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[(est)-8(imator)-245(of)-236.8(the)-240.2(species)-249.2(tree)-239(topolog)-10.9(y)-234.1(whe)-8(n)-234.1(inco)-7.6(mplete)-244.8(lineage)-243.8(sortin)-7.6(g)-239.8(i)0(s)-238.8(taken)-243.5(to)-237.6(be)-242.3(the)-240.2(sole)-242.1(source)-244.6(of)-236.8(gene)]TJ
T*
[(tre)-8.8(e/species)-260.9(tree)-256.1(discorda)-9.9(nce.)-256.6(To)-251.7(estim)-10.2(ate)-253.3(the)-251.5(speci)-11.3(es)-254.9(tree)-256.1(using)-252.5(the)-257.2(GLASS)-260.3(method,)-257.7(for)-250.9(each)-258.8(pair)-254.3(of)-253.9(taxa)]TJ
/F6 1 Tf
42.5881 0 TD
(A)Tj
/F1 1 Tf
-42.5881 -1.2007 TD
(and)Tj
/F6 1 Tf
1.6673 0 TD
(B)Tj
/F1 1 Tf
.6146 0 TD
[(,)-216.6(one)-220.3(rst)-218.7(obta)-7.6(ins)-216.8(an)-219.6(estimat)-10.5(e)]TJ
/F7 1 Tf
11.7339 .1138 TD
(^)Tj
/F6 1 Tf
.0285 -.1138 TD
(t)Tj
6.9738 0 0 6.9738 216.8503 642.2738 Tm
(AB)Tj
/F1 1 Tf
9.9626 0 0 9.9626 228.0755 643.7479 Tm
[(of)-219.7(the)-217.4(dive)-7.6(rgence)-222.5(time)]TJ
/F8 1 Tf
9.139 0 TD
(s)Tj
/F6 1 Tf
7.4718 0 0 6.641 323.4897 642.1038 Tm
(AB)Tj
/F1 1 Tf
9.9626 0 0 9.9626 334.8282 643.7479 Tm
[(betwee)-10.9(n)]TJ
/F6 1 Tf
3.568 0 TD
(A)Tj
/F1 1 Tf
.8308 0 TD
(and)Tj
/F6 1 Tf
1.6673 0 TD
(B)Tj
/F1 1 Tf
.6146 0 TD
[(.)-216.6(The)-220.1(estimat)-10.5(e)]TJ
/F7 1 Tf
5.793 .1138 TD
(^)Tj
/F6 1 Tf
.0341 -.1138 TD
(t)Tj
6.9738 0 0 6.9738 462.2172 642.2738 Tm
(AB)Tj
/F1 1 Tf
9.9626 0 0 9.9626 473.4424 643.7479 Tm
[(is)-221.7(given)]TJ
-40.0842 -1.2007 TD
[(by)-246.2(the)-251.5(minimum)-254.8(interspeci)-13(c)-241.6(coal)-9.4(escence)-254.5(time)-247.2(betwee)-10.9(n)-245.5(a)-247.2(lineage)-249.5(from)-249.5(taxo)-7.6(n)]TJ
/F6 1 Tf
31.2582 0 TD
(A)Tj
/F1 1 Tf
.8593 0 TD
[(and)-248.8(a)-247.2(lineage)-249.5(from)-249.5(taxo)-7.6(n)]TJ
/F6 1 Tf
10.2202 0 TD
(B)Tj
/F1 1 Tf
.6146 0 TD
(,)Tj
-42.9523 -1.2007 TD
[(whe)-8(re)-227.2(the)-223.1(minimum)-232(is)-221.7(take)-9.4(n)-222.7(over)-228.7(all)-225.8(such)-228(lineage)-226.8(pair)-9.6(s)-218.2(and)-231.7(over)-223.1(all)-225.8(loci.)-227(Th)-7(e)-224.5(species)-232.1(tree)-227.6(is)-221.7(then)-229.5(construc)-9.9(ted)]TJ
0 -1.195 TD
[(from)-289.4(the)-280(pairw)-8.6(ise)-281.2(est)-8(imates)-285.8(by)-280.4(sing)-7(le-linkag)-9.3(e)-281.4(clusteri)-9.7(ng)-280.4(\(Gordon)-7.5(,)-279.2(1996;)-285.4(Moss)-7.4(el)-279.2(and)-282.9(Roc)-8.8(h,)-280(2010\).)]TJ
1.0015 -1.2007 TD
[(The)-345.3(data)-345.1(for)-336.3(the)-342.6(GLA)-10(SS)-341.4(method)-342.7(consist)-345.1(of)-344.9(genotypes)-344.4(at)-341.8(each)-344.2(of)]TJ
/F6 1 Tf
26.996 0 TD
(L)Tj
/F1 1 Tf
.8877 0 TD
[(loci)-346.1(for)-342(a)-338.3(numb)-6.6(er)-341(of)-339.2(indivi)-7.2(duals)-339.6(in)]TJ
-28.8852 -1.2007 TD
[(each)-372.6(taxo)-7.6(n.)-365.3(Speci)-9.4(cally,)-371.8(for)-364.7(a)-372.4(set)-366.5(of)]TJ
/F6 1 Tf
15.4612 0 TD
(L)Tj
/F1 1 Tf
.9162 0 TD
[(loci)-374.6(indexed)-370.2(by)]TJ
/F9 1 Tf
6.7945 0 TD
()Tj
/F10 1 Tf
.5747 0 TD
()Tj
/F1 1 Tf
.9389 0 TD
(1)Tj
/F7 1 Tf
1.1723 0 TD
.1682 Tc
(...)Tj
/F1 1 Tf
1.3145 0 TD
0 Tc
()Tj
/F6 1 Tf
.4951 0 TD
(L)Tj
/F1 1 Tf
.5577 0 TD
[(,)-364.6(let)]TJ
/F10 1 Tf
1.9917 0 TD
(f)Tj
/F6 1 Tf
.5008 0 TD
(a)Tj
/F9 1 Tf
6.9738 0 0 6.9738 385.1149 587.6219 Tm
()Tj
/F6 1 Tf
0 -.9186 TD
(i)Tj
/F10 1 Tf
9.9626 0 0 9.9626 388.4597 583.9935 Tm
(g)Tj
/F6 1 Tf
6.9738 0 0 6.9738 393.4487 590.2864 Tm
(n)Tj
4.9813 0 0 4.9813 396.9637 589.2093 Tm
(A)Tj
/F9 1 Tf
.6146 -.3528 TD
()Tj
/F6 1 Tf
6.9738 0 0 6.9738 393.4487 581.1589 Tm
(i)Tj
/F10 1 Tf
.4471 0 TD
()Tj
/F1 1 Tf
.943 0 TD
(1)Tj
9.9626 0 0 9.9626 410.7401 583.9935 Tm
(and)Tj
/F10 1 Tf
1.8153 0 TD
(f)Tj
/F6 1 Tf
.5065 0 TD
(b)Tj
/F9 1 Tf
6.9738 0 0 6.9738 438.8597 587.6219 Tm
()Tj
/F6 1 Tf
0 -.9186 TD
(j)Tj
/F10 1 Tf
9.9626 0 0 9.9626 442.1479 583.9935 Tm
(g)Tj
/F6 1 Tf
6.9738 0 0 6.9738 447.1369 590.2864 Tm
(n)Tj
4.9813 0 0 4.9813 450.6518 589.2093 Tm
(B)Tj
/F9 1 Tf
.6146 -.3528 TD
()Tj
/F6 1 Tf
6.9738 0 0 6.9738 447.1369 581.1589 Tm
(j)Tj
/F10 1 Tf
.4553 0 TD
()Tj
/F1 1 Tf
.9349 0 TD
(1)Tj
9.9626 0 0 9.9626 464.4849 583.9935 Tm
[(be)-367.5(sets)-368.5(of)]TJ
-39.1851 -1.2007 TD
[(lin)-7.8(eages)-334.7(sam)-8.8(pled)-332(at)-336.1(locus)]TJ
/F9 1 Tf
10.8291 0 TD
()Tj
/F1 1 Tf
.7341 0 TD
[(from)-340.6(taxa)]TJ
/F6 1 Tf
4.2964 0 TD
(A)Tj
/F1 1 Tf
.9503 0 TD
(and)Tj
/F6 1 Tf
1.7811 0 TD
(B)Tj
/F1 1 Tf
.6146 0 TD
[(,)-330.4(resp)-8(ective)-9.8(ly.)-329(Le)-8.8(t)]TJ
/F6 1 Tf
7.705 0 TD
(T)Tj
6.9738 0 0 6.9738 347.7542 569.5369 Tm
(a)Tj
/F9 1 Tf
4.9813 0 0 4.9813 351.2125 571.9747 Tm
()Tj
/F6 1 Tf
0 -.9788 TD
(i)Tj
/F1 1 Tf
6.9738 0 0 6.9738 353.7637 569.5369 Tm
()Tj
/F6 1 Tf
.4959 0 TD
(b)Tj
/F9 1 Tf
4.9813 0 0 4.9813 360.7369 571.9747 Tm
()Tj
/F6 1 Tf
0 -.9788 TD
(j)Tj
/F1 1 Tf
9.9626 0 0 9.9626 367.0865 572.0314 Tm
[(be)-333.4(an)-333.4(estimat)-10.5(e)-332.6(o)0(f)-333.6(the)-336.9(coalescence)]TJ
-29.4088 -1.2007 TD
[(time)-241.5(betwee)-10.9(n)-234.1(l)0(i)-7.1(neages)]TJ
/F6 1 Tf
9.1504 0 TD
(a)Tj
/F9 1 Tf
6.9738 0 0 6.9738 170.3055 563.6975 Tm
()Tj
/F6 1 Tf
0 -.9186 TD
(i)Tj
/F1 1 Tf
9.9626 0 0 9.9626 175.9747 560.0692 Tm
(and)Tj
/F6 1 Tf
1.6844 0 TD
(b)Tj
/F9 1 Tf
6.9738 0 0 6.9738 197.7448 563.6975 Tm
()Tj
/F6 1 Tf
0 -.9186 TD
(j)Tj
/F1 1 Tf
9.9626 0 0 9.9626 201.0897 560.0692 Tm
[(,)-239.4(and)-237.4(let)]TJ
/F6 1 Tf
3.42 0 TD
(T)Tj
/F11 1 Tf
6.9738 0 0 6.9738 241.5117 564.9447 Tm
(\()Tj
/F9 1 Tf
.3252 0 TD
()Tj
/F11 1 Tf
.4065 0 TD
(\))Tj
/F6 1 Tf
-.8536 -1.0975 TD
(AB)Tj
/F10 1 Tf
9.9626 0 0 9.9626 251.433 560.0692 Tm
()Tj
/F1 1 Tf
1.104 0 TD
(min)Tj
/F6 1 Tf
6.9738 0 0 6.9738 278.0219 558.5951 Tm
(i)Tj
/F1 1 Tf
.2845 0 TD
()Tj
/F6 1 Tf
.504 0 TD
(j)Tj
9.9626 0 0 9.9626 287.6031 560.0692 Tm
(T)Tj
6.9738 0 0 6.9738 293.159 557.5746 Tm
(a)Tj
/F9 1 Tf
4.9813 0 0 4.9813 296.6172 560.0125 Tm
()Tj
/F6 1 Tf
0 -.9674 TD
(i)Tj
6.9738 0 0 6.9738 299.1684 557.5746 Tm
(b)Tj
/F9 1 Tf
4.9813 0 0 4.9813 302.6267 560.0125 Tm
()Tj
/F6 1 Tf
T*
(j)Tj
/F1 1 Tf
9.9626 0 0 9.9626 305.6881 560.0692 Tm
.2337 Tc
[(.I)233.7(f)]TJ
/F8 1 Tf
1.3885 0 TD
0 Tc
(s)Tj
/F6 1 Tf
7.4718 0 0 6.641 323.8865 558.425 Tm
(AB)Tj
/F1 1 Tf
9.9626 0 0 9.9626 335.4519 560.0692 Tm
[(is)-233.1(the)-240.2(true)-242.9(divergen)-8.7(ce)-238.4(time)-241.5(betwee)-10.9(n)-234.1(taxa)]TJ
/F6 1 Tf
16.3546 0 TD
(A)Tj
/F1 1 Tf
-42.5881 -1.2007 TD
(and)Tj
/F6 1 Tf
1.7185 0 TD
(B)Tj
/F1 1 Tf
.6146 0 TD
[(,)-267.8(then)-269.4(the)-268.6(GLASS)-271.7(estimat)-10.5(e)-264.3(o)0(f)]TJ
/F8 1 Tf
12.1607 0 TD
(s)Tj
/F6 1 Tf
7.4718 0 0 6.641 222.9165 546.4629 Tm
(AB)Tj
/F1 1 Tf
9.9626 0 0 9.9626 234.7086 548.1069 Tm
[(is)-267.2(give)-7.6(n)-262.5(b)0(y)]TJ
/F7 1 Tf
4.6663 .1138 TD
(^)Tj
/F6 1 Tf
.0341 -.1138 TD
(t)Tj
6.9738 0 0 6.9738 284.3149 546.6329 Tm
(AB)Tj
/F10 1 Tf
9.9626 0 0 9.9626 295.0865 548.1069 Tm
()Tj
/F1 1 Tf
1.104 0 TD
(min)Tj
/F9 1 Tf
6.9738 0 0 6.9738 321.6755 546.6329 Tm
()Tj
/F6 1 Tf
9.9626 0 0 9.9626 326.7212 548.1069 Tm
(T)Tj
/F11 1 Tf
6.9738 0 0 6.9738 333.0141 552.9825 Tm
(\()Tj
/F9 1 Tf
.3252 0 TD
()Tj
/F11 1 Tf
.4065 0 TD
(\))Tj
/F6 1 Tf
-.8455 -1.0975 TD
(AB)Tj
/F1 1 Tf
9.9626 0 0 9.9626 341.2913 548.1069 Tm
[(,)-267.8(i.e.,)-269(the)-268.6(shortest)-273.8(time)-270(to)-266.1(an)-265.1(inters)-9.4(pecic)]TJ
-26.8196 -1.2007 TD
[(coal)-9.4(escence)-339.8(at)-336.1(som)-7(e)-332.6(locu)-7.6(s)-332(\(Fig.)-337.4(1\).)]TJ
1.0015 -1.2007 TD
[(The)-294.1(GLAS)-9.9(S)-290.2(estimate)]TJ
/F7 1 Tf
9.0537 .239 TD
(^)Tj
/F6 1 Tf
-.0967 -.239 TD
(S)Tj
/F1 1 Tf
.791 0 TD
[(of)-288(the)-297.1(species)-294.7(tree)]TJ
/F6 1 Tf
7.6367 0 TD
(S)Tj
/F1 1 Tf
.791 0 TD
[(is)-290(then)-292.1(const)-9.6(ructed)-297.4(by)-291.7(applying)-292.2(sing)-7(le-linkag)-9.3(e)-292.8(clusteri)-9.7(ng)-286.1(to)]TJ
-19.1772 -1.195 TD
[(the)-427.9(set)-423.4(of)-424.6(est)-8(imates)]TJ
/F10 1 Tf
8.6212 0 TD
(f)Tj
/F7 1 Tf
.4666 .1081 TD
(^)Tj
/F6 1 Tf
.0341 -.1081 TD
(t)Tj
6.9738 0 0 6.9738 167.811 510.7463 Tm
(AB)Tj
/F10 1 Tf
9.9626 0 0 9.9626 176.8818 512.277 Tm
(g)Tj
/F6 1 Tf
6.9738 0 0 6.9738 181.8708 509.4991 Tm
(A)Tj
/F1 1 Tf
.6178 0 TD
()Tj
/F6 1 Tf
.4959 0 TD
(B)Tj
/F10 1 Tf
.6178 0 TD
(2S)Tj
/F1 1 Tf
9.9626 0 0 9.9626 203.5275 512.277 Tm
[(,)-421.5(whe)-8(re)]TJ
/F10 1 Tf
3.5452 0 TD
(S)Tj
/F1 1 Tf
1.0698 0 TD
[(is)-426.6(the)-422.3(taxo)-7.6(n)-421.9(set)-423.4(of)-424.6(the)-427.9(species)-431.2(tree.)-427.2(Speci)-9.3(cally,)-428.7(the)-422.3(GLAS)-9.9(S)]TJ
-17.6066 -1.2007 TD
[(est)-8(imate)]TJ
/F7 1 Tf
3.7785 .2447 TD
(^)Tj
/F6 1 Tf
-.1081 -.2447 TD
(d)Tj
6.9738 0 0 6.9738 115.6535 498.7841 Tm
(CC)Tj
/F10 1 Tf
4.9813 0 0 4.9813 125.1779 500.8251 Tm
(0)Tj
/F1 1 Tf
9.9626 0 0 9.9626 130.5637 500.3148 Tm
[(of)-310.8(the)-308.4(distanc)-9.9(e)-304.2(betwee)-10.9(n)-308.1(two)-310.6(sets)-311.6(of)-305.1(taxa)]TJ
/F6 1 Tf
16.6904 0 TD
(C)Tj
/F1 1 Tf
.9731 0 TD
(and)Tj
/F6 1 Tf
1.7584 0 TD
(C)Tj
/F10 1 Tf
6.9738 0 0 6.9738 330.6897 503.8865 Tm
(0)Tj
/F1 1 Tf
9.9626 0 0 9.9626 336.1322 500.3148 Tm
[(is)-307.1(dened)-314.7(by)]TJ
/F7 1 Tf
5.6564 .2447 TD
(^)Tj
/F6 1 Tf
-.1138 -.2447 TD
(d)Tj
6.9738 0 0 6.9738 396.3401 498.7841 Tm
(CC)Tj
/F10 1 Tf
4.9813 0 0 4.9813 405.8645 500.8251 Tm
(0)Tj
9.9626 0 0 9.9626 409.8896 500.3148 Tm
()Tj
/F1 1 Tf
1.104 0 TD
(min)Tj
/F6 1 Tf
6.9738 0 0 6.9738 436.4786 498.7841 Tm
(A)Tj
/F10 1 Tf
.6178 0 TD
(2)Tj
/F6 1 Tf
.6585 0 TD
(C)Tj
/F1 1 Tf
.6991 0 TD
()Tj
/F6 1 Tf
.4959 0 TD
(B)Tj
/F10 1 Tf
.6178 0 TD
(2)Tj
/F6 1 Tf
.6585 0 TD
(C)Tj
/F10 1 Tf
4.9813 0 0 4.9813 467.4896 500.8251 Tm
(0)Tj
/F7 1 Tf
9.9626 0 0 9.9626 471.1747 501.392 Tm
(^)Tj
/F6 1 Tf
.0285 -.1081 TD
(t)Tj
6.9738 0 0 6.9738 474.2928 498.7841 Tm
(AB)Tj
/F1 1 Tf
9.9626 0 0 9.9626 483.3636 500.3148 Tm
[(.)-307.7(The)]TJ
-41.0801 -1.2007 TD
[(sing)-7(le-linkag)-9.3(e)-537.5(clus)-8.8(tering)-543.1(procedure)-545.4(involv)-10.1(es)-539.4(grouping)-545.8(the)-541.8(two)-538.2(taxo)-7.6(n)-535.7(sets)-544.9(with)-541.7(shortes)-8.6(t)-538.4(distance,)-547.8(re-)]TJ
T*
[(com)-7.6(puting)-340.2(the)-336.9(distances)-338.8(amo)-7.6(ng)-331.6(g)-6.5(roups,)-337.4(and)-334.1(repe)-8.6(ating)-335.5(the)-336.9(proce)-9.4(ss)-334(until)-336.5(a)-332.6(sing)-7(le)-336.1(cluster)-342(remains.)]TJ
1.0015 -1.2007 TD
[(The)-248.6(quantity)]TJ
/F7 1 Tf
5.3207 .1081 TD
(^)Tj
/F6 1 Tf
.0285 -.1081 TD
(t)Tj
6.9738 0 0 6.9738 140.2015 462.9542 Tm
(AB)Tj
/F1 1 Tf
9.9626 0 0 9.9626 151.7102 464.4282 Tm
[(is)-244.5(a)-241.6(consist)-9.3(ent)-245.8(estimat)-10.5(or)-242.5(of)-242.5(the)-251.5(pairwise)-249.9(dive)-7.6(rgence)-250.9(time)]TJ
/F8 1 Tf
22.7451 0 TD
(s)Tj
/F6 1 Tf
7.4718 0 0 6.641 382.6771 462.7841 Tm
(AB)Tj
/F1 1 Tf
9.9626 0 0 9.9626 391.8613 464.4282 Tm
[(,)-245.1(because)-252.7(for)-245.2(any)]TJ
/F9 1 Tf
7.0221 0 TD
.4472 Tc
(>)Tj
/F1 1 Tf
2.06 0 TD
0 Tc
[(0,)-245.8(the)]TJ
-40.9776 -1.2007 TD
[(proba)-7.6(bility)-345.7(is)-341.2(posi)-7(tive)-340.4(that)-346.1(at)-341.8(locus)]TJ
/F9 1 Tf
14.6702 0 TD
()Tj
/F1 1 Tf
.4097 0 TD
(,)Tj
/F6 1 Tf
.5861 0 TD
(T)Tj
/F11 1 Tf
6.9738 0 0 6.9738 236.5228 457.3416 Tm
(\()Tj
/F9 1 Tf
.3252 0 TD
()Tj
/F11 1 Tf
.4065 0 TD
(\))Tj
/F6 1 Tf
-.8455 -1.0975 TD
(AB)Tj
/F1 1 Tf
9.9626 0 0 9.9626 248.2015 452.466 Tm
[(will)-339.6(excee)-11(d)-342.2(the)-342.6(divergen)-8.7(ce)-340.8(time)-349.6(by)-337.3(no)-343(more)-346.1(than)]TJ
/F12 1 Tf
20.6624 0 TD
(e)Tj
/F1 1 Tf
.7284 0 TD
[(time)-343.9(units.)]TJ
-38.8665 -1.2007 TD
[(Th)-7(us,)-355.9(as)-363(more)-363.2(loci)-363.2(are)-360.7(sample)-9.9(d,)-359.7(it)-359.9(becomes)-368.2(increasing)-10.3(ly)-357.1(likel)-8.2(y)-359.3(that)-357.5(an)-361.8(inters)-9.4(pecic)-364.7(coalesc)-10.7(ence)-361.2(at)-364.6(some)]TJ
T*
[(locu)-7.6(s)-366.2(will)-368.1(occur)-373.6(within)]TJ
/F12 1 Tf
9.9528 0 TD
(e)Tj
/F1 1 Tf
.7512 0 TD
[(time)-366.7(u)-6.5(nits)-368.3(of)-367.7(the)-365.3(dive)-7.6(rgence)-370.4(ti)-7(me)]TJ
/F8 1 Tf
14.215 0 TD
(s)Tj
/F6 1 Tf
7.4718 0 0 6.641 326.7212 426.8975 Tm
(AB)Tj
/F1 1 Tf
9.9626 0 0 9.9626 335.9054 428.5416 Tm
[(.)-370.3(The)-368.1(GLAS)-9.9(S)-364.2(estimat)-10.5(or)]TJ
/F7 1 Tf
10.2828 .239 TD
(^)Tj
/F6 1 Tf
-.091 -.239 TD
(S)Tj
/F1 1 Tf
.865 0 TD
[(is)-369.7(a)-366.8(consist)-9.3(ent)]TJ
-37.3357 -1.195 TD
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