013_4191brc_m013_4192brc_m013_4193..brc_m013_4194brc_m013_4195..brc_m013_4206brc_m013_4207..brc_m013_4210brc_m013_4211..brc_m013_4213brc_m013_4214brc_m013_4215..brc_m013_4217brc_m013_4218..brc_m013_4221brc_m013_4222..brc_m013_4223brc_m013_4224..brc_m013_4231brc_m013_4232..brc_m013_4234brc_m013_4235..brc_m013_4239brc_m013_4240..brc_m013_4246brc_m013_4247..brc_m013_4248brc_m013_4249..brc_m013_4258brc_m013_4259..brc_m013_4260brc_m013_4261..brc_m013_4269brc_m013_4270..brc_m013_4271brc_m013_4272..brc_m013_4278brc_m013_4279..brc_m013_4280brc_m013_4281..brc_m013_4284brc_m013_4285brc_m013_4286..brc_m013_4288brc_m013_4289..brc_m013_4294brc_m013_4295..brc_m013_4296brc_m013_4297..brc_m013_4301brc_m013_4302..brc_m013_4313brc_m013_4314..brc_m013_4320brc_m013_4321..brc_m013_4322brc_m013_4323..brc_m013_4345brc_m013_4346..brc_m013_4351
0
20
40
60
LG14brc_m013_4352..brc_m013_4366brc_m013_4367brc_m013_4368brc_m013_4369..brc_m013_4373brc_m013_4374..brc_m013_4381brc_m013_4382..brc_m013_4383brc_m013_4384..brc_m013_4385brc_m013_4386brc_m013_4387..brc_m013_4388brc_m013_4389brc_m013_4390..brc_m013_4404brc_m013_4405brc_m013_4406..brc_m013_4409brc_m013_4410..brc_m013_4411brc_m013_4412..brc_m013_4418brc_m013_4419..brc_m013_4434brc_m013_4435..brc_m013_4442brc_m013_4443..brc_m013_4448brc_m013_4449..brc_m013_4451brc_m013_4452..brc_m013_4461brc_m013_4462..brc_m013_4471brc_m013_4472..brc_m013_4475brc_m013_4476..brc_m013_4477brc_m013_4478brc_m013_4479brc_m013_4480..brc_m013_4485brc_m013_4486brc_m013_4487..brc_m013_4491brc_m013_4492brc_m013_4493brc_m013_4494..brc_m013_4495brc_m013_4496..brc_m013_4501brc_m013_4502..brc_m013_4510brc_m013_4511..brc_m013_4531brc_m013_4532brc_m013_4533..brc_m013_4534brc_m013_4535..brc_m013_4541brc_m013_4542..brc_m013_4543brc_m013_4544..brc_m013_4545brc_m013_4546..brc_m013_4548brc_m013_4549..brc_m013_4551brc_m013_4552..brc_m013_4555brc_m013_4556..brc_m013_4561
0
20
40
60
LG15
brc_m013_4562..brc_m013_4577brc_m013_4578..brc_m013_4594brc_m013_4595..brc_m013_4599brc_m013_4600..brc_m013_4625brc_m013_4626..brc_m013_4638brc_m013_4639..brc_m013_4642brc_m013_4643..brc_m013_4644brc_m013_4645..brc_m013_4650brc_m013_4651..brc_m013_4663brc_m013_4664..brc_m013_4668brc_m013_4669..brc_m013_4670brc_m013_4671..brc_m013_4674brc_m013_4675..brc_m013_4679brc_m013_4680..brc_m013_4681brc_m013_4682brc_m013_4683..brc_m013_4688brc_m013_4689..brc_m013_4692brc_m013_4693..brc_m013_4695brc_m013_4696..brc_m013_4701brc_m013_4702brc_m013_4703..brc_m013_4712brc_m013_4713..brc_m013_4717brc_m013_4718..brc_m013_4720brc_m013_4721brc_m013_4722..brc_m013_4726brc_m013_4727..brc_m013_4728brc_m013_4729..brc_m013_4742brc_m013_4743brc_m013_4744..brc_m013_4746brc_m013_4747brc_m013_4748..brc_m013_4749brc_m013_4750..brc_m013_4752
brc_m013_4753..brc_m013_4756brc_m013_4757..brc_m013_4759brc_m013_4760..brc_m013_4762brc_m013_4763brc_m013_4764..brc_m013_4766brc_m013_4767..brc_m013_4769brc_m013_4770brc_m013_4771..brc_m013_4774brc_m013_4775..brc_m013_4776brc_m013_4777..brc_m013_4778brc_m013_4779..brc_m013_4780brc_m013_4781..brc_m013_4793brc_m013_4794brc_m013_4795..brc_m013_4798brc_m013_4799..brc_m013_4802brc_m013_4803..brc_m013_4806brc_m013_4807brc_m013_4808..brc_m013_4814brc_m013_4815..brc_m013_4819brc_m013_4820brc_m013_4821brc_m013_4822..brc_m013_4823brc_m013_4824brc_m013_4825..brc_m013_4855brc_m013_4856..brc_m013_4858brc_m013_4859..brc_m013_4863brc_m013_4864..brc_m013_4865brc_m013_4866..brc_m013_4875brc_m013_4876..brc_m013_4881brc_m013_4882..brc_m013_4891brc_m013_4892..brc_m013_4895brc_m013_4896..brc_m013_4911brc_m013_4912..brc_m013_4938brc_m013_4939brc_m013_4940..brc_m013_4957brc_m013_4958..brc_m013_4959brc_m013_4960..brc_m013_4972brc_m013_4973..brc_m013_4981brc_m013_4982..brc_m013_4983
0
20
40
60
80
100
120
LGSB
Gp-9
Figure 1a b
Si_gnF.scaffold00779_nt2778431.7
Si_gnF.scaffold00779_nt1255229Si_gnF.scaffold02684_nt10884.2
Si_gnF.scaffold00779_nt1633919Si_gnF.scaffold00779_nt17842486.5
Si_gnF.scaffold00779_nt3746833Si_gnF.scaffold00779_nt374687927.3Si_gnF.scaffold00779_nt382158728.5
Si_gnF.scaffold00779_nt417489034.2
Si_gnF.scaffold09607_nt698300Si_gnF.scaffold09607_nt69848340.2
Si_gnF.scaffold09758_nt22273252.8
Si_gnF.scaffold05266_nt63430678.4Si_gnF.scaffold05266_nt65952779.7
Si_gnF.scaffold05266_nt733643Si_gnF.scaffold05266_nt75364482.8
Si_gnF.scaffold07090_nt71001087.6
Si_gnF.scaffold07090_nt105177192.7
Si_gnF.scaffold00255_nt314067Si_gnF.scaffold00255_nt40777897.5
Si_gnF.scaffold03404_nt128925Si_gnF.scaffold03404_nt228606Si_gnF.scaffold03404_nt241461
104.4
Si_gnF.scaffold00413_nt676115107.3
Si_gnF.scaffold00413_nt1035856109.6Si_gnF.scaffold01573_nt108462110.8Si_gnF.scaffold01573_nt447618112.1Si_gnF.scaffold00899_nt377419Si_gnF.scaffold00899_nt686574114.4Si_gnF.scaffold00899_nt236146Si_gnF.scaffold00899_nt332715Si_gnF.scaffold00899_nt335756
115.8
Si_gnF.scaffold00469_nt794118.0Si_gnF.scaffold00690_nt229012Si_gnF.scaffold00690_nt415290119.3
Si_gnF.scaffold06914_nt297673125.1
Si_gnF.scaffold01957_nt412242Si_gnF.scaffold02848_nt41846127.6
LGS Bfrom M013
Si_gnF.scaffold00779_nt2778430.0Si_gnF.scaffold00779_nt1255229Si_gnF.scaffold02684_nt10881.2
Si_gnF.scaffold00779_nt1633919Si_gnF.scaffold00779_nt17842486.7
Si_gnF.scaffold00779_nt3746833Si_gnF.scaffold00779_nt3746879Si_gnF.scaffold00779_nt3821587
22.2
Si_gnF.scaffold00779_nt417489029.2
Si_gnF.scaffold09607_nt698300Si_gnF.scaffold09607_nt69848361.9
Si_gnF.scaffold01573_nt10846280.7Si_gnF.scaffold00255_nt314067Si_gnF.scaffold00255_nt407778Si_gnF.scaffold00413_nt1035856Si_gnF.scaffold00413_nt676115Si_gnF.scaffold00469_nt794Si_gnF.scaffold00690_nt229012Si_gnF.scaffold00690_nt415290Si_gnF.scaffold00899_nt236146Si_gnF.scaffold00899_nt332715Si_gnF.scaffold00899_nt335756Si_gnF.scaffold00899_nt377419Si_gnF.scaffold00899_nt686574Si_gnF.scaffold01573_nt447618Si_gnF.scaffold01957_nt412242Si_gnF.scaffold03404_nt128925Si_gnF.scaffold03404_nt228606Si_gnF.scaffold03404_nt241461Si_gnF.scaffold05266_nt634306Si_gnF.scaffold05266_nt659527Si_gnF.scaffold05266_nt733643Si_gnF.scaffold05266_nt753644Si_gnF.scaffold06914_nt297673Si_gnF.scaffold07090_nt1051771Si_gnF.scaffold07090_nt710010Si_gnF.scaffold09758_nt222732
81.8
Si_gnF.scaffold02848_nt4184690.5
LGS B/bfrom P034
Gp-9
Total285 non-recombiningmarkersbrc_m013_0001..brc_m013_0005
brc_m013_0006..brc_m013_0014brc_m013_0015..brc_m013_0017brc_m013_0018brc_m013_0019..brc_m013_0020brc_m013_0021..brc_m013_0029brc_m013_0030..brc_m013_0031brc_m013_0032..brc_m013_0034brc_m013_0035..brc_m013_0036brc_m013_0037..brc_m013_0038brc_m013_0039..brc_m013_0043brc_m013_0044brc_m013_0045brc_m013_0046..brc_m013_0048brc_m013_0049brc_m013_0050..brc_m013_0051brc_m013_0052..brc_m013_0056brc_m013_0057..brc_m013_0061
brc_m013_0062..brc_m013_0075brc_m013_0076..brc_m013_0078brc_m013_0079..brc_m013_0081
brc_m013_0082..brc_m013_0088
brc_m013_0089..brc_m013_0092
brc_m013_0093..brc_m013_0096brc_m013_0097brc_m013_0098..brc_m013_0113brc_m013_0114..brc_m013_0119brc_m013_0120..brc_m013_0130brc_m013_0131brc_m013_0132..brc_m013_0134brc_m013_0135..brc_m013_0136brc_m013_0137..brc_m013_0139brc_m013_0140..brc_m013_0142brc_m013_0143brc_m013_0144..brc_m013_0146brc_m013_0147..brc_m013_0154brc_m013_0155
brc_m013_0156brc_m013_0157..brc_m013_0180brc_m013_0181brc_m013_0182brc_m013_0183..brc_m013_0188brc_m013_0189..brc_m013_0208brc_m013_0209brc_m013_0210..brc_m013_0211brc_m013_0212..brc_m013_0215brc_m013_0216brc_m013_0217brc_m013_0218..brc_m013_0224brc_m013_0225..brc_m013_0228brc_m013_0229..brc_m013_0237brc_m013_0238..brc_m013_0245
brc_m013_0246..brc_m013_0270
brc_m013_0271..brc_m013_0274brc_m013_0275brc_m013_0276..brc_m013_0278
brc_m013_0279
brc_m013_0280
brc_m013_0281..brc_m013_0294
brc_m013_0295..brc_m013_0303brc_m013_0304brc_m013_0305..brc_m013_0307brc_m013_0308brc_m013_0309..brc_m013_0314brc_m013_0315..brc_m013_0317brc_m013_0318..brc_m013_0320brc_m013_0321..brc_m013_0326brc_m013_0327brc_m013_0328brc_m013_0329..brc_m013_0330brc_m013_0331..brc_m013_0333brc_m013_0334..brc_m013_0339brc_m013_0340brc_m013_0341..brc_m013_0343brc_m013_0344brc_m013_0345..brc_m013_0349brc_m013_0350
brc_m013_0351..brc_m013_0354brc_m013_0355brc_m013_0356brc_m013_0357..brc_m013_0361brc_m013_0362..brc_m013_0376brc_m013_0377..brc_m013_0390brc_m013_0391..brc_m013_0393brc_m013_0394..brc_m013_0400brc_m013_0401..brc_m013_0439brc_m013_0440..brc_m013_0478brc_m013_0479..brc_m013_0480
0
20
40
60
80
100
120
140
160
180
LG1brc_m013_0481brc_m013_0482..brc_m013_0484brc_m013_0485..brc_m013_0488brc_m013_0489..brc_m013_0502brc_m013_0503brc_m013_0504..brc_m013_0519brc_m013_0520..brc_m013_0532brc_m013_0533..brc_m013_0534brc_m013_0535..brc_m013_0537brc_m013_0538..brc_m013_0540brc_m013_0541..brc_m013_0543brc_m013_0544..brc_m013_0545brc_m013_0546..brc_m013_0549
brc_m013_0550..brc_m013_0554
brc_m013_0555..brc_m013_0560
brc_m013_0561..brc_m013_0562brc_m013_0563..brc_m013_0565
brc_m013_0566brc_m013_0567brc_m013_0568..brc_m013_0570brc_m013_0571..brc_m013_0573
brc_m013_0574..brc_m013_0575brc_m013_0576..brc_m013_0578brc_m013_0579..brc_m013_0580brc_m013_0581brc_m013_0582..brc_m013_0584brc_m013_0585brc_m013_0586brc_m013_0587brc_m013_0588..brc_m013_0591brc_m013_0592brc_m013_0593brc_m013_0594..brc_m013_0612brc_m013_0613..brc_m013_0614brc_m013_0615..brc_m013_0632brc_m013_0633brc_m013_0634..brc_m013_0648brc_m013_0649..brc_m013_0655brc_m013_0656brc_m013_0657..brc_m013_0694brc_m013_0695..brc_m013_0703brc_m013_0704brc_m013_0705brc_m013_0706..brc_m013_0707brc_m013_0708brc_m013_0709..brc_m013_0711brc_m013_0712..brc_m013_0715brc_m013_0716..brc_m013_0721brc_m013_0722brc_m013_0723brc_m013_0724..brc_m013_0728brc_m013_0729brc_m013_0730brc_m013_0731brc_m013_0732..brc_m013_0735brc_m013_0736..brc_m013_0769brc_m013_0770..brc_m013_0771brc_m013_0772..brc_m013_0773brc_m013_0774..brc_m013_0775brc_m013_0776..brc_m013_0782brc_m013_0783brc_m013_0784..brc_m013_0795brc_m013_0796..brc_m013_0798brc_m013_0799..brc_m013_0801brc_m013_0802..brc_m013_0805brc_m013_0806..brc_m013_0809brc_m013_0810..brc_m013_0811brc_m013_0812..brc_m013_0824brc_m013_0825..brc_m013_0826brc_m013_0827..brc_m013_0829brc_m013_0830..brc_m013_0831brc_m013_0832..brc_m013_0842brc_m013_0843..brc_m013_0854brc_m013_0855..brc_m013_0861brc_m013_0862brc_m013_0863..brc_m013_0864brc_m013_0865..brc_m013_0867brc_m013_0868..brc_m013_0883brc_m013_0884..brc_m013_0893brc_m013_0894brc_m013_0895..brc_m013_0897brc_m013_0898..brc_m013_0906brc_m013_0907..brc_m013_0910brc_m013_0911..brc_m013_0925brc_m013_0926..brc_m013_0928brc_m013_0929..brc_m013_0931
0
20
40
60
80
100
120
140
LG2brc_m013_0932..brc_m013_0941brc_m013_0942..brc_m013_0943brc_m013_0944..brc_m013_0945brc_m013_0946..brc_m013_0949brc_m013_0950..brc_m013_0952
brc_m013_0953..brc_m013_0975
brc_m013_0976..brc_m013_1019brc_m013_1020brc_m013_1021brc_m013_1022..brc_m013_1061brc_m013_1062brc_m013_1063
brc_m013_1064..brc_m013_1065
brc_m013_1066..brc_m013_1068brc_m013_1069brc_m013_1070
brc_m013_1071..brc_m013_1074
brc_m013_1075
brc_m013_1076..brc_m013_1081
brc_m013_1082..brc_m013_1086brc_m013_1087..brc_m013_1088brc_m013_1089..brc_m013_1098brc_m013_1099..brc_m013_1106brc_m013_1107..brc_m013_1116brc_m013_1117brc_m013_1118..brc_m013_1121brc_m013_1122..brc_m013_1127brc_m013_1128brc_m013_1129..brc_m013_1136brc_m013_1137..brc_m013_1138brc_m013_1139..brc_m013_1141brc_m013_1142..brc_m013_1144brc_m013_1145..brc_m013_1156brc_m013_1157brc_m013_1158..brc_m013_1170brc_m013_1171..brc_m013_1181brc_m013_1182..brc_m013_1185brc_m013_1186brc_m013_1187..brc_m013_1205brc_m013_1206..brc_m013_1218brc_m013_1219..brc_m013_1220brc_m013_1221..brc_m013_1224brc_m013_1225..brc_m013_1228brc_m013_1229brc_m013_1230..brc_m013_1236brc_m013_1237brc_m013_1238..brc_m013_1247brc_m013_1248..brc_m013_1251
brc_m013_1252brc_m013_1253..brc_m013_1268brc_m013_1269..brc_m013_1270brc_m013_1271..brc_m013_1273brc_m013_1274brc_m013_1275..brc_m013_1280brc_m013_1281
brc_m013_1282..brc_m013_1286brc_m013_1287..brc_m013_1298brc_m013_1299..brc_m013_1307brc_m013_1308brc_m013_1309..brc_m013_1313brc_m013_1314..brc_m013_1317brc_m013_1318..brc_m013_1319brc_m013_1320..brc_m013_1326brc_m013_1327..brc_m013_1340brc_m013_1341..brc_m013_1362brc_m013_1363..brc_m013_1385
0
20
40
60
80
100
120
140
LG3brc_m013_1386..brc_m013_1388brc_m013_1389..brc_m013_1398brc_m013_1399..brc_m013_1406brc_m013_1407..brc_m013_1411brc_m013_1412..brc_m013_1413brc_m013_1414..brc_m013_1416
brc_m013_1417brc_m013_1418..brc_m013_1420brc_m013_1421..brc_m013_1424brc_m013_1425..brc_m013_1432brc_m013_1433..brc_m013_1442brc_m013_1443brc_m013_1444..brc_m013_1450brc_m013_1451brc_m013_1452brc_m013_1453..brc_m013_1455brc_m013_1456..brc_m013_1467brc_m013_1468..brc_m013_1469brc_m013_1470brc_m013_1471..brc_m013_1474brc_m013_1475brc_m013_1476brc_m013_1477brc_m013_1478..brc_m013_1482brc_m013_1483
brc_m013_1484brc_m013_1485..brc_m013_1487brc_m013_1488..brc_m013_1490
brc_m013_1491brc_m013_1492..brc_m013_1494brc_m013_1495..brc_m013_1496
brc_m013_1497..brc_m013_1500brc_m013_1501brc_m013_1502..brc_m013_1513brc_m013_1514..brc_m013_1562brc_m013_1563..brc_m013_1565brc_m013_1566..brc_m013_1567
brc_m013_1568..brc_m013_1580brc_m013_1581..brc_m013_1587brc_m013_1588..brc_m013_1591brc_m013_1592..brc_m013_1593brc_m013_1594..brc_m013_1604brc_m013_1605..brc_m013_1607brc_m013_1608..brc_m013_1609brc_m013_1610..brc_m013_1611brc_m013_1612..brc_m013_1616brc_m013_1617..brc_m013_1618brc_m013_1619..brc_m013_1620brc_m013_1621..brc_m013_1629brc_m013_1630..brc_m013_1633brc_m013_1634..brc_m013_1638brc_m013_1639..brc_m013_1647brc_m013_1648..brc_m013_1649brc_m013_1650..brc_m013_1656brc_m013_1657..brc_m013_1665brc_m013_1666..brc_m013_1672brc_m013_1673..brc_m013_1674brc_m013_1675..brc_m013_1678brc_m013_1679..brc_m013_1682brc_m013_1683brc_m013_1684brc_m013_1685..brc_m013_1686brc_m013_1687..brc_m013_1700brc_m013_1701..brc_m013_1702brc_m013_1703brc_m013_1704..brc_m013_1707brc_m013_1708..brc_m013_1709brc_m013_1710..brc_m013_1714brc_m013_1715..brc_m013_1728brc_m013_1729..brc_m013_1742
0
20
40
60
80
100
120
140
LG4brc_m013_1743..brc_m013_1750
brc_m013_1751..brc_m013_1766brc_m013_1767brc_m013_1768
brc_m013_1769..brc_m013_1772
brc_m013_1773..brc_m013_1779brc_m013_1780brc_m013_1781brc_m013_1782..brc_m013_1783brc_m013_1784brc_m013_1785..brc_m013_1786
brc_m013_1787
brc_m013_1788brc_m013_1789..brc_m013_1790brc_m013_1791..brc_m013_1793brc_m013_1794..brc_m013_1797brc_m013_1798..brc_m013_1800brc_m013_1801..brc_m013_1804brc_m013_1805brc_m013_1806..brc_m013_1808brc_m013_1809brc_m013_1810..brc_m013_1813brc_m013_1814..brc_m013_1818brc_m013_1819..brc_m013_1820brc_m013_1821..brc_m013_1822brc_m013_1823..brc_m013_1824brc_m013_1825brc_m013_1826..brc_m013_1840brc_m013_1841..brc_m013_1842brc_m013_1843brc_m013_1844..brc_m013_1848brc_m013_1849brc_m013_1850brc_m013_1851..brc_m013_1853brc_m013_1854..brc_m013_1858brc_m013_1859..brc_m013_1866brc_m013_1867..brc_m013_1868brc_m013_1869brc_m013_1870..brc_m013_1874brc_m013_1875..brc_m013_1876brc_m013_1877..brc_m013_1878brc_m013_1879..brc_m013_1883brc_m013_1884brc_m013_1885brc_m013_1886..brc_m013_1888brc_m013_1889..brc_m013_1895brc_m013_1896..brc_m013_1899brc_m013_1900..brc_m013_1913brc_m013_1914brc_m013_1915..brc_m013_1922brc_m013_1923brc_m013_1924..brc_m013_1928brc_m013_1929..brc_m013_1942brc_m013_1943..brc_m013_1946brc_m013_1947..brc_m013_1948brc_m013_1949brc_m013_1950..brc_m013_1953brc_m013_1954..brc_m013_1955brc_m013_1956brc_m013_1957..brc_m013_1963brc_m013_1964..brc_m013_1966brc_m013_1967..brc_m013_1968brc_m013_1969..brc_m013_1970brc_m013_1971brc_m013_1972brc_m013_1973..brc_m013_1980brc_m013_1981..brc_m013_1983brc_m013_1984..brc_m013_1990brc_m013_1991..brc_m013_1993brc_m013_1994..brc_m013_1996brc_m013_1997..brc_m013_2009
0
20
40
60
80
100
120
LG5brc_m013_2010..brc_m013_2028
brc_m013_2029..brc_m013_2038brc_m013_2039
brc_m013_2040..brc_m013_2041brc_m013_2042..brc_m013_2047brc_m013_2048..brc_m013_2050brc_m013_2051..brc_m013_2053brc_m013_2054..brc_m013_2062brc_m013_2063brc_m013_2064..brc_m013_2065brc_m013_2066..brc_m013_2067brc_m013_2068brc_m013_2069..brc_m013_2071brc_m013_2072..brc_m013_2081brc_m013_2082
brc_m013_2083brc_m013_2084brc_m013_2085..brc_m013_2099brc_m013_2100brc_m013_2101..brc_m013_2102brc_m013_2103..brc_m013_2107brc_m013_2108brc_m013_2109..brc_m013_2112
brc_m013_2113..brc_m013_2114brc_m013_2115..brc_m013_2123brc_m013_2124..brc_m013_2131brc_m013_2132brc_m013_2133brc_m013_2134..brc_m013_2136
brc_m013_2137
brc_m013_2138..brc_m013_2139
brc_m013_2140..brc_m013_2142brc_m013_2143..brc_m013_2150brc_m013_2151..brc_m013_2152brc_m013_2153..brc_m013_2161brc_m013_2162..brc_m013_2163
brc_m013_2164..brc_m013_2165brc_m013_2166..brc_m013_2170brc_m013_2171..brc_m013_2172brc_m013_2173brc_m013_2174..brc_m013_2182brc_m013_2183..brc_m013_2186brc_m013_2187..brc_m013_2190brc_m013_2191..brc_m013_2193brc_m013_2194brc_m013_2195..brc_m013_2201brc_m013_2202..brc_m013_2203brc_m013_2204..brc_m013_2220brc_m013_2221..brc_m013_2232brc_m013_2233..brc_m013_2239brc_m013_2240..brc_m013_2261brc_m013_2262..brc_m013_2267brc_m013_2268..brc_m013_2269brc_m013_2270..brc_m013_2271brc_m013_2272..brc_m013_2282brc_m013_2283..brc_m013_2284brc_m013_2285..brc_m013_2299brc_m013_2300..brc_m013_2301brc_m013_2302..brc_m013_2305brc_m013_2306..brc_m013_2307brc_m013_2308..brc_m013_2330brc_m013_2331..brc_m013_2337brc_m013_2338..brc_m013_2352
0
20
40
60
80
100
120
LG6brc_m013_2353..brc_m013_2365brc_m013_2366..brc_m013_2369
brc_m013_2370..brc_m013_2372brc_m013_2373..brc_m013_2378brc_m013_2379..brc_m013_2386brc_m013_2387brc_m013_2388..brc_m013_2394brc_m013_2395..brc_m013_2397brc_m013_2398brc_m013_2399brc_m013_2400brc_m013_2401brc_m013_2402..brc_m013_2407brc_m013_2408..brc_m013_2411brc_m013_2412..brc_m013_2416brc_m013_2417brc_m013_2418brc_m013_2419..brc_m013_2436brc_m013_2437..brc_m013_2441brc_m013_2442brc_m013_2443..brc_m013_2444brc_m013_2445brc_m013_2446..brc_m013_2453brc_m013_2454brc_m013_2455..brc_m013_2460brc_m013_2461brc_m013_2462..brc_m013_2470brc_m013_2471..brc_m013_2474brc_m013_2475..brc_m013_2482brc_m013_2483brc_m013_2484..brc_m013_2487brc_m013_2488brc_m013_2489..brc_m013_2492brc_m013_2493..brc_m013_2496brc_m013_2497brc_m013_2498..brc_m013_2504brc_m013_2505brc_m013_2506..brc_m013_2510brc_m013_2511..brc_m013_2523brc_m013_2524..brc_m013_2531brc_m013_2532..brc_m013_2536brc_m013_2537..brc_m013_2555brc_m013_2556..brc_m013_2571brc_m013_2572..brc_m013_2573brc_m013_2574..brc_m013_2579brc_m013_2580..brc_m013_2581brc_m013_2582..brc_m013_2587brc_m013_2588brc_m013_2589..brc_m013_2594
brc_m013_2595
brc_m013_2596..brc_m013_2597brc_m013_2598..brc_m013_2604brc_m013_2605brc_m013_2606..brc_m013_2616brc_m013_2617..brc_m013_2619brc_m013_2620..brc_m013_2623
brc_m013_2624brc_m013_2625..brc_m013_2626brc_m013_2627..brc_m013_2628
brc_m013_2629..brc_m013_2630
0
20
40
60
80
100
LG7brc_m013_2631..brc_m013_2632brc_m013_2633brc_m013_2634..brc_m013_2635brc_m013_2636..brc_m013_2642brc_m013_2643..brc_m013_2657brc_m013_2658..brc_m013_2659brc_m013_2660..brc_m013_2661brc_m013_2662
brc_m013_2663
brc_m013_2664brc_m013_2665..brc_m013_2666
brc_m013_2667..brc_m013_2668brc_m013_2669..brc_m013_2670brc_m013_2671..brc_m013_2680brc_m013_2681..brc_m013_2682brc_m013_2683brc_m013_2684..brc_m013_2685brc_m013_2686..brc_m013_2694
brc_m013_2695..brc_m013_2698brc_m013_2699..brc_m013_2713
brc_m013_2714..brc_m013_2725brc_m013_2726..brc_m013_2727brc_m013_2728..brc_m013_2731brc_m013_2732brc_m013_2733..brc_m013_2753brc_m013_2754..brc_m013_2758brc_m013_2759..brc_m013_2763brc_m013_2764..brc_m013_2779brc_m013_2780brc_m013_2781brc_m013_2782..brc_m013_2784brc_m013_2785..brc_m013_2787brc_m013_2788..brc_m013_2791brc_m013_2792..brc_m013_2797brc_m013_2798..brc_m013_2799brc_m013_2800brc_m013_2801..brc_m013_2804brc_m013_2805..brc_m013_2809
brc_m013_2810..brc_m013_2811
brc_m013_2812..brc_m013_2813brc_m013_2814..brc_m013_2817brc_m013_2818..brc_m013_2827brc_m013_2828brc_m013_2829..brc_m013_2832brc_m013_2833brc_m013_2834..brc_m013_2840brc_m013_2841..brc_m013_2846brc_m013_2847brc_m013_2848..brc_m013_2852brc_m013_2853brc_m013_2854..brc_m013_2856brc_m013_2857..brc_m013_2862brc_m013_2863..brc_m013_2868brc_m013_2869..brc_m013_2874brc_m013_2875..brc_m013_2896
0
20
40
60
80
100
LG8
brc_m013_2897..brc_m013_2920brc_m013_2921..brc_m013_2928brc_m013_2929..brc_m013_2931brc_m013_2932
brc_m013_2933
brc_m013_2934..brc_m013_2935brc_m013_2936brc_m013_2937..brc_m013_2943brc_m013_2944brc_m013_2945..brc_m013_2946brc_m013_2947brc_m013_2948brc_m013_2949..brc_m013_2950brc_m013_2951..brc_m013_2957brc_m013_2958..brc_m013_2961brc_m013_2962..brc_m013_2970brc_m013_2971..brc_m013_2980brc_m013_2981..brc_m013_2992brc_m013_2993..brc_m013_2996brc_m013_2997..brc_m013_2998brc_m013_2999..brc_m013_3000brc_m013_3001brc_m013_3002..brc_m013_3003brc_m013_3004brc_m013_3005brc_m013_3006..brc_m013_3010brc_m013_3011..brc_m013_3014brc_m013_3015brc_m013_3016..brc_m013_3019brc_m013_3020brc_m013_3021..brc_m013_3030brc_m013_3031..brc_m013_3032brc_m013_3033..brc_m013_3034brc_m013_3035..brc_m013_3036brc_m013_3037..brc_m013_3045brc_m013_3046..brc_m013_3052brc_m013_3053brc_m013_3054..brc_m013_3061brc_m013_3062..brc_m013_3066brc_m013_3067..brc_m013_3068brc_m013_3069..brc_m013_3076brc_m013_3077..brc_m013_3084brc_m013_3085..brc_m013_3087brc_m013_3088..brc_m013_3089brc_m013_3090..brc_m013_3096brc_m013_3097..brc_m013_3100brc_m013_3101..brc_m013_3104brc_m013_3105brc_m013_3106..brc_m013_3112brc_m013_3113..brc_m013_3122brc_m013_3123..brc_m013_3124brc_m013_3125..brc_m013_3127brc_m013_3128..brc_m013_3145brc_m013_3146..brc_m013_3159brc_m013_3160..brc_m013_3172
0
20
40
60
80
100
LG9brc_m013_3173..brc_m013_3175brc_m013_3176..brc_m013_3180brc_m013_3181..brc_m013_3189brc_m013_3190..brc_m013_3198brc_m013_3199brc_m013_3200..brc_m013_3201brc_m013_3202..brc_m013_3203brc_m013_3204brc_m013_3205..brc_m013_3206brc_m013_3207..brc_m013_3211brc_m013_3212..brc_m013_3214brc_m013_3215..brc_m013_3227brc_m013_3228..brc_m013_3230brc_m013_3231..brc_m013_3235brc_m013_3236..brc_m013_3238brc_m013_3239..brc_m013_3242brc_m013_3243..brc_m013_3244brc_m013_3245brc_m013_3246..brc_m013_3247brc_m013_3248..brc_m013_3249brc_m013_3250..brc_m013_3252brc_m013_3253..brc_m013_3257brc_m013_3258brc_m013_3259brc_m013_3260..brc_m013_3261brc_m013_3262..brc_m013_3263brc_m013_3264brc_m013_3265..brc_m013_3269brc_m013_3270..brc_m013_3274brc_m013_3275..brc_m013_3276brc_m013_3277..brc_m013_3281brc_m013_3282..brc_m013_3284brc_m013_3285brc_m013_3286..brc_m013_3289brc_m013_3290..brc_m013_3296brc_m013_3297brc_m013_3298..brc_m013_3300brc_m013_3301..brc_m013_3302brc_m013_3303..brc_m013_3305brc_m013_3306..brc_m013_3308brc_m013_3309..brc_m013_3314brc_m013_3315..brc_m013_3317brc_m013_3318..brc_m013_3329brc_m013_3330..brc_m013_3331brc_m013_3332..brc_m013_3338brc_m013_3339..brc_m013_3340brc_m013_3341..brc_m013_3344brc_m013_3345..brc_m013_3349brc_m013_3350..brc_m013_3357brc_m013_3358..brc_m013_3359brc_m013_3360brc_m013_3361..brc_m013_3368brc_m013_3369..brc_m013_3372brc_m013_3373..brc_m013_3376brc_m013_3377brc_m013_3378..brc_m013_3386brc_m013_3387..brc_m013_3388brc_m013_3389..brc_m013_3395brc_m013_3396..brc_m013_3399
0
20
40
60
80
LG10brc_m013_3400..brc_m013_3411brc_m013_3412brc_m013_3413..brc_m013_3424brc_m013_3425brc_m013_3426brc_m013_3427..brc_m013_3429
brc_m013_3430
brc_m013_3431..brc_m013_3432brc_m013_3433..brc_m013_3435brc_m013_3436brc_m013_3437..brc_m013_3439
brc_m013_3440..brc_m013_3441brc_m013_3442
brc_m013_3443..brc_m013_3445brc_m013_3446..brc_m013_3447brc_m013_3448..brc_m013_3449brc_m013_3450..brc_m013_3454brc_m013_3455brc_m013_3456..brc_m013_3462brc_m013_3463..brc_m013_3464brc_m013_3465brc_m013_3466..brc_m013_3467brc_m013_3468..brc_m013_3472brc_m013_3473brc_m013_3474..brc_m013_3476brc_m013_3477..brc_m013_3487brc_m013_3488brc_m013_3489..brc_m013_3491brc_m013_3492..brc_m013_3500brc_m013_3501..brc_m013_3512brc_m013_3513..brc_m013_3514brc_m013_3515..brc_m013_3524brc_m013_3525..brc_m013_3527brc_m013_3528..brc_m013_3531brc_m013_3532..brc_m013_3547brc_m013_3548..brc_m013_3557brc_m013_3558..brc_m013_3566brc_m013_3567..brc_m013_3568brc_m013_3569..brc_m013_3570brc_m013_3571..brc_m013_3574brc_m013_3575..brc_m013_3582brc_m013_3583..brc_m013_3592brc_m013_3593..brc_m013_3605brc_m013_3606..brc_m013_3616brc_m013_3617..brc_m013_3618brc_m013_3619..brc_m013_3622brc_m013_3623..brc_m013_3624brc_m013_3625..brc_m013_3628brc_m013_3629..brc_m013_3635
0
20
40
60
80
LG11
brc_m013_3636..brc_m013_3661brc_m013_3662..brc_m013_3665
brc_m013_3666..brc_m013_3667brc_m013_3668brc_m013_3669..brc_m013_3671
brc_m013_3672
brc_m013_3673..brc_m013_3674brc_m013_3675..brc_m013_3682
brc_m013_3683..brc_m013_3685
brc_m013_3686..brc_m013_3688
brc_m013_3689..brc_m013_3693
brc_m013_3694..brc_m013_3698brc_m013_3699
brc_m013_3700brc_m013_3701..brc_m013_3702brc_m013_3703..brc_m013_3704brc_m013_3705..brc_m013_3712brc_m013_3713brc_m013_3714..brc_m013_3716brc_m013_3717..brc_m013_3724brc_m013_3725..brc_m013_3730brc_m013_3731..brc_m013_3752brc_m013_3753..brc_m013_3758brc_m013_3759..brc_m013_3789brc_m013_3790..brc_m013_3801brc_m013_3802..brc_m013_3814brc_m013_3815..brc_m013_3818brc_m013_3819..brc_m013_3822brc_m013_3823..brc_m013_3826brc_m013_3827..brc_m013_3832brc_m013_3833..brc_m013_3837brc_m013_3838brc_m013_3839..brc_m013_3841brc_m013_3842..brc_m013_3847
brc_m013_3848..brc_m013_3853brc_m013_3854..brc_m013_3858brc_m013_3859..brc_m013_3868brc_m013_3869..brc_m013_3871brc_m013_3872..brc_m013_3901brc_m013_3902brc_m013_3903..brc_m013_3909brc_m013_3910brc_m013_3911..brc_m013_3926brc_m013_3927..brc_m013_3931brc_m013_3932..brc_m013_3948
0
20
40
60
80
LG12
brc_m013_3949..brc_m013_3952brc_m013_3953..brc_m013_3958brc_m013_3959..brc_m013_3970brc_m013_3971
brc_m013_3972..brc_m013_3975brc_m013_3976
brc_m013_3977..brc_m013_3985
brc_m013_3986brc_m013_3987..brc_m013_3994brc_m013_3995..brc_m013_3997brc_m013_3998..brc_m013_4004
brc_m013_4005..brc_m013_4006brc_m013_4007..brc_m013_4008brc_m013_4009..brc_m013_4010brc_m013_4011..brc_m013_4013brc_m013_4014brc_m013_4015brc_m013_4016..brc_m013_4019brc_m013_4020..brc_m013_4021brc_m013_4022..brc_m013_4025brc_m013_4026..brc_m013_4032brc_m013_4033..brc_m013_4036brc_m013_4037..brc_m013_4041brc_m013_4042..brc_m013_4043
brc_m013_4044..brc_m013_4046brc_m013_4047..brc_m013_4056brc_m013_4057brc_m013_4058..brc_m013_4063brc_m013_4064..brc_m013_4071brc_m013_4072..brc_m013_4075brc_m013_4076brc_m013_4077brc_m013_4078..brc_m013_4085brc_m013_4086..brc_m013_4089brc_m013_4090..brc_m013_4091brc_m013_4092..brc_m013_4093brc_m013_4094..brc_m013_4095brc_m013_4096..brc_m013_4114brc_m013_4115..brc_m013_4117brc_m013_4118..brc_m013_4131brc_m013_4132..brc_m013_4133brc_m013_4134..brc_m013_4146
0
20
40
60
80
LG13
brc_m013_4147..brc_m013_4150brc_m013_4151..brc_m013_4167
brc_m013_4168brc_m013_4169
brc_m013_4170brc_m013_4171..brc_m013_4172brc_m013_4173..brc_m013_4175brc_m013_4176brc_m013_4177..brc_m013_4178brc_m013_4179..brc_m013_4183brc_m013_4184..brc_m013_4185brc_m013_4186..brc_m013_4187brc_m013_4188..brc_m013_4191brc_m013_4192brc_m013_4193..brc_m013_4194brc_m013_4195..brc_m013_4206brc_m013_4207..brc_m013_4210brc_m013_4211..brc_m013_4213brc_m013_4214brc_m013_4215..brc_m013_4217brc_m013_4218..brc_m013_4221brc_m013_4222..brc_m013_4223brc_m013_4224..brc_m013_4231brc_m013_4232..brc_m013_4234brc_m013_4235..brc_m013_4239brc_m013_4240..brc_m013_4246brc_m013_4247..brc_m013_4248brc_m013_4249..brc_m013_4258brc_m013_4259..brc_m013_4260brc_m013_4261..brc_m013_4269brc_m013_4270..brc_m013_4271brc_m013_4272..brc_m013_4278brc_m013_4279..brc_m013_4280brc_m013_4281..brc_m013_4284brc_m013_4285brc_m013_4286..brc_m013_4288brc_m013_4289..brc_m013_4294brc_m013_4295..brc_m013_4296brc_m013_4297..brc_m013_4301brc_m013_4302..brc_m013_4313brc_m013_4314..brc_m013_4320brc_m013_4321..brc_m013_4322brc_m013_4323..brc_m013_4345brc_m013_4346..brc_m013_4351
0
20
40
60
LG14brc_m013_4352..brc_m013_4366brc_m013_4367brc_m013_4368brc_m013_4369..brc_m013_4373brc_m013_4374..brc_m013_4381brc_m013_4382..brc_m013_4383brc_m013_4384..brc_m013_4385brc_m013_4386brc_m013_4387..brc_m013_4388brc_m013_4389brc_m013_4390..brc_m013_4404brc_m013_4405brc_m013_4406..brc_m013_4409brc_m013_4410..brc_m013_4411brc_m013_4412..brc_m013_4418brc_m013_4419..brc_m013_4434brc_m013_4435..brc_m013_4442brc_m013_4443..brc_m013_4448brc_m013_4449..brc_m013_4451brc_m013_4452..brc_m013_4461brc_m013_4462..brc_m013_4471brc_m013_4472..brc_m013_4475brc_m013_4476..brc_m013_4477brc_m013_4478brc_m013_4479brc_m013_4480..brc_m013_4485brc_m013_4486brc_m013_4487..brc_m013_4491brc_m013_4492brc_m013_4493brc_m013_4494..brc_m013_4495brc_m013_4496..brc_m013_4501brc_m013_4502..brc_m013_4510brc_m013_4511..brc_m013_4531brc_m013_4532brc_m013_4533..brc_m013_4534brc_m013_4535..brc_m013_4541brc_m013_4542..brc_m013_4543brc_m013_4544..brc_m013_4545brc_m013_4546..brc_m013_4548brc_m013_4549..brc_m013_4551brc_m013_4552..brc_m013_4555brc_m013_4556..brc_m013_4561
0
20
40
60
LG15
brc_m013_4562..brc_m013_4577brc_m013_4578..brc_m013_4594brc_m013_4595..brc_m013_4599brc_m013_4600..brc_m013_4625brc_m013_4626..brc_m013_4638brc_m013_4639..brc_m013_4642brc_m013_4643..brc_m013_4644brc_m013_4645..brc_m013_4650brc_m013_4651..brc_m013_4663brc_m013_4664..brc_m013_4668brc_m013_4669..brc_m013_4670brc_m013_4671..brc_m013_4674brc_m013_4675..brc_m013_4679brc_m013_4680..brc_m013_4681brc_m013_4682brc_m013_4683..brc_m013_4688brc_m013_4689..brc_m013_4692brc_m013_4693..brc_m013_4695brc_m013_4696..brc_m013_4701brc_m013_4702brc_m013_4703..brc_m013_4712brc_m013_4713..brc_m013_4717brc_m013_4718..brc_m013_4720brc_m013_4721brc_m013_4722..brc_m013_4726brc_m013_4727..brc_m013_4728brc_m013_4729..brc_m013_4742brc_m013_4743brc_m013_4744..brc_m013_4746brc_m013_4747brc_m013_4748..brc_m013_4749brc_m013_4750..brc_m013_4752
brc_m013_4753..brc_m013_4756brc_m013_4757..brc_m013_4759brc_m013_4760..brc_m013_4762brc_m013_4763brc_m013_4764..brc_m013_4766brc_m013_4767..brc_m013_4769brc_m013_4770brc_m013_4771..brc_m013_4774brc_m013_4775..brc_m013_4776brc_m013_4777..brc_m013_4778brc_m013_4779..brc_m013_4780brc_m013_4781..brc_m013_4793brc_m013_4794brc_m013_4795..brc_m013_4798brc_m013_4799..brc_m013_4802brc_m013_4803..brc_m013_4806brc_m013_4807brc_m013_4808..brc_m013_4814brc_m013_4815..brc_m013_4819brc_m013_4820brc_m013_4821brc_m013_4822..brc_m013_4823brc_m013_4824brc_m013_4825..brc_m013_4855brc_m013_4856..brc_m013_4858brc_m013_4859..brc_m013_4863brc_m013_4864..brc_m013_4865brc_m013_4866..brc_m013_4875brc_m013_4876..brc_m013_4881brc_m013_4882..brc_m013_4891brc_m013_4892..brc_m013_4895brc_m013_4896..brc_m013_4911brc_m013_4912..brc_m013_4938brc_m013_4939brc_m013_4940..brc_m013_4957brc_m013_4958..brc_m013_4959brc_m013_4960..brc_m013_4972brc_m013_4973..brc_m013_4981brc_m013_4982..brc_m013_4983
0
20
40
60
80
100
120
LGSB
Gp-9
Figure 1a b
Si_gnF.scaffold00779_nt2778431.7
Si_gnF.scaffold00779_nt1255229Si_gnF.scaffold02684_nt10884.2
Si_gnF.scaffold00779_nt1633919Si_gnF.scaffold00779_nt17842486.5
Si_gnF.scaffold00779_nt3746833Si_gnF.scaffold00779_nt374687927.3Si_gnF.scaffold00779_nt382158728.5
Si_gnF.scaffold00779_nt417489034.2
Si_gnF.scaffold09607_nt698300Si_gnF.scaffold09607_nt69848340.2
Si_gnF.scaffold09758_nt22273252.8
Si_gnF.scaffold05266_nt63430678.4Si_gnF.scaffold05266_nt65952779.7
Si_gnF.scaffold05266_nt733643Si_gnF.scaffold05266_nt75364482.8
Si_gnF.scaffold07090_nt71001087.6
Si_gnF.scaffold07090_nt105177192.7
Si_gnF.scaffold00255_nt314067Si_gnF.scaffold00255_nt40777897.5
Si_gnF.scaffold03404_nt128925Si_gnF.scaffold03404_nt228606Si_gnF.scaffold03404_nt241461
104.4
Si_gnF.scaffold00413_nt676115107.3
Si_gnF.scaffold00413_nt1035856109.6Si_gnF.scaffold01573_nt108462110.8Si_gnF.scaffold01573_nt447618112.1Si_gnF.scaffold00899_nt377419Si_gnF.scaffold00899_nt686574114.4Si_gnF.scaffold00899_nt236146Si_gnF.scaffold00899_nt332715Si_gnF.scaffold00899_nt335756
115.8
Si_gnF.scaffold00469_nt794118.0Si_gnF.scaffold00690_nt229012Si_gnF.scaffold00690_nt415290119.3
Si_gnF.scaffold06914_nt297673125.1
Si_gnF.scaffold01957_nt412242Si_gnF.scaffold02848_nt41846127.6
LGS Bfrom M013
Si_gnF.scaffold00779_nt2778430.0Si_gnF.scaffold00779_nt1255229Si_gnF.scaffold02684_nt10881.2
Si_gnF.scaffold00779_nt1633919Si_gnF.scaffold00779_nt17842486.7
Si_gnF.scaffold00779_nt3746833Si_gnF.scaffold00779_nt3746879Si_gnF.scaffold00779_nt3821587
22.2
Si_gnF.scaffold00779_nt417489029.2
Si_gnF.scaffold09607_nt698300Si_gnF.scaffold09607_nt69848361.9
Si_gnF.scaffold01573_nt10846280.7Si_gnF.scaffold00255_nt314067Si_gnF.scaffold00255_nt407778Si_gnF.scaffold00413_nt1035856Si_gnF.scaffold00413_nt676115Si_gnF.scaffold00469_nt794Si_gnF.scaffold00690_nt229012Si_gnF.scaffold00690_nt415290Si_gnF.scaffold00899_nt236146Si_gnF.scaffold00899_nt332715Si_gnF.scaffold00899_nt335756Si_gnF.scaffold00899_nt377419Si_gnF.scaffold00899_nt686574Si_gnF.scaffold01573_nt447618Si_gnF.scaffold01957_nt412242Si_gnF.scaffold03404_nt128925Si_gnF.scaffold03404_nt228606Si_gnF.scaffold03404_nt241461Si_gnF.scaffold05266_nt634306Si_gnF.scaffold05266_nt659527Si_gnF.scaffold05266_nt733643Si_gnF.scaffold05266_nt753644Si_gnF.scaffold06914_nt297673Si_gnF.scaffold07090_nt1051771Si_gnF.scaffold07090_nt710010Si_gnF.scaffold09758_nt222732
81.8
Si_gnF.scaffold02848_nt4184690.5
LGS B/bfrom P034
Gp-9
Total285 non-recombiningmarkers
>4% of genome linked to Gp-9
No recombination between B and b over ⅔ of a chromosme!
Gp-9
Wang & Wurm et al 2013 Nature
• Is this gene the single überregulator?
maybe 1/14th of the genome?•Only 14 allozyme markers
Social form completely associated to Gp-9 locus
BB BB Bb
Single queen form Multiple queen form(>15% ) (< 5% )
x xx
✖✔
Locus!
0.3!0.4!0.5!0.6!0.7!0.8!0.9!1.0!
Single queen!Multiple queen!
Est-6!Est-4!G3pdh-1!Ca-4!Pgm-4!Ddh-1!Pro-5!
Pgm-3!
Acoh-5!
acoh-1!
Acy-1!
Pgm-1!
Aat-2!
Gp-9!
Sex chromosomes
X Y
Gp-9 B
Gp-9 b
SB Sb
?
1. Why non-recombining?
“Social chromosomes”= supergene
2. Are SB and Sb differentiated?3. What are the differences?
SBSBSBSb
Single queen form Multiple queen form
SBSB SB Sb
Single queen colony Multiple queen colony
SBSB SB Sb
Single queen colony Multiple queen colony
Summary: Fire ants have two colony types
Summary: this is determined by a pair of social chromosomes
Research themes
• Biomedical approaches • International population genomics surveys • Monitoring via sequencing
• Major social transitions » social chromosomes » convergence » eusociality, queen number, parasitism...
• 100-fold intra-specific variation in lifespan • Strengths of selection • Candidate genes/pathway
Pollinator health
Genome evolution Social evolution
Modern bioinformatics tools & approaches(some at https://wurmlab.github.io )
“Can you BLAST this for me?”
BLAST
But: •convoluted interface•challenging on custom data
Antgenomes.org SequenceServer BLAST made easy
is the most commonly used tool: >100,000 citations
http://www.sequenceserver.com/
If no config file: Asks interactive setup questions. If needed: Downloads BLAST binariesIf needed: Formats FASTA into BLAST database.
1. Installinggem install sequenceserver
### Launched SequenceServer at: http://0.0.0.0:4567
2. Launchsequenceserver
DemoAnurag Priyam - @yeban
Timewasters
• Client vs server-side code.
• Workflows stalling (data download, cluster queues…)
• Fragmented efforts - having to learn additional languages for specific tools
+ project-specific needs
Bionode
Bruno Vieira @bmpvieira
Philosophy for flexibility
Modules should:•(also) work in the web browser (when possible)•(also) work in the command-line•support streaming input/output
gittergitter join chatjoin chat
http://bionode.io
Bruno Vieira @bmpvieira
Difficulty writing scalable, reproducible andcomplex bioinformatic pipelines.Solution: Node.js everywhereStreams var ncbi = require('bionode-ncbi') var tool = require('tool-stream') var through = require('through2') var fork1 = through.obj() var fork2 = through.obj()
ncbi .search('sra', 'Solenopsis invicta') .pipe(fork1) .pipe(dat.reads)
fork1 .pipe(tool.extractProperty('expxml.Biosample.id')) .pipe(ncbi.search('biosample')) .pipe(dat.samples)
fork1 .pipe(tool.extractProperty('uid')) .pipe(ncbi.link('sra', 'pubmed'))
Node/Bionode for complex pipelines
@bmpvieira
#"Get"descriptions"for"papers"related"to"SRA"search!bionode!ncbi!search!sra!Solenopsis!invicta!|!!!!!!!!!!tool3stream!extractProperty!uid!|!!!!!!!!!!bionode!ncbi!link!sra!pubmed!|!!!!!!!!!!tool3stream!extractProperty!destUID!|! !!!!!!!!bionode!ncbi!search!pubmed
#"Get"URL"of"Solenopsis"invicta"genome"bionode3ncbi!urls!assembly!Solenopsis!invicta!|!json|!grep!genomic.fna!!http://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000188075.1_Si_gnG/GCA_000188075.1_Si_gnG_genomic.fna.gz
http://bionode.io in the terminal
#"Get"all"FASTQ"of"Arthropod"short"reads"bionode3ncbi!download!sra!arthropoda!|!bionode3sra!fastq3dump!3
#"Get"all"GFF"of"bacterial"genome"annotations"bionode3ncbi!download!gff!bacteria!
@bmpvieira
Bruno Vieira @bmpvieira
Philosophy for flexibility
Modules should:•(also) work in the web browser (when possible)•(also) work in the command-line•support streaming input/output
Modules:•decentralised management.•small - just do one thing well.•few strict rules, but some strong recommendations (style, interfaces etc).
gittergitter join chatjoin chat
Bruno Vieira @bmpvieira
Contributors
gittergitter join chatjoin chat
YOU?
BioJS for visualisation Bionode for data handling
Geoffrey Chang: Crystallographer• Beckman Foundation Young Investigator
Award
• Presidential Early Career Award
Journal of Molecular Biology (2003) Chang. Structure of MsbA from Vibrio cholera: a multidrug resistance ABC transporter homolog in a closed conformation.
PNAS (2004) Ma & Chang. Structure of the multidrug resistance efflux transporter EmrE from Escherichia coli.Science (2005) Reyes & Chang. Structure of the ABC transporter MsbA in complex with ADP vanadate and lipopolysaccharide.
Science (2005) Pornillos et al. X-ray structure of the EmrE multidrug transporter in complex with a substrate.
Science (2001) Chang & Roth. Structure of MsbA from E. coli: a homolog of the multidrug resistance ATP binding cassette (ABC) transporters.
Science (2001) Chang & Roth.
1856
NEWS>>
THIS WEEK A dolphin’s
demise
Indians wary of
nuclear pact
1860 1863
Until recently, Geoffrey Chang’s career was ona trajectory most young scientists only dreamabout. In 1999, at the age of 28, the proteincrystallographer landed a faculty position atthe prestigious Scripps Research Institute inSan Diego, California. The next year, in a cer-emony at the White House, Chang received aPresidential Early Career Awardfor Scientists and Engineers, thecountry’s highest honor for youngresearchers. His lab generated astream of high-prof ile papersdetailing the molecular structuresof important proteins embedded incell membranes.
Then the dream turned into anightmare. In September, Swissresearchers published a paper inNature that cast serious doubt on aprotein structure Chang’s grouphad described in a 2001 Science
paper. When he investigated,Chang was horrified to discoverthat a homemade data-analysis pro-gram had flipped two columns ofdata, inverting the electron-densitymap from which his team hadderived the final protein structure.Unfortunately, his group had usedthe program to analyze data forother proteins. As a result, on page 1875,Chang and his colleagues retract three Science
papers and report that two papers in other jour-nals also contain erroneous structures.
“I’ve been devastated,” Chang says. “I hopepeople will understand that it was a mistake,and I’m very sorry for it.” Other researchersdon’t doubt that the error was unintentional,and although some say it has cost them timeand effort, many praise Chang for setting therecord straight promptly and forthrightly. “I’mvery pleased he’s done this because there hasbeen some confusion” about the original struc-tures, says Christopher Higgins, a biochemistat Imperial College London. “Now the fieldcan really move forward.”
The most influential of Chang’s retractedpublications, other researchers say, was the
2001 Science paper, which described the struc-ture of a protein called MsbA, isolated from thebacterium Escherichia coli. MsbA belongs to ahuge and ancient family of molecules that useenergy from adenosine triphosphate to trans-port molecules across cell membranes. Theseso-called ABC transporters perform many
essential biological duties and are of great clin-ical interest because of their roles in drug resist-ance. Some pump antibiotics out of bacterialcells, for example; others clear chemotherapydrugs from cancer cells. Chang’s MsbA struc-ture was the first molecular portrait of an entireABC transporter, and many researchers saw itas a major contribution toward figuring out howthese crucial proteins do their jobs. That paperalone has been cited by 364 publications,according to Google Scholar.
Two subsequent papers, both now beingretracted, describe the structure of MsbA fromother bacteria, Vibrio cholera (published inMolecular Biology in 2003) and Salmonella
typhimurium (published in Science in 2005).The other retractions, a 2004 paper in theProceedings of the National Academy of
Sciences and a 2005 Science paper, describedEmrE, a different type of transporter protein.
Crystallizing and obtaining structures offive membrane proteins in just over 5 yearswas an incredible feat, says Chang’s formerpostdoc adviser Douglas Rees of the Califor-nia Institute of Technology in Pasadena. Suchproteins are a challenge for crystallographersbecause they are large, unwieldy, and notori-ously diff icult to coax into the crystalsneeded for x-ray crystallography. Rees saysdetermination was at the root of Chang’s suc-cess: “He has an incredible drive and workethic. He really pushed the field in the sense
of getting things to crystallize thatno one else had been able to do.”Chang’s data are good, Rees says,but the faulty software threweverything off.
Ironically, another former post-doc in Rees’s lab, Kaspar Locher,exposed the mistake. In the 14 Sep-tember issue of Nature, Locher,now at the Swiss Federal Instituteof Technology in Zurich, describedthe structure of an ABC transportercalled Sav1866 from Staphylococcus
aureus. The structure was dramati-cally—and unexpectedly—differ-ent from that of MsbA. Afterpulling up Sav1866 and Chang’sMsbA from S. typhimurium on acomputer screen, Locher says herealized in minutes that the MsbAstructure was inverted. Interpretingthe “hand” of a molecule is alwaysa challenge for crystallographers,
Locher notes, and many mistakes can lead toan incorrect mirror-image structure. Gettingthe wrong hand is “in the category of monu-mental blunders,” Locher says.
On reading the Nature paper, Changquickly traced the mix-up back to the analysisprogram, which he says he inherited fromanother lab. Locher suspects that Changwould have caught the mistake if he’d takenmore time to obtain a higher resolution struc-ture. “I think he was under immense pressureto get the first structure, and that’s what madehim push the limits of his data,” he says. Oth-ers suggest that Chang might have caught theproblem if he’d paid closer attention to bio-chemical findings that didn’t jibe well with theMsbA structure. “When the first structurecame out, we and others said, ‘We really
A Scientist’s Nightmare: Software
Problem Leads to Five Retractions
SCIENTIFIC PUBLISHING
CR
ED
IT: R
. J. P.
DA
WS
ON
AN
D K
. P.
LO
CH
ER
, N
AT
UR
E4
43
, 1
80
( 2
00
6)
22 DECEMBER 2006 VOL 314 SCIENCE www.sciencemag.org
Flipping fiasco. The structures of MsbA (purple) and Sav1866 (green) overlap
little (left) until MsbA is inverted (right).
▲
Published by AAAS
on
Janu
ary
5, 2
007
ww
w.s
cien
cem
ag.o
rgD
ownl
oade
d fro
m
1856
NEWS>>
THIS WEEK A dolphin’s
demise
Indians wary of
nuclear pact
1860 1863
Until recently, Geoffrey Chang’s career was ona trajectory most young scientists only dreamabout. In 1999, at the age of 28, the proteincrystallographer landed a faculty position atthe prestigious Scripps Research Institute inSan Diego, California. The next year, in a cer-emony at the White House, Chang received aPresidential Early Career Awardfor Scientists and Engineers, thecountry’s highest honor for youngresearchers. His lab generated astream of high-prof ile papersdetailing the molecular structuresof important proteins embedded incell membranes.
Then the dream turned into anightmare. In September, Swissresearchers published a paper inNature that cast serious doubt on aprotein structure Chang’s grouphad described in a 2001 Science
paper. When he investigated,Chang was horrified to discoverthat a homemade data-analysis pro-gram had flipped two columns ofdata, inverting the electron-densitymap from which his team hadderived the final protein structure.Unfortunately, his group had usedthe program to analyze data forother proteins. As a result, on page 1875,Chang and his colleagues retract three Science
papers and report that two papers in other jour-nals also contain erroneous structures.
“I’ve been devastated,” Chang says. “I hopepeople will understand that it was a mistake,and I’m very sorry for it.” Other researchersdon’t doubt that the error was unintentional,and although some say it has cost them timeand effort, many praise Chang for setting therecord straight promptly and forthrightly. “I’mvery pleased he’s done this because there hasbeen some confusion” about the original struc-tures, says Christopher Higgins, a biochemistat Imperial College London. “Now the fieldcan really move forward.”
The most influential of Chang’s retractedpublications, other researchers say, was the
2001 Science paper, which described the struc-ture of a protein called MsbA, isolated from thebacterium Escherichia coli. MsbA belongs to ahuge and ancient family of molecules that useenergy from adenosine triphosphate to trans-port molecules across cell membranes. Theseso-called ABC transporters perform many
essential biological duties and are of great clin-ical interest because of their roles in drug resist-ance. Some pump antibiotics out of bacterialcells, for example; others clear chemotherapydrugs from cancer cells. Chang’s MsbA struc-ture was the first molecular portrait of an entireABC transporter, and many researchers saw itas a major contribution toward figuring out howthese crucial proteins do their jobs. That paperalone has been cited by 364 publications,according to Google Scholar.
Two subsequent papers, both now beingretracted, describe the structure of MsbA fromother bacteria, Vibrio cholera (published inMolecular Biology in 2003) and Salmonella
typhimurium (published in Science in 2005).The other retractions, a 2004 paper in theProceedings of the National Academy of
Sciences and a 2005 Science paper, describedEmrE, a different type of transporter protein.
Crystallizing and obtaining structures offive membrane proteins in just over 5 yearswas an incredible feat, says Chang’s formerpostdoc adviser Douglas Rees of the Califor-nia Institute of Technology in Pasadena. Suchproteins are a challenge for crystallographersbecause they are large, unwieldy, and notori-ously diff icult to coax into the crystalsneeded for x-ray crystallography. Rees saysdetermination was at the root of Chang’s suc-cess: “He has an incredible drive and workethic. He really pushed the field in the sense
of getting things to crystallize thatno one else had been able to do.”Chang’s data are good, Rees says,but the faulty software threweverything off.
Ironically, another former post-doc in Rees’s lab, Kaspar Locher,exposed the mistake. In the 14 Sep-tember issue of Nature, Locher,now at the Swiss Federal Instituteof Technology in Zurich, describedthe structure of an ABC transportercalled Sav1866 from Staphylococcus
aureus. The structure was dramati-cally—and unexpectedly—differ-ent from that of MsbA. Afterpulling up Sav1866 and Chang’sMsbA from S. typhimurium on acomputer screen, Locher says herealized in minutes that the MsbAstructure was inverted. Interpretingthe “hand” of a molecule is alwaysa challenge for crystallographers,
Locher notes, and many mistakes can lead toan incorrect mirror-image structure. Gettingthe wrong hand is “in the category of monu-mental blunders,” Locher says.
On reading the Nature paper, Changquickly traced the mix-up back to the analysisprogram, which he says he inherited fromanother lab. Locher suspects that Changwould have caught the mistake if he’d takenmore time to obtain a higher resolution struc-ture. “I think he was under immense pressureto get the first structure, and that’s what madehim push the limits of his data,” he says. Oth-ers suggest that Chang might have caught theproblem if he’d paid closer attention to bio-chemical findings that didn’t jibe well with theMsbA structure. “When the first structurecame out, we and others said, ‘We really
A Scientist’s Nightmare: Software
Problem Leads to Five Retractions
SCIENTIFIC PUBLISHING
CR
ED
IT: R
. J. P.
DA
WSO
N A
ND
K. P.
LO
CH
ER
, N
AT
UR
E4
43
, 180 ( 2
006)
22 DECEMBER 2006 VOL 314 SCIENCE www.sciencemag.org
Flipping fiasco. The structures of MsbA (purple) and Sav1866 (green) overlap
little (left) until MsbA is inverted (right).
▲
Published by AAAS
on
Janu
ary
5, 2
007
ww
w.s
cien
cem
ag.o
rgD
ownl
oade
d fro
m
Sav1866 Dawson & Locher (2006) NatureScience (2001) Chang & Roth.Science (2001) Chang & Roth.
Comparison with 3D structure of ortholog
Science (2001) Chang & Roth.
http://wurmlab.github.io
www.sciencemag.org SCIENCE VOL 314 22 DECEMBER 2006 1875
Aquaculture in
Offshore Zones
THE EDITORIAL BY ROSAMOND NAYLOR,“Offshore aquaculture legislation” (8 Sept.,
p. 1363), suggests that the motivation for
moving aquaculture into the open ocean is
that “marine f ish farming near the shore
is limited by state regulations.” Although
unworkable regulations may exist in a few
states, in the larger scheme this is irrele-
vant. Of the offshore aquaculture projects
currently under way, none are occurring in
the U.S. Exclusive Economic Zone (EEZ);
rather, they are happening in state waters.
Even historically, only two aquaculture
projects have ever occurred in federal
waters (1).
Much of Naylor’s stated concern over
offshore aquaculture is based on historical
experience with near-shore fish farms. This
is in spite of years of more relevant offshore
operations that reveal little, if any, negative
impact on the environment or local ecosys-
tems (2, 3). Naylor criticizes the National
Offshore Aquaculture Act of 2005 because
it lacks specific environmental standards.
Yet, she recommends California’s recent
Sustainable Oceans Act as a legislative
model, although it is similarly silent, leaving
those details to rule-making in response to
the best available science.
Naylor criticizes the use of fishmeal as
an aquaculture ingredient, ignoring the fact
that industrial fisheries are well managed
and would occur with or without aquacul-
ture’s demand. Naylor ignores the higher
efficiency of using fishmeal to feed fish
compared with its use in land-based live-
stock operations (4). Also ignored is the
inefficiency of using small pelagic fish in
the natural setting to feed predator fish (5).
Researchers and entrepreneurs currently
developing the technologies needed for offshore
aquaculture share a vision of a well-managed
industry governed by regulations with a rational
basis in the ecology of the oceans and the eco-
nomic realities of the marketplace.CLIFFORD A. GOUDEY
Massachusetts Institute of Technology, Cambridge, MA02139, USA.
References and Notes1. The SeaStead project a decade ago, four miles off
Massachusetts (see www.nmfs.noaa.gov/mb/sk/saltonstallken/enhancement.htm) and the recentOffshore Aquaculture Consortium experimental cageoperation 22 miles off Mississippi (see www.masgc.org/oac/).
2. See www.lib.noaa.gov/docaqua/reports_noaaresearch/hooarrprept.htm/.
3. See www.blackpearlsinc.com/PDF/hoarpi.pdf.4. See www.salmonoftheamericas.com/env_food.html.5. D. Pauly, V. Christensen, Nature 374, 255 (2002).
IN HER PROVOCATIVE EDITORIAL “OFFSHOREaquaculture legislation” (8 Sept., p. 1363),
R. Naylor raises valid points regarding regu-
lation of oceanic aquaculture, since it is
sure to grow in the future because of dwin-
dling global fishery supplies. This growth is
LETTERS I BOOKS I POLICY FORUM I EDUCATION FORUM I PERSPECTIVES
1878
Generating new sciencein the classroom
How proteins connect
1880 1882
Mathematicalperspectives
LETTERSedited by Etta Kavanagh
Retraction
WE WISH TO RETRACT OUR RESEARCH ARTICLE “STRUCTURE OFMsbA from E. coli: A homolog of the multidrug resistance ATP bind-
ing cassette (ABC) transporters” and both of our Reports “Structure of
the ABC transporter MsbA in complex with ADP•vanadate and
lipopolysaccharide” and “X-ray structure of the EmrE multidrug trans-
porter in complex with a substrate” (1–3).
The recently reported structure of Sav1866 (4) indicated that our
MsbA structures (1, 2, 5) were incorrect in both the hand of the struc-
ture and the topology. Thus, our biological interpretations based on
these inverted models for MsbA are invalid.
An in-house data reduction program introduced a change in sign for
anomalous differences. This program, which was not part of a conven-
tional data processing package, converted the anomalous pairs (I+ and
I-) to (F- and F+), thereby introducing a sign change. As the diffrac-
tion data collected for each set of MsbA crystals and for the EmrE
crystals were processed with the same program, the structures reported
in (1–3, 5, 6) had the wrong hand.
The error in the topology of the original MsbA structure was a con-
sequence of the low resolution of the data as well as breaks in the elec-
tron density for the connecting loop regions. Unfortunately, the use of
the multicopy refinement procedure still allowed us to obtain reason-
able refinement values for the wrong structures.
The Protein Data Bank (PDB) files 1JSQ, 1PF4, and 1Z2R for
MsbA and 1S7B and 2F2M for EmrE have been moved to the archive
of obsolete PDB entries. The MsbA and EmrE structures will be
recalculated from the original data using the proper sign for the anom-
alous differences, and the new Ca coordinates and structure factors
will be deposited.
We very sincerely regret the confusion that these papers have
caused and, in particular, subsequent research efforts that were unpro-
ductive as a result of our original findings.GEOFFREY CHANG, CHRISTOPHER B. ROTH,
CHRISTOPHER L. REYES, OWEN PORNILLOS,
YEN-JU CHEN, ANDY P. CHEN
Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.
References1. G. Chang, C. B. Roth, Science 293, 1793 (2001).2. C. L. Reyes, G. Chang, Science 308, 1028 (2005).3. O. Pornillos, Y.-J. Chen, A. P. Chen, G. Chang, Science 310, 1950 (2005).4. R. J. Dawson, K. P. Locher, Nature 443, 180 (2006).5. G. Chang, J. Mol. Biol. 330, 419 (2003).6. C. Ma, G. Chang, Proc. Natl. Acad. Sci. U.S.A. 101, 2852 (2004).
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www.sciencemag.org SCIENCE VOL 314 22 DECEMBER 2006 1875
Aquaculture in
Offshore Zones
THE EDITORIAL BY ROSAMOND NAYLOR,“Offshore aquaculture legislation” (8 Sept.,
p. 1363), suggests that the motivation for
moving aquaculture into the open ocean is
that “marine f ish farming near the shore
is limited by state regulations.” Although
unworkable regulations may exist in a few
states, in the larger scheme this is irrele-
vant. Of the offshore aquaculture projects
currently under way, none are occurring in
the U.S. Exclusive Economic Zone (EEZ);
rather, they are happening in state waters.
Even historically, only two aquaculture
projects have ever occurred in federal
waters (1).
Much of Naylor’s stated concern over
offshore aquaculture is based on historical
experience with near-shore fish farms. This
is in spite of years of more relevant offshore
operations that reveal little, if any, negative
impact on the environment or local ecosys-
tems (2, 3). Naylor criticizes the National
Offshore Aquaculture Act of 2005 because
it lacks specific environmental standards.
Yet, she recommends California’s recent
Sustainable Oceans Act as a legislative
model, although it is similarly silent, leaving
those details to rule-making in response to
the best available science.
Naylor criticizes the use of fishmeal as
an aquaculture ingredient, ignoring the fact
that industrial fisheries are well managed
and would occur with or without aquacul-
ture’s demand. Naylor ignores the higher
efficiency of using fishmeal to feed fish
compared with its use in land-based live-
stock operations (4). Also ignored is the
inefficiency of using small pelagic fish in
the natural setting to feed predator fish (5).
Researchers and entrepreneurs currently
developing the technologies needed for offshore
aquaculture share a vision of a well-managed
industry governed by regulations with a rational
basis in the ecology of the oceans and the eco-
nomic realities of the marketplace.CLIFFORD A. GOUDEY
Massachusetts Institute of Technology, Cambridge, MA02139, USA.
References and Notes1. The SeaStead project a decade ago, four miles off
Massachusetts (see www.nmfs.noaa.gov/mb/sk/saltonstallken/enhancement.htm) and the recentOffshore Aquaculture Consortium experimental cageoperation 22 miles off Mississippi (see www.masgc.org/oac/).
2. See www.lib.noaa.gov/docaqua/reports_noaaresearch/hooarrprept.htm/.
3. See www.blackpearlsinc.com/PDF/hoarpi.pdf.4. See www.salmonoftheamericas.com/env_food.html.5. D. Pauly, V. Christensen, Nature 374, 255 (2002).
IN HER PROVOCATIVE EDITORIAL “OFFSHOREaquaculture legislation” (8 Sept., p. 1363),
R. Naylor raises valid points regarding regu-
lation of oceanic aquaculture, since it is
sure to grow in the future because of dwin-
dling global fishery supplies. This growth is
LETTERS I BOOKS I POLICY FORUM I EDUCATION FORUM I PERSPECTIVES
1878
Generating new sciencein the classroom
How proteins connect
1880 1882
Mathematicalperspectives
LETTERSedited by Etta Kavanagh
Retraction
WE WISH TO RETRACT OUR RESEARCH ARTICLE “STRUCTURE OFMsbA from E. coli: A homolog of the multidrug resistance ATP bind-
ing cassette (ABC) transporters” and both of our Reports “Structure of
the ABC transporter MsbA in complex with ADP•vanadate and
lipopolysaccharide” and “X-ray structure of the EmrE multidrug trans-
porter in complex with a substrate” (1–3).
The recently reported structure of Sav1866 (4) indicated that our
MsbA structures (1, 2, 5) were incorrect in both the hand of the struc-
ture and the topology. Thus, our biological interpretations based on
these inverted models for MsbA are invalid.
An in-house data reduction program introduced a change in sign for
anomalous differences. This program, which was not part of a conven-
tional data processing package, converted the anomalous pairs (I+ and
I-) to (F- and F+), thereby introducing a sign change. As the diffrac-
tion data collected for each set of MsbA crystals and for the EmrE
crystals were processed with the same program, the structures reported
in (1–3, 5, 6) had the wrong hand.
The error in the topology of the original MsbA structure was a con-
sequence of the low resolution of the data as well as breaks in the elec-
tron density for the connecting loop regions. Unfortunately, the use of
the multicopy refinement procedure still allowed us to obtain reason-
able refinement values for the wrong structures.
The Protein Data Bank (PDB) files 1JSQ, 1PF4, and 1Z2R for
MsbA and 1S7B and 2F2M for EmrE have been moved to the archive
of obsolete PDB entries. The MsbA and EmrE structures will be
recalculated from the original data using the proper sign for the anom-
alous differences, and the new Ca coordinates and structure factors
will be deposited.
We very sincerely regret the confusion that these papers have
caused and, in particular, subsequent research efforts that were unpro-
ductive as a result of our original findings.GEOFFREY CHANG, CHRISTOPHER B. ROTH,
CHRISTOPHER L. REYES, OWEN PORNILLOS,
YEN-JU CHEN, ANDY P. CHEN
Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.
References1. G. Chang, C. B. Roth, Science 293, 1793 (2001).2. C. L. Reyes, G. Chang, Science 308, 1028 (2005).3. O. Pornillos, Y.-J. Chen, A. P. Chen, G. Chang, Science 310, 1950 (2005).4. R. J. Dawson, K. P. Locher, Nature 443, 180 (2006).5. G. Chang, J. Mol. Biol. 330, 419 (2003).6. C. Ma, G. Chang, Proc. Natl. Acad. Sci. U.S.A. 101, 2852 (2004).
COMMENTARY
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1856
NEWS>>
THIS WEEK A dolphin’s
demise
Indians wary of
nuclear pact
1860 1863
Until recently, Geoffrey Chang’s career was ona trajectory most young scientists only dreamabout. In 1999, at the age of 28, the proteincrystallographer landed a faculty position atthe prestigious Scripps Research Institute inSan Diego, California. The next year, in a cer-emony at the White House, Chang received aPresidential Early Career Awardfor Scientists and Engineers, thecountry’s highest honor for youngresearchers. His lab generated astream of high-prof ile papersdetailing the molecular structuresof important proteins embedded incell membranes.
Then the dream turned into anightmare. In September, Swissresearchers published a paper inNature that cast serious doubt on aprotein structure Chang’s grouphad described in a 2001 Science
paper. When he investigated,Chang was horrified to discoverthat a homemade data-analysis pro-gram had flipped two columns ofdata, inverting the electron-densitymap from which his team hadderived the final protein structure.Unfortunately, his group had usedthe program to analyze data forother proteins. As a result, on page 1875,Chang and his colleagues retract three Science
papers and report that two papers in other jour-nals also contain erroneous structures.
“I’ve been devastated,” Chang says. “I hopepeople will understand that it was a mistake,and I’m very sorry for it.” Other researchersdon’t doubt that the error was unintentional,and although some say it has cost them timeand effort, many praise Chang for setting therecord straight promptly and forthrightly. “I’mvery pleased he’s done this because there hasbeen some confusion” about the original struc-tures, says Christopher Higgins, a biochemistat Imperial College London. “Now the fieldcan really move forward.”
The most influential of Chang’s retractedpublications, other researchers say, was the
2001 Science paper, which described the struc-ture of a protein called MsbA, isolated from thebacterium Escherichia coli. MsbA belongs to ahuge and ancient family of molecules that useenergy from adenosine triphosphate to trans-port molecules across cell membranes. Theseso-called ABC transporters perform many
essential biological duties and are of great clin-ical interest because of their roles in drug resist-ance. Some pump antibiotics out of bacterialcells, for example; others clear chemotherapydrugs from cancer cells. Chang’s MsbA struc-ture was the first molecular portrait of an entireABC transporter, and many researchers saw itas a major contribution toward figuring out howthese crucial proteins do their jobs. That paperalone has been cited by 364 publications,according to Google Scholar.
Two subsequent papers, both now beingretracted, describe the structure of MsbA fromother bacteria, Vibrio cholera (published inMolecular Biology in 2003) and Salmonella
typhimurium (published in Science in 2005).The other retractions, a 2004 paper in theProceedings of the National Academy of
Sciences and a 2005 Science paper, describedEmrE, a different type of transporter protein.
Crystallizing and obtaining structures offive membrane proteins in just over 5 yearswas an incredible feat, says Chang’s formerpostdoc adviser Douglas Rees of the Califor-nia Institute of Technology in Pasadena. Suchproteins are a challenge for crystallographersbecause they are large, unwieldy, and notori-ously diff icult to coax into the crystalsneeded for x-ray crystallography. Rees saysdetermination was at the root of Chang’s suc-cess: “He has an incredible drive and workethic. He really pushed the field in the sense
of getting things to crystallize thatno one else had been able to do.”Chang’s data are good, Rees says,but the faulty software threweverything off.
Ironically, another former post-doc in Rees’s lab, Kaspar Locher,exposed the mistake. In the 14 Sep-tember issue of Nature, Locher,now at the Swiss Federal Instituteof Technology in Zurich, describedthe structure of an ABC transportercalled Sav1866 from Staphylococcus
aureus. The structure was dramati-cally—and unexpectedly—differ-ent from that of MsbA. Afterpulling up Sav1866 and Chang’sMsbA from S. typhimurium on acomputer screen, Locher says herealized in minutes that the MsbAstructure was inverted. Interpretingthe “hand” of a molecule is alwaysa challenge for crystallographers,
Locher notes, and many mistakes can lead toan incorrect mirror-image structure. Gettingthe wrong hand is “in the category of monu-mental blunders,” Locher says.
On reading the Nature paper, Changquickly traced the mix-up back to the analysisprogram, which he says he inherited fromanother lab. Locher suspects that Changwould have caught the mistake if he’d takenmore time to obtain a higher resolution struc-ture. “I think he was under immense pressureto get the first structure, and that’s what madehim push the limits of his data,” he says. Oth-ers suggest that Chang might have caught theproblem if he’d paid closer attention to bio-chemical findings that didn’t jibe well with theMsbA structure. “When the first structurecame out, we and others said, ‘We really
A Scientist’s Nightmare: Software
Problem Leads to Five Retractions
SCIENTIFIC PUBLISHING
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22 DECEMBER 2006 VOL 314 SCIENCE www.sciencemag.org
Flipping fiasco. The structures of MsbA (purple) and Sav1866 (green) overlap
little (left) until MsbA is inverted (right).
▲
Published by AAAS
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Geoffrey Chang• Beckman Foundation Young Investigator
Award
• Presidential Early Career Award
Science (2001) Chang & Roth. Structure of MsbA from E. coli: a homolog of the multidrug resistance ATP binding cassette (ABC) transporters.Journal of Molecular Biology (2003) Chang. Structure of MsbA from Vibrio cholera: a multidrug resistance ABC transporter homolog in a closed conformation.
PNAS (2004) Ma & Chang. Structure of the multidrug resistance efflux transporter EmrE from Escherichia coli.Science (2005) Reyes & Chang. Structure of the ABC transporter MsbA in complex with ADP vanadate and lipopolysaccharide.
Science (2005) Pornillos et al. X-ray structure of the EmrE multidrug transporter in complex with a substrate.
1856
NEWS>>
THIS WEEK A dolphin’s
demise
Indians wary of
nuclear pact
1860 1863
Until recently, Geoffrey Chang’s career was ona trajectory most young scientists only dreamabout. In 1999, at the age of 28, the proteincrystallographer landed a faculty position atthe prestigious Scripps Research Institute inSan Diego, California. The next year, in a cer-emony at the White House, Chang received aPresidential Early Career Awardfor Scientists and Engineers, thecountry’s highest honor for youngresearchers. His lab generated astream of high-prof ile papersdetailing the molecular structuresof important proteins embedded incell membranes.
Then the dream turned into anightmare. In September, Swissresearchers published a paper inNature that cast serious doubt on aprotein structure Chang’s grouphad described in a 2001 Science
paper. When he investigated,Chang was horrified to discoverthat a homemade data-analysis pro-gram had flipped two columns ofdata, inverting the electron-densitymap from which his team hadderived the final protein structure.Unfortunately, his group had usedthe program to analyze data forother proteins. As a result, on page 1875,Chang and his colleagues retract three Science
papers and report that two papers in other jour-nals also contain erroneous structures.
“I’ve been devastated,” Chang says. “I hopepeople will understand that it was a mistake,and I’m very sorry for it.” Other researchersdon’t doubt that the error was unintentional,and although some say it has cost them timeand effort, many praise Chang for setting therecord straight promptly and forthrightly. “I’mvery pleased he’s done this because there hasbeen some confusion” about the original struc-tures, says Christopher Higgins, a biochemistat Imperial College London. “Now the fieldcan really move forward.”
The most influential of Chang’s retractedpublications, other researchers say, was the
2001 Science paper, which described the struc-ture of a protein called MsbA, isolated from thebacterium Escherichia coli. MsbA belongs to ahuge and ancient family of molecules that useenergy from adenosine triphosphate to trans-port molecules across cell membranes. Theseso-called ABC transporters perform many
essential biological duties and are of great clin-ical interest because of their roles in drug resist-ance. Some pump antibiotics out of bacterialcells, for example; others clear chemotherapydrugs from cancer cells. Chang’s MsbA struc-ture was the first molecular portrait of an entireABC transporter, and many researchers saw itas a major contribution toward figuring out howthese crucial proteins do their jobs. That paperalone has been cited by 364 publications,according to Google Scholar.
Two subsequent papers, both now beingretracted, describe the structure of MsbA fromother bacteria, Vibrio cholera (published inMolecular Biology in 2003) and Salmonella
typhimurium (published in Science in 2005).The other retractions, a 2004 paper in theProceedings of the National Academy of
Sciences and a 2005 Science paper, describedEmrE, a different type of transporter protein.
Crystallizing and obtaining structures offive membrane proteins in just over 5 yearswas an incredible feat, says Chang’s formerpostdoc adviser Douglas Rees of the Califor-nia Institute of Technology in Pasadena. Suchproteins are a challenge for crystallographersbecause they are large, unwieldy, and notori-ously diff icult to coax into the crystalsneeded for x-ray crystallography. Rees saysdetermination was at the root of Chang’s suc-cess: “He has an incredible drive and workethic. He really pushed the field in the sense
of getting things to crystallize thatno one else had been able to do.”Chang’s data are good, Rees says,but the faulty software threweverything off.
Ironically, another former post-doc in Rees’s lab, Kaspar Locher,exposed the mistake. In the 14 Sep-tember issue of Nature, Locher,now at the Swiss Federal Instituteof Technology in Zurich, describedthe structure of an ABC transportercalled Sav1866 from Staphylococcus
aureus. The structure was dramati-cally—and unexpectedly—differ-ent from that of MsbA. Afterpulling up Sav1866 and Chang’sMsbA from S. typhimurium on acomputer screen, Locher says herealized in minutes that the MsbAstructure was inverted. Interpretingthe “hand” of a molecule is alwaysa challenge for crystallographers,
Locher notes, and many mistakes can lead toan incorrect mirror-image structure. Gettingthe wrong hand is “in the category of monu-mental blunders,” Locher says.
On reading the Nature paper, Changquickly traced the mix-up back to the analysisprogram, which he says he inherited fromanother lab. Locher suspects that Changwould have caught the mistake if he’d takenmore time to obtain a higher resolution struc-ture. “I think he was under immense pressureto get the first structure, and that’s what madehim push the limits of his data,” he says. Oth-ers suggest that Chang might have caught theproblem if he’d paid closer attention to bio-chemical findings that didn’t jibe well with theMsbA structure. “When the first structurecame out, we and others said, ‘We really
A Scientist’s Nightmare: Software
Problem Leads to Five Retractions
SCIENTIFIC PUBLISHING
CR
ED
IT: R
. J. P.
DA
WS
ON
AN
D K
. P.
LO
CH
ER
, N
AT
UR
E4
43
, 1
80
( 2
00
6)
22 DECEMBER 2006 VOL 314 SCIENCE www.sciencemag.org
Flipping fiasco. The structures of MsbA (purple) and Sav1866 (green) overlap
little (left) until MsbA is inverted (right).
▲
Published by AAAS
on
Janu
ary
5, 2
007
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http://wurmlab.github.io
This is costlyFor: •the individual•collaborators•the institution•1000s of researchers performing follow-up work
•science•society
http://wurmlab.github.io
• Understanding/visualising/analysing/massaging big data is hard.• Biology/life is complex.• Biologists lack computational training. • Field is young.• Analysis tools (generally) suck:
• badly written• badly tested• hard to install• output quality… often questionable.
• Data sizes keep growing!• Data formats keep changing :(
Genome bioinformatics is hard Biology is harder than (many) other data sciences
http://wurmlab.github.io
Community Page
Best Practices for Scientific ComputingGreg Wilson1*, D. A. Aruliah2, C. Titus Brown3, Neil P. Chue Hong4, Matt Davis5, Richard T. Guy6¤,
Steven H. D. Haddock7, Kathryn D. Huff8, Ian M. Mitchell9, Mark D. Plumbley10, Ben Waugh11,
Ethan P. White12, Paul Wilson13
1 Mozilla Foundation, Toronto, Ontario, Canada, 2 University of Ontario Institute of Technology, Oshawa, Ontario, Canada, 3 Michigan State University, East Lansing,
Michigan, United States of America, 4 Software Sustainability Institute, Edinburgh, United Kingdom, 5 Space Telescope Science Institute, Baltimore, Maryland, United
States of America, 6 University of Toronto, Toronto, Ontario, Canada, 7 Monterey Bay Aquarium Research Institute, Moss Landing, California, United States of America,
8 University of California Berkeley, Berkeley, California, United States of America, 9 University of British Columbia, Vancouver, British Columbia, Canada, 10 Queen Mary
University of London, London, United Kingdom, 11 University College London, London, United Kingdom, 12 Utah State University, Logan, Utah, United States of America,
13 University of Wisconsin, Madison, Wisconsin, United States of America
Introduction
Scientists spend an increasing amount of time building andusing software. However, most scientists are never taught how todo this efficiently. As a result, many are unaware of tools andpractices that would allow them to write more reliable andmaintainable code with less effort. We describe a set of bestpractices for scientific software development that have solidfoundations in research and experience, and that improvescientists’ productivity and the reliability of their software.
Software is as important to modern scientific research astelescopes and test tubes. From groups that work exclusively oncomputational problems, to traditional laboratory and fieldscientists, more and more of the daily operation of science revolvesaround developing new algorithms, managing and analyzing thelarge amounts of data that are generated in single researchprojects, combining disparate datasets to assess synthetic problems,and other computational tasks.
Scientists typically develop their own software for these purposesbecause doing so requires substantial domain-specific knowledge.As a result, recent studies have found that scientists typically spend30% or more of their time developing software [1,2]. However,90% or more of them are primarily self-taught [1,2], and thereforelack exposure to basic software development practices such aswriting maintainable code, using version control and issuetrackers, code reviews, unit testing, and task automation.
We believe that software is just another kind of experimentalapparatus [3] and should be built, checked, and used as carefullyas any physical apparatus. However, while most scientists arecareful to validate their laboratory and field equipment, most donot know how reliable their software is [4,5]. This can lead toserious errors impacting the central conclusions of publishedresearch [6]: recent high-profile retractions, technical comments,and corrections because of errors in computational methodsinclude papers in Science [7,8], PNAS [9], the Journal of MolecularBiology [10], Ecology Letters [11,12], the Journal of Mammalogy [13],Journal of the American College of Cardiology [14], Hypertension [15], andThe American Economic Review [16].
In addition, because software is often used for more than a singleproject, and is often reused by other scientists, computing errors canhave disproportionate impacts on the scientific process. This type ofcascading impact caused several prominent retractions when an
error from another group’s code was not discovered until afterpublication [6]. As with bench experiments, not everything must bedone to the most exacting standards; however, scientists need to beaware of best practices both to improve their own approaches andfor reviewing computational work by others.
This paper describes a set of practices that are easy to adopt andhave proven effective in many research settings. Our recommenda-tions are based on several decades of collective experience bothbuilding scientific software and teaching computing to scientists[17,18], reports from many other groups [19–25], guidelines forcommercial and open source software development [26,27], and onempirical studies of scientific computing [28–31] and softwaredevelopment in general (summarized in [32]). None of these practiceswill guarantee efficient, error-free software development, but used inconcert they will reduce the number of errors in scientific software,make it easier to reuse, and save the authors of the software time andeffort that can used for focusing on the underlying scientific questions.
Our practices are summarized in Box 1; labels in the main textsuch as ‘‘(1a)’’ refer to items in that summary. For reasons of space,we do not discuss the equally important (but independent) issues ofreproducible research, publication and citation of code and data,and open science. We do believe, however, that all of these will bemuch easier to implement if scientists have the skills we describe.
The Community Page is a forum for organizations and societies to highlight theirefforts to enhance the dissemination and value of scientific knowledge.
Citation: Wilson G, Aruliah DA, Brown CT, Chue Hong NP, Davis M, etal. (2014) Best Practices for Scientific Computing. PLoS Biol 12(1): e1001745.doi:10.1371/journal.pbio.1001745
Academic Editor: Jonathan A. Eisen, University of California Davis, United Statesof America
Published January 7, 2014
Copyright: ! 2014 Wilson et al. This is an open-access article distributed underthe terms of the Creative Commons Attribution License, which permitsunrestricted use, distribution, and reproduction in any medium, provided theoriginal author and source are credited.
Funding: Neil Chue Hong was supported by the UK Engineering and PhysicalSciences Research Council (EPSRC) Grant EP/H043160/1 for the UK SoftwareSustainability Institute. Ian M. Mitchell was supported by NSERC Discovery Grant#298211. Mark Plumbley was supported by EPSRC through a LeadershipFellowship (EP/G007144/1) and a grant (EP/H043101/1) for SoundSoftware.ac.uk.Ethan White was supported by a CAREER grant from the US National ScienceFoundation (DEB 0953694). Greg Wilson was supported by a grant from the SloanFoundation. The funders had no role in study design, data collection and analysis,decision to publish, or preparation of the manuscript.
Competing Interests: The lead author (GVW) is involved in a pilot study of codereview in scientific computing with PLOS Computational Biology.
* E-mail: [email protected]
¤ Current address: Microsoft, Inc., Seattle, Washington, United States ofAmerica
PLOS Biology | www.plosbiology.org 1 January 2014 | Volume 12 | Issue 1 | e1001745
Education
A Quick Guide to Organizing Computational BiologyProjectsWilliam Stafford Noble1,2*
1 Department of Genome Sciences, School of Medicine, University of Washington, Seattle, Washington, United States of America, 2 Department of Computer Science and
Engineering, University of Washington, Seattle, Washington, United States of America
Introduction
Most bioinformatics coursework focus-es on algorithms, with perhaps somecomponents devoted to learning pro-gramming skills and learning how touse existing bioinformatics software. Un-fortunately, for students who are prepar-ing for a research career, this type ofcurriculum fails to address many of theday-to-day organizational challenges as-sociated with performing computationalexperiments. In practice, the principlesbehind organizing and documentingcomputational experiments are oftenlearned on the fly, and this learning isstrongly influenced by personal predilec-tions as well as by chance interactionswith collaborators or colleagues.
The purpose of this article is to describeone good strategy for carrying out com-putational experiments. I will not describeprofound issues such as how to formulatehypotheses, design experiments, or drawconclusions. Rather, I will focus onrelatively mundane issues such as organiz-ing files and directories and documentingprogress. These issues are importantbecause poor organizational choices canlead to significantly slower research pro-gress. I do not claim that the strategies Ioutline here are optimal. These are simplythe principles and practices that I havedeveloped over 12 years of bioinformaticsresearch, augmented with various sugges-tions from other researchers with whom Ihave discussed these issues.
Principles
The core guiding principle is simple:Someone unfamiliar with your projectshould be able to look at your computerfiles and understand in detail what you didand why. This ‘‘someone’’ could be any of avariety of people: someone who read yourpublished article and wants to try toreproduce your work, a collaborator whowants to understand the details of yourexperiments, a future student working inyour lab who wants to extend your workafter you have moved on to a new job, yourresearch advisor, who may be interested in
understanding your work or who may beevaluating your research skills. Most com-monly, however, that ‘‘someone’’ is you. Afew months from now, you may notremember what you were up to when youcreated a particular set of files, or you maynot remember what conclusions you drew.You will either have to then spend timereconstructing your previous experimentsor lose whatever insights you gained fromthose experiments.
This leads to the second principle,which is actually more like a version ofMurphy’s Law: Everything you do, youwill probably have to do over again.Inevitably, you will discover some flaw inyour initial preparation of the data beinganalyzed, or you will get access to newdata, or you will decide that your param-eterization of a particular model was notbroad enough. This means that theexperiment you did last week, or eventhe set of experiments you’ve been work-ing on over the past month, will probablyneed to be redone. If you have organizedand documented your work clearly, thenrepeating the experiment with the newdata or the new parameterization will bemuch, much easier.
To see how these two principles areapplied in practice, let’s begin by consid-ering the organization of directories andfiles with respect to a particular project.
File and Directory Organization
When you begin a new project, youwill need to decide upon some organiza-tional structure for the relevant directo-ries. It is generally a good idea to storeall of the files relevant to one project
under a common root directory. Theexception to this rule is source code orscripts that are used in multiple projects.Each such program might have a projectdirectory of its own.
Within a given project, I use a top-levelorganization that is logical, with chrono-logical organization at the next level, andlogical organization below that. A sampleproject, called msms, is shown in Figure 1.At the root of most of my projects, I have adata directory for storing fixed data sets, aresults directory for tracking computa-tional experiments peformed on that data,a doc directory with one subdirectory permanuscript, and directories such as srcfor source code and bin for compiledbinaries or scripts.
Within the data and results directo-ries, it is often tempting to apply a similar,logical organization. For example, youmay have two or three data sets againstwhich you plan to benchmark youralgorithms, so you could create onedirectory for each of them under data.In my experience, this approach is risky,because the logical structure of your finalset of experiments may look drasticallydifferent from the form you initiallydesigned. This is particularly true underthe results directory, where you maynot even know in advance what kinds ofexperiments you will need to perform. Ifyou try to give your directories logicalnames, you may end up with a very longlist of directories with names that, sixmonths from now, you no longer knowhow to interpret.
Instead, I have found that organizingmy data and results directories chro-nologically makes the most sense. Indeed,
Citation: Noble WS (2009) A Quick Guide to Organizing Computational Biology Projects. PLoS ComputBiol 5(7): e1000424. doi:10.1371/journal.pcbi.1000424
Editor: Fran Lewitter, Whitehead Institute, United States of America
Published July 31, 2009
Copyright: ! 2009 William Stafford Noble. This is an open-access article distributed under the terms of theCreative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in anymedium, provided the original author and source are credited.
Funding: The author received no specific funding for writing this article.
Competing Interests: The author has declared that no competing interests exist.
* E-mail: [email protected]
PLoS Computational Biology | www.ploscompbiol.org 1 July 2009 | Volume 5 | Issue 7 | e1000424
http://wurmlab.github.io
Specific Approaches/Tools
1. Write code for humans
http://wurmlab.github.io
Write code for humans (not computers!)• For
• yourself• colleagues / collaborators• reviewers• other random people who may reuse/improve your code
• Respect conventions (e.g., a style guide)
Programming better
• variable naming
• coding width: 100 characters
• indenting
• Follow conventions -eg “Google R Style”
• Versioning: DropBox & http://github.com/
• Automated testing
• “being able to use understand and improve your code in 6 months & in 60 years” - approximate Damian Conway
preprocess_snps <- function(snp_table, testing=FALSE) { if (testing) { # run a bunch of tests of extreme situations. # quit if a test gives a weird result. } # real part of function. }
Friday, 22 June 12
Use whitespace/indentation!
Programming better
• variable naming
• coding width: 100 characters
• indenting
• Follow conventions -eg “Google R Style”
• Versioning: DropBox & http://github.com/
• Automated testing
• “being able to use understand and improve your code in 6 months & in 60 years” - approximate Damian Conway
preprocess_snps <- function(snp_table, testing=FALSE) { if (testing) { # run a bunch of tests of extreme situations. # quit if a test gives a weird result. } # real part of function. }
Friday, 22 June 12
Programming better
• variable naming
• coding width: 100 characters
• indenting
• Follow conventions -eg “Google R Style”
• Versioning: DropBox & http://github.com/
• Automated testing
• “being able to use understand and improve your code in 6 months & in 60 years” - approximate Damian Conway
preprocess_snps <- function(snp_table, testing=FALSE) { if (testing) { # run a bunch of tests of extreme situations. # quit if a test gives a weird result. } # real part of function. }
Friday, 22 June 12
Same information
Line length Strive to limit your code to 80 characters per line. This fits comfortably on a printed page with a reasonably sized font. If you find yourself running out of room, this is a good indication that you should encapsulate some of the work in a separate function.
ant_measurements <- read.table(file = '~/Downloads/Web/ant_measurements.txt', header=TRUE, sep='\t', col.names = c('colony', 'individual', 'headwidth', ‘mass'))
ant_measurements <- read.table(file = '~/Downloads/Web/ant_measurements.txt', header = TRUE, sep = '\t', col.names = c('colony', 'individual', 'headwidth', 'mass') )
ant_measurements <- read.table(file = '~/Downloads/Web/ant_measurements.txt', header=TRUE, sep='\t', col.names = c('colony', 'individual', 'headwidth', 'mass'))
R style guide extracthttp://r-pkgs.had.co.nz/style.html
http://wurmlab.github.io
Write code for humans (not computers!)• For
• yourself• colleagues / collaborators• reviewers• other random people who may want to reuse your code
• Respect conventions (e.g., a style guide)
• Don't optimise (generally…)
http://wurmlab.github.io
Code reviews: ask a peer to (critically) read your analysis code.
Or do peer-programming sessions
http://wurmlab.github.io
Specific Approaches/Tools
1. Write code for humans
2. Organise mindfully
http://wurmlab.github.io
Organise mindfully http://bit.ly/projectstruct
Choose a standard/template and stick to it!
Choose a standard/template and stick to it!
http://wurmlab.github.io
Specific Approaches/Tools
1. Write code for humans
2. Organise mindfully
3. Plan for mistakes
Automatically check consistency with style guide
install.packages("lint") # once
library(lint) # everytime lint("file_to_check.R")
http://wurmlab.github.io
Create code tests that are easy to run• Unit tests == checking edge cases to see if the function works
# do your stuff # e.g. define speed() function
library(testthat)
expect_that(speed(km = 0, minutes = 60), equals(0)) expect_that(speed(km = 60, minutes = 60), equals(1)) expect_that(speed(km = -4, minutes = 60), throws_error()) expect_that(nrow(significant_SNPs), 42) expect_that(my_model, is_a("lm"))
• Integration tests == "full analysis" but on small data with known results
• e.g. on fake VCF genotype file of 2 loci (one true positive, one true negative)
• Add sanity checks. E.g. the following should fail rather than return something incorrect.speed(km= "twenty", minutes=20) speed(km = -4, minutes = 60)
http://wurmlab.github.io
"Continuous integration": Tests should run automagically.
So you don't have to remember (or find time) to do it.
"http://github.org
Tests run automaticallyhttp://travis-ci.org
If unexpected result:#
http://wurmlab.github.io
Specific Approaches/Tools
1. Write code for humans
2. Organise mindfully
3. Plan for mistakes
4. Use tools that reduce risks
http://wurmlab.github.io
Use tools that reduce risks• Ensure computers are set up for productivity. E.g.,:
• use GNU parallel on an 80-core machine when more appropriate than submitting to queue
• If you need to make a "pipeline", use software designed for this. E.g.:
• Snakemake• Nextflow• (etc)
• too many examples to discuss here
knitr/rmarkdown/jupyter
Analysis & report in one.
analysis.Rmd
A minimal R Markdown example
I know the value of pi is 3.1416, and 2 times pi is 6.2832. To compile me type:
library(knitr); knit(�minimal.Rmd�)
A paragraph here. A code chunk below:
1+1
## [1] 2
.4-.7+.3 # what? it is not zero!
## [1] 5.551e-17
Graphics work too
library(ggplot2)
qplot(speed, dist, data = cars) + geom_smooth()
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5 10 15 20 25speed
dist
Figure 1: A scatterplot of cars
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How to get users to adopt good practices?
• Carrot (dual-benefit): • Use their motivation to have an easier life.
"their motivation is the database" "they see it, they understand it" -Thomasz? on SEEK
• Piggyback off that so they do things better ("by stealth" -Carol)
• Stick:• When you're reviewing publications/grants
• Politics:• Encourage funders / journals to require good practices.
[email protected]@yannick__
https://wurmlab.github.io
@ Queen Mary U London Rodrigo Pracana Anurag Priyam @yeban Eckart Stolle Bruno Vieira @bmpvieira R Nichols & sbcsEvolve R Christie & T King / ITSR Apocrita
Laurent Keller lab @ Lausanne J Wang, D Shoemaker,O Riba-Grognuz, M Nipitwattanaphon Ioannis Xenarios @ SIB DeWayne Shoemaker @ USDA
Thanks!