forked from tbegum/Testing_the_ortholog_conjecture
-
Notifications
You must be signed in to change notification settings - Fork 0
/
TM.bib
1320 lines (1216 loc) · 42.6 KB
/
TM.bib
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
572
573
574
575
576
577
578
579
580
581
582
583
584
585
586
587
588
589
590
591
592
593
594
595
596
597
598
599
600
601
602
603
604
605
606
607
608
609
610
611
612
613
614
615
616
617
618
619
620
621
622
623
624
625
626
627
628
629
630
631
632
633
634
635
636
637
638
639
640
641
642
643
644
645
646
647
648
649
650
651
652
653
654
655
656
657
658
659
660
661
662
663
664
665
666
667
668
669
670
671
672
673
674
675
676
677
678
679
680
681
682
683
684
685
686
687
688
689
690
691
692
693
694
695
696
697
698
699
700
701
702
703
704
705
706
707
708
709
710
711
712
713
714
715
716
717
718
719
720
721
722
723
724
725
726
727
728
729
730
731
732
733
734
735
736
737
738
739
740
741
742
743
744
745
746
747
748
749
750
751
752
753
754
755
756
757
758
759
760
761
762
763
764
765
766
767
768
769
770
771
772
773
774
775
776
777
778
779
780
781
782
783
784
785
786
787
788
789
790
791
792
793
794
795
796
797
798
799
800
801
802
803
804
805
806
807
808
809
810
811
812
813
814
815
816
817
818
819
820
821
822
823
824
825
826
827
828
829
830
831
832
833
834
835
836
837
838
839
840
841
842
843
844
845
846
847
848
849
850
851
852
853
854
855
856
857
858
859
860
861
862
863
864
865
866
867
868
869
870
871
872
873
874
875
876
877
878
879
880
881
882
883
884
885
886
887
888
889
890
891
892
893
894
895
896
897
898
899
900
901
902
903
904
905
906
907
908
909
910
911
912
913
914
915
916
917
918
919
920
921
922
923
924
925
926
927
928
929
930
931
932
933
934
935
936
937
938
939
940
941
942
943
944
945
946
947
948
949
950
951
952
953
954
955
956
957
958
959
960
961
962
963
964
965
966
967
968
969
970
971
972
973
974
975
976
977
978
979
980
981
982
983
984
985
986
987
988
989
990
991
992
993
994
995
996
997
998
999
1000
@article{RN380,
author = {Akaike, Hirotugu.},
title = {New look at statistical-model identification},
journal = {Automatic Control, IEEE Transactions on},
volume = {19},
number = {6},
pages = {716-723},
ISSN = {0018-9286},
DOI = {10.1109/tac.1974.1100705},
year = {1974},
type = {Journal Article}
}
@article{RN790,
author = {Altenhoff, A. M. and Studer, R. A. and Robinson-Rechavi, M. and Dessimoz, C.},
title = {Resolving the ortholog conjecture: orthologs tend to be weakly, but significantly, more similar in function than paralogs},
journal = {PLoS Comput Biol},
volume = {8},
number = {5},
pages = {e1002514},
ISSN = {1553-7358},
DOI = {10.1371/journal.pcbi.1002514},
url = {https://www.ncbi.nlm.nih.gov/pubmed/22615551},
year = {2012},
type = {Journal Article}
}
@article{RN834,
author = {Benjamini, Y. and Drai, D. and Elmer, G. and Kafkafi, N. and Golani, I.},
title = {Controlling the false discovery rate in behavior genetics research},
journal = {Behav Brain Res},
volume = {125},
number = {1-2},
pages = {279-84},
ISSN = {0166-4328},
url = {https://www.ncbi.nlm.nih.gov/pubmed/11682119},
year = {2001},
type = {Journal Article}
}
@article{RN833,
author = {Benjamini, Y. and Yekutieli, D.},
title = {Quantitative trait Loci analysis using the false discovery rate},
journal = {Genetics},
volume = {171},
number = {2},
pages = {783-90},
ISSN = {0016-6731},
DOI = {10.1534/genetics.104.036699},
url = {https://www.ncbi.nlm.nih.gov/pubmed/15956674},
year = {2005},
type = {Journal Article}
}
@article{RN800,
author = {Blomberg, S. P. and Garland, T. and Ives, A. R.},
title = {Testing for phylogenetic signal in comparative data: behavioral traits are more labile},
journal = {Evolution},
volume = {57},
number = {4},
pages = {717-45},
ISSN = {0014-3820},
url = {https://www.ncbi.nlm.nih.gov/pubmed/12778543},
year = {2003},
type = {Journal Article}
}
@article{RN810,
author = {Blomberg, S. P. and Garland, T. and Ives, A. R.},
title = {Testing for phylogenetic signal in comparative data: behavioral traits are more labile},
journal = {Evolution},
volume = {57},
number = {4},
pages = {717-45},
ISSN = {0014-3820},
url = {https://www.ncbi.nlm.nih.gov/pubmed/12778543},
year = {2003},
type = {Journal Article}
}
@article{RN808,
author = {Blomberg, S. P. and Lefevre, J. G. and Wells, J. A. and Waterhouse, M.},
title = {Independent contrasts and PGLS regression estimators are equivalent},
journal = {Syst Biol},
volume = {61},
number = {3},
pages = {382-91},
ISSN = {1076-836X},
DOI = {10.1093/sysbio/syr118},
url = {https://www.ncbi.nlm.nih.gov/pubmed/22215720},
year = {2012},
type = {Journal Article}
}
@article{RN827,
author = {Braasch, I. and Bobe, J. and Guiguen, Y. and Postlethwait, J. H.},
title = {Reply to: 'Subfunctionalization versus neofunctionalization after whole-genome duplication'},
journal = {Nat Genet},
volume = {50},
number = {7},
pages = {910-911},
ISSN = {1546-1718},
DOI = {10.1038/s41588-018-0163-3},
url = {https://www.ncbi.nlm.nih.gov/pubmed/29955179},
year = {2018},
type = {Journal Article}
}
@article{RN829,
author = {Braasch, I. and Gehrke, A. R. and Smith, J. J. and Kawasaki, K. and Manousaki, T. and Pasquier, J. and Amores, A. and Desvignes, T. and Batzel, P. and Catchen, J. and Berlin, A. M. and Campbell, M. S. and Barrell, D. and Martin, K. J. and Mulley, J. F. and Ravi, V. and Lee, A. P. and Nakamura, T. and Chalopin, D. and Fan, S. and Wcisel, D. and Cañestro, C. and Sydes, J. and Beaudry, F. E. and Sun, Y. and Hertel, J. and Beam, M. J. and Fasold, M. and Ishiyama, M. and Johnson, J. and Kehr, S. and Lara, M. and Letaw, J. H. and Litman, G. W. and Litman, R. T. and Mikami, M. and Ota, T. and Saha, N. R. and Williams, L. and Stadler, P. F. and Wang, H. and Taylor, J. S. and Fontenot, Q. and Ferrara, A. and Searle, S. M. and Aken, B. and Yandell, M. and Schneider, I. and Yoder, J. A. and Volff, J. N. and Meyer, A. and Amemiya, C. T. and Venkatesh, B. and Holland, P. W. and Guiguen, Y. and Bobe, J. and Shubin, N. H. and Di Palma, F. and Alföldi, J. and Lindblad-Toh, K. and Postlethwait, J. H.},
title = {The spotted gar genome illuminates vertebrate evolution and facilitates human-teleost comparisons},
journal = {Nat Genet},
volume = {48},
number = {4},
pages = {427-37},
ISSN = {1546-1718},
DOI = {10.1038/ng.3526},
url = {https://www.ncbi.nlm.nih.gov/pubmed/26950095},
year = {2016},
type = {Journal Article}
}
@article{RN793,
author = {Chen, X. and Zhang, J.},
title = {The ortholog conjecture is untestable by the current gene ontology but is supported by RNA sequencing data},
journal = {PLoS Comput Biol},
volume = {8},
number = {11},
pages = {e1002784},
ISSN = {1553-7358},
DOI = {10.1371/journal.pcbi.1002784},
url = {https://www.ncbi.nlm.nih.gov/pubmed/23209392},
year = {2012},
type = {Journal Article}
}
@article{RN764,
author = {Chira, A. M. and Thomas, G. H.},
title = {The impact of rate heterogeneity on inference of phylogenetic models of trait evolution},
journal = {J Evol Biol},
volume = {29},
number = {12},
pages = {2502-2518},
ISSN = {1420-9101},
DOI = {10.1111/jeb.12979},
url = {https://www.ncbi.nlm.nih.gov/pubmed/27653965},
year = {2016},
type = {Journal Article}
}
@article{RN805,
author = {Church, S. H. and Ryan, J. F. and Dunn, C. W.},
title = {Automation and Evaluation of the SOWH Test with SOWHAT},
journal = {Syst Biol},
volume = {64},
number = {6},
pages = {1048-58},
ISSN = {1076-836X},
DOI = {10.1093/sysbio/syv055},
url = {https://www.ncbi.nlm.nih.gov/pubmed/26231182},
year = {2015},
type = {Journal Article}
}
@article{RN822,
author = {Church, S. H. and Ryan, J. F. and Dunn, C. W.},
title = {Automation and Evaluation of the SOWH Test with SOWHAT},
journal = {Syst Biol},
volume = {64},
number = {6},
pages = {1048-58},
ISSN = {1076-836X},
DOI = {10.1093/sysbio/syv055},
url = {https://www.ncbi.nlm.nih.gov/pubmed/26231182},
year = {2015},
type = {Journal Article}
}
@article{RN781,
author = {Cooper, N. and Thomas, G. H. and FitzJohn, R. G.},
title = {Shedding light on the 'dark side' of phylogenetic comparative methods},
journal = {Methods Ecol Evol},
volume = {7},
number = {6},
pages = {693-699},
ISSN = {2041-210X},
DOI = {10.1111/2041-210X.12533},
url = {https://www.ncbi.nlm.nih.gov/pubmed/27499839},
year = {2016},
type = {Journal Article}
}
@article{RN766,
author = {Davis, J. C. and Petrov, D. A.},
title = {Preferential duplication of conserved proteins in eukaryotic genomes},
journal = {PLoS Biol},
volume = {2},
number = {3},
pages = {E55},
ISSN = {1545-7885},
DOI = {10.1371/journal.pbio.0020055},
url = {https://www.ncbi.nlm.nih.gov/pubmed/15024414},
year = {2004},
type = {Journal Article}
}
@article{RN788,
author = {Domazet-Lošo, T. and Tautz, D.},
title = {A phylogenetically based transcriptome age index mirrors ontogenetic divergence patterns},
journal = {Nature},
volume = {468},
number = {7325},
pages = {815-8},
ISSN = {1476-4687},
DOI = {10.1038/nature09632},
url = {https://www.ncbi.nlm.nih.gov/pubmed/21150997},
year = {2010},
type = {Journal Article}
}
@article{RN760,
author = {Dunn, C. W. and Zapata, F. and Munro, C. and Siebert, S. and Hejnol, A.},
title = {Pairwise comparisons across species are problematic when analyzing functional genomic data},
journal = {Proc Natl Acad Sci U S A},
volume = {115},
number = {3},
pages = {E409-E417},
ISSN = {1091-6490},
DOI = {10.1073/pnas.1707515115},
url = {https://www.ncbi.nlm.nih.gov/pubmed/29301966},
year = {2018},
type = {Journal Article}
}
@article{RN782,
author = {Díaz-Uriarte, R. and Garland, T.},
title = {Effects of branch length errors on the performance of phylogenetically independent contrasts},
journal = {Syst Biol},
volume = {47},
number = {4},
pages = {654-72},
ISSN = {1063-5157},
url = {https://www.ncbi.nlm.nih.gov/pubmed/12066309},
year = {1998},
type = {Journal Article}
}
@article{RN772,
author = {Eng, K. H. and Bravo, H. C. and Keleş, S.},
title = {A phylogenetic mixture model for the evolution of gene expression},
journal = {Mol Biol Evol},
volume = {26},
number = {10},
pages = {2363-72},
ISSN = {1537-1719},
DOI = {10.1093/molbev/msp149},
url = {https://www.ncbi.nlm.nih.gov/pubmed/19602540},
year = {2009},
type = {Journal Article}
}
@article{RN773,
author = {Felsenstein, J.},
title = {Confidence limits on phylogenies: an approach using the bootstrap},
journal = {Evolution},
volume = {39},
number = {4},
pages = {783-791},
ISSN = {1558-5646},
DOI = {10.1111/j.1558-5646.1985.tb00420.x},
url = {https://www.ncbi.nlm.nih.gov/pubmed/28561359},
year = {1985},
type = {Journal Article}
}
@article{RN807,
author = {Felsenstein, Joseph.},
title = {Phylogenies and the comparative method},
journal = {The American Naturalist},
volume = {125},
number = {1},
pages = {1-15},
url = {https://www.jstor.org/stable/2461605},
year = {1985},
type = {Journal Article}
}
@article{RN596,
author = {Flicek, P and Ahmed, I and Amode, MR and Barrell, D and Beal, K and Brent, S and Carvalho-Silva, D and Clapham, P and Coates, G and Fairley, S and Fitzgerald, S and Gil, L and Garcia-Giron, C and Gordon, L and Hourlier, T and Hunt, S and Juettemann, T and Kahari, AK and Keenan, S and Komorowska, M and Kulesha, E and Longden, I and Maurel, T and McLaren, WM and Muffato, M and Nag, R and Overduin, B and Pignatelli, M and Pritchard, B and Pritchard, E and Riat, HS and Ritchie, GRS and Ruffier, M and Schuster, M and Sheppard, D and Sobral, D and Taylor, K and Thormann, A and Trevanion, S and White, S and Wilder, SP and Aken, BL and Birney, E and Cunningham, F and Dunham, I and Harrow, J and Herrero, J and Hubbard, TJP and Johnson, N and Kinsella, R and Parker, A and Spudich, G and Yates, A and Zadissa, A and Searle, SMJ},
title = {Ensembl 2013},
journal = {Nucleic Acids Research},
volume = {41},
number = {D1},
pages = {D48-D55},
ISSN = {0305-1048},
DOI = {10.1093/nar/gks1236},
year = {2013},
type = {Journal Article}
}
@article{RN809,
author = {Freckleton, R. P.},
title = {The seven deadly sins of comparative analysis},
journal = {J Evol Biol},
volume = {22},
number = {7},
pages = {1367-75},
ISSN = {1420-9101},
DOI = {10.1111/j.1420-9101.2009.01757.x},
url = {https://www.ncbi.nlm.nih.gov/pubmed/19508410},
year = {2009},
type = {Journal Article}
}
@article{RN783,
author = {Freckleton, R. P. and Harvey, P. H.},
title = {Detecting non-Brownian trait evolution in adaptive radiations},
journal = {PLoS Biol},
volume = {4},
number = {11},
pages = {e373},
ISSN = {1545-7885},
DOI = {10.1371/journal.pbio.0040373},
url = {https://www.ncbi.nlm.nih.gov/pubmed/17090217},
year = {2006},
type = {Journal Article}
}
@article{RN826,
author = {Freckleton, R.P. and Harvey, P.H. and Pagel, M.},
title = {Phylogenetic analysis and comparative data: a test and review of evidence.},
journal = {American Naturalist},
volume = {160},
pages = {712-726},
year = {2002},
type = {Journal Article}
}
@article{RN770,
author = {Gabaldón, T. and Koonin, E. V.},
title = {Functional and evolutionary implications of gene orthology},
journal = {Nat Rev Genet},
volume = {14},
number = {5},
pages = {360-6},
ISSN = {1471-0064},
DOI = {10.1038/nrg3456},
url = {https://www.ncbi.nlm.nih.gov/pubmed/23552219},
year = {2013},
type = {Journal Article}
}
@article{RN791,
author = {Gabaldón, T. and Koonin, E. V.},
title = {Functional and evolutionary implications of gene orthology},
journal = {Nat Rev Genet},
volume = {14},
number = {5},
pages = {360-6},
ISSN = {1471-0064},
DOI = {10.1038/nrg3456},
url = {https://www.ncbi.nlm.nih.gov/pubmed/23552219},
year = {2013},
type = {Journal Article}
}
@article{RN816,
author = {Garland, T Jr. and Harvey, PH. and Ives, AR.},
title = {Procedure for the analysis of comparative data using phylogenetically independent contrasts},
journal = {Systematic Biology},
volume = {41},
pages = {18-32},
year = {1992},
type = {Journal Article}
}
@article{RN779,
author = {Garland, T.},
title = {Rate tests for phenotypic evolution using phylogenetically independent contrasts},
journal = {Am Nat},
volume = {140},
number = {3},
pages = {509-19},
ISSN = {0003-0147},
DOI = {10.1086/285424},
url = {https://www.ncbi.nlm.nih.gov/pubmed/19426053},
year = {1992},
type = {Journal Article}
}
@article{RN780,
author = {Garland, T. and Bennett, A. F. and Rezende, E. L.},
title = {Phylogenetic approaches in comparative physiology},
journal = {J Exp Biol},
volume = {208},
number = {Pt 16},
pages = {3015-35},
ISSN = {0022-0949},
DOI = {10.1242/jeb.01745},
url = {https://www.ncbi.nlm.nih.gov/pubmed/16081601},
year = {2005},
type = {Journal Article}
}
@article{RN784,
author = {Glasauer, S. M. and Neuhauss, S. C.},
title = {Whole-genome duplication in teleost fishes and its evolutionary consequences},
journal = {Mol Genet Genomics},
volume = {289},
number = {6},
pages = {1045-60},
ISSN = {1617-4623},
DOI = {10.1007/s00438-014-0889-2},
url = {https://www.ncbi.nlm.nih.gov/pubmed/25092473},
year = {2014},
type = {Journal Article}
}
@article{RN823,
author = {Guangchuang, Yu.},
title = {treeio: Base classes and functions for phylogenetic tree input and output},
url = {https://guangchuangyu.github.io/software/treeio},
year = {2018},
type = {Journal Article}
}
@article{RN821,
author = {Guangchuang, Yu. and David, Smith. and Huachen, Zhu. and Yi, Guan. and Tommy, Tsan-Yuk Lam.},
title = {ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data},
journal = {Methods in Ecology and Evolution},
volume = {8},
number = {1},
pages = {28-36},
year = {2017},
type = {Journal Article}
}
@article{RN787,
author = {Hahn, M. W.},
title = {Bias in phylogenetic tree reconciliation methods: implications for vertebrate genome evolution},
journal = {Genome Biol},
volume = {8},
number = {7},
pages = {R141},
ISSN = {1474-760X},
DOI = {10.1186/gb-2007-8-7-r141},
url = {https://www.ncbi.nlm.nih.gov/pubmed/17634151},
year = {2007},
type = {Journal Article}
}
@article{RN789,
author = {Hahn, M. W.},
title = {Distinguishing among evolutionary models for the maintenance of gene duplicates},
journal = {J Hered},
volume = {100},
number = {5},
pages = {605-17},
ISSN = {1465-7333},
DOI = {10.1093/jhered/esp047},
url = {https://www.ncbi.nlm.nih.gov/pubmed/19596713},
year = {2009},
type = {Journal Article}
}
@article{RN798,
author = {Herrero, J. and Muffato, M. and Beal, K. and Fitzgerald, S. and Gordon, L. and Pignatelli, M. and Vilella, A. J. and Searle, S. M. and Amode, R. and Brent, S. and Spooner, W. and Kulesha, E. and Yates, A. and Flicek, P.},
title = {Ensembl comparative genomics resources},
journal = {Database (Oxford)},
volume = {2016},
ISSN = {1758-0463},
DOI = {10.1093/database/baw053},
url = {https://www.ncbi.nlm.nih.gov/pubmed/27141089},
year = {2016},
type = {Journal Article}
}
@article{RN835,
author = {Hochberg, Y. and Benjamini, Y.},
title = {More powerful procedures for multiple significance testing},
journal = {Stat Med},
volume = {9},
number = {7},
pages = {811-8},
ISSN = {0277-6715},
url = {https://www.ncbi.nlm.nih.gov/pubmed/2218183},
year = {1990},
type = {Journal Article}
}
@article{RN795,
author = {Ives, A. R. and Midford, P. E. and Garland, T.},
title = {Within-species variation and measurement error in phylogenetic comparative methods},
journal = {Syst Biol},
volume = {56},
number = {2},
pages = {252-70},
ISSN = {1063-5157},
DOI = {10.1080/10635150701313830},
url = {https://www.ncbi.nlm.nih.gov/pubmed/17464881},
year = {2007},
type = {Journal Article}
}
@article{RN824,
author = {Jones , K E. and Purvis, A.},
title = {An optimum body size for mammals ? comparative evidence from bats.},
journal = {Functional Ecology},
volume = {11},
number = {6},
pages = {751-756},
DOI = {https://doi.org/10.1046/j.1365-2435.1997.00149.x},
year = {1997},
type = {Journal Article}
}
@article{RN817,
author = {Keck, F. and Rimet, F. and Bouchez, A. and Franc, A.},
title = {phylosignal: an R package to measure, test, and explore the phylogenetic signal},
journal = {Ecol Evol},
volume = {6},
number = {9},
pages = {2774-80},
ISSN = {2045-7758},
DOI = {10.1002/ece3.2051},
url = {https://www.ncbi.nlm.nih.gov/pubmed/27066252},
year = {2016},
type = {Journal Article}
}
@article{RN792,
author = {Koonin, E. V.},
title = {Orthologs, paralogs, and evolutionary genomics},
journal = {Annu Rev Genet},
volume = {39},
pages = {309-38},
ISSN = {0066-4197},
DOI = {10.1146/annurev.genet.39.073003.114725},
url = {https://www.ncbi.nlm.nih.gov/pubmed/16285863},
year = {2005},
type = {Journal Article}
}
@article{RN762,
author = {Kryuchkova-Mostacci, N. and Robinson-Rechavi, M.},
title = {Tissue-Specificity of Gene Expression Diverges Slowly between Orthologs, and Rapidly between Paralogs},
journal = {PLoS Comput Biol},
volume = {12},
number = {12},
pages = {e1005274},
ISSN = {1553-7358},
DOI = {10.1371/journal.pcbi.1005274},
url = {https://www.ncbi.nlm.nih.gov/pubmed/28030541},
year = {2016},
type = {Journal Article}
}
@article{RN832,
author = {Lan, X. and Pritchard, J. K.},
title = {Coregulation of tandem duplicate genes slows evolution of subfunctionalization in mammals},
journal = {Science},
volume = {352},
number = {6288},
pages = {1009-13},
ISSN = {1095-9203},
DOI = {10.1126/science.aad8411},
url = {https://www.ncbi.nlm.nih.gov/pubmed/27199432},
year = {2016},
type = {Journal Article}
}
@article{RN778,
author = {Laurent, S. and Robinson-Rechavi, M. and Salamin, N.},
title = {Detecting patterns of species diversification in the presence of both rate shifts and mass extinctions},
journal = {BMC Evol Biol},
volume = {15},
pages = {157},
ISSN = {1471-2148},
DOI = {10.1186/s12862-015-0432-z},
url = {https://www.ncbi.nlm.nih.gov/pubmed/26260305},
year = {2015},
type = {Journal Article}
}
@article{RN767,
author = {Laurent, S. and Salamin, N. and Robinson-Rechavi, M.},
title = {No evidence for the radiation time lag model after whole genome duplications in Teleostei},
journal = {PLoS One},
volume = {12},
number = {4},
pages = {e0176384},
ISSN = {1932-6203},
DOI = {10.1371/journal.pone.0176384},
url = {https://www.ncbi.nlm.nih.gov/pubmed/28426792},
year = {2017},
type = {Journal Article}
}
@article{RN831,
author = {Lien, S. and Koop, B. F. and Sandve, S. R. and Miller, J. R. and Kent, M. P. and Nome, T. and Hvidsten, T. R. and Leong, J. S. and Minkley, D. R. and Zimin, A. and Grammes, F. and Grove, H. and Gjuvsland, A. and Walenz, B. and Hermansen, R. A. and von Schalburg, K. and Rondeau, E. B. and Di Genova, A. and Samy, J. K. and Olav Vik, J. and Vigeland, M. D. and Caler, L. and Grimholt, U. and Jentoft, S. and Våge, D. I. and de Jong, P. and Moen, T. and Baranski, M. and Palti, Y. and Smith, D. R. and Yorke, J. A. and Nederbragt, A. J. and Tooming-Klunderud, A. and Jakobsen, K. S. and Jiang, X. and Fan, D. and Hu, Y. and Liberles, D. A. and Vidal, R. and Iturra, P. and Jones, S. J. and Jonassen, I. and Maass, A. and Omholt, S. W. and Davidson, W. S.},
title = {The Atlantic salmon genome provides insights into rediploidization},
journal = {Nature},
volume = {533},
number = {7602},
pages = {200-5},
ISSN = {1476-4687},
DOI = {10.1038/nature17164},
url = {https://www.ncbi.nlm.nih.gov/pubmed/27088604},
year = {2016},
type = {Journal Article}
}
@article{RN811,
author = {Losos, J. B.},
title = {Seeing the forest for the trees: the limitations of phylogenies in comparative biology. (American Society of Naturalists Address)},
journal = {Am Nat},
volume = {177},
number = {6},
pages = {709-27},
ISSN = {1537-5323},
DOI = {10.1086/660020},
url = {https://www.ncbi.nlm.nih.gov/pubmed/21597249},
year = {2011},
type = {Journal Article}
}
@article{RN830,
author = {Lynch, M. and Conery, J. S.},
title = {The evolutionary fate and consequences of duplicate genes},
journal = {Science},
volume = {290},
number = {5494},
pages = {1151-5},
ISSN = {0036-8075},
url = {https://www.ncbi.nlm.nih.gov/pubmed/11073452},
year = {2000},
type = {Journal Article}
}
@article{RN786,
author = {Malmstrøm, M. and Matschiner, M. and Tørresen, O. K. and Star, B. and Snipen, L. G. and Hansen, T. F. and Baalsrud, H. T. and Nederbragt, A. J. and Hanel, R. and Salzburger, W. and Stenseth, N. C. and Jakobsen, K. S. and Jentoft, S.},
title = {Evolution of the immune system influences speciation rates in teleost fishes},
journal = {Nat Genet},
volume = {48},
number = {10},
pages = {1204-10},
ISSN = {1546-1718},
DOI = {10.1038/ng.3645},
url = {https://www.ncbi.nlm.nih.gov/pubmed/27548311},
year = {2016},
type = {Journal Article}
}
@article{RN785,
author = {Meyer, A. and Van de Peer, Y.},
title = {From 2R to 3R: evidence for a fish-specific genome duplication (FSGD)},
journal = {Bioessays},
volume = {27},
number = {9},
pages = {937-45},
ISSN = {0265-9247},
DOI = {10.1002/bies.20293},
url = {https://www.ncbi.nlm.nih.gov/pubmed/16108068},
year = {2005},
type = {Journal Article}
}
@article{RN768,
author = {Molina-Venegas, R. and Rodríguez, M.},
title = {Revisiting phylogenetic signal; strong or negligible impacts of polytomies and branch length information?},
journal = {BMC Evol Biol},
volume = {17},
number = {1},
pages = {53},
ISSN = {1471-2148},
DOI = {10.1186/s12862-017-0898-y},
url = {https://www.ncbi.nlm.nih.gov/pubmed/28201989},
year = {2017},
type = {Journal Article}
}
@article{RN819,
author = {Münkemüller, T. and Lavergne, S. and Bzeznik, B. and Dray, S. and Jombart, T. and Schiffers, K. and Thuiller, W.},
title = {How to measure and test phylogenetic signal},
journal = {Methods in Ecology and Evolution},
volume = {3},
pages = {743-756},
DOI = {doi:
10.1111/j.2041-210X.2012.00196.x},
year = {2012},
type = {Journal Article}
}
@article{RN774,
author = {Nehrt, N. L. and Clark, W. T. and Radivojac, P. and Hahn, M. W.},
title = {Testing the ortholog conjecture with comparative functional genomic data from mammals},
journal = {PLoS Comput Biol},
volume = {7},
number = {6},
pages = {e1002073},
ISSN = {1553-7358},
DOI = {10.1371/journal.pcbi.1002073},
url = {https://www.ncbi.nlm.nih.gov/pubmed/21695233},
year = {2011},
type = {Journal Article}
}
@article{RN825,
author = {Orme, D.},
title = {The caper package: comparative analysis of phylogenetics and evolution in R},
url = {https://cran.r-project.org/web/packages/caper/vignettes/caper.pdf},
year = {2018},
type = {Journal Article}
}
@article{RN820,
author = {Pagel, M.},
title = {Inferring the historical patterns of biological evolution},
journal = {Nature},
volume = {401},
pages = {877-884},
year = {1999},
type = {Journal Article}
}
@article{RN803,
author = {Paradis, E. and Claude, J. and Strimmer, K.},
title = {APE: Analyses of Phylogenetics and Evolution in R language},
journal = {Bioinformatics},
volume = {20},
number = {2},
pages = {289-90},
ISSN = {1367-4803},
url = {https://www.ncbi.nlm.nih.gov/pubmed/14734327},
year = {2004},
type = {Journal Article}
}
@article{RN763,
author = {Pasquier, J. and Cabau, C. and Nguyen, T. and Jouanno, E. and Severac, D. and Braasch, I. and Journot, L. and Pontarotti, P. and Klopp, C. and Postlethwait, J. H. and Guiguen, Y. and Bobe, J.},
title = {Gene evolution and gene expression after whole genome duplication in fish: the PhyloFish database},
journal = {BMC Genomics},
volume = {17},
pages = {368},
ISSN = {1471-2164},
DOI = {10.1186/s12864-016-2709-z},
url = {https://www.ncbi.nlm.nih.gov/pubmed/27189481},
year = {2016},
type = {Journal Article}
}
@article{RN796,
author = {Pennell, M. W. and Eastman, J. M. and Slater, G. J. and Brown, J. W. and Uyeda, J. C. and FitzJohn, R. G. and Alfaro, M. E. and Harmon, L. J.},
title = {geiger v2.0: an expanded suite of methods for fitting macroevolutionary models to phylogenetic trees},
journal = {Bioinformatics},
volume = {30},
number = {15},
pages = {2216-8},
ISSN = {1367-4811},
DOI = {10.1093/bioinformatics/btu181},
url = {https://www.ncbi.nlm.nih.gov/pubmed/24728855},
year = {2014},
type = {Journal Article}
}
@article{RN797,
author = {Posada, D. and Buckley, T. R.},
title = {Model selection and model averaging in phylogenetics: advantages of akaike information criterion and bayesian approaches over likelihood ratio tests},
journal = {Syst Biol},
volume = {53},
number = {5},
pages = {793-808},
ISSN = {1063-5157},
DOI = {10.1080/10635150490522304},
url = {https://www.ncbi.nlm.nih.gov/pubmed/15545256},
year = {2004},
type = {Journal Article}
}
@article{RN813,
author = {Purvis, A. and Rambaut, A.},
title = {Comparative analysis by independent contrasts (CAIC): an Apple Macintosh application for analysing comparative data},
journal = {Comput Appl Biosci},
volume = {11},
number = {3},
pages = {247-51},
ISSN = {0266-7061},
url = {https://www.ncbi.nlm.nih.gov/pubmed/7583692},
year = {1995},
type = {Journal Article}
}
@article{RN804,
author = {Revell, Liam J.},
title = {phytools: An R package for phylogenetic comparative biology (and other things).},
journal = {Methods in Ecology and Evolution},
volume = {3},
pages = {217-223},
DOI = {doi:10.1111/j.2041-210X.2011.00169.x},
year = {2012},
type = {Journal Article}
}
@article{RN765,
author = {Rodrigo, G. and Fares, M. A.},
title = {Intrinsic adaptive value and early fate of gene duplication revealed by a bottom-up approach},
journal = {Elife},
volume = {7},
ISSN = {2050-084X},
DOI = {10.7554/eLife.29739},
url = {https://www.ncbi.nlm.nih.gov/pubmed/29303479},
year = {2018},
type = {Journal Article}
}
@article{RN794,
author = {Rogozin, I. B. and Managadze, D. and Shabalina, S. A. and Koonin, E. V.},
title = {Gene family level comparative analysis of gene expression in mammals validates the ortholog conjecture},
journal = {Genome Biol Evol},
volume = {6},
number = {4},
pages = {754-62},
ISSN = {1759-6653},
DOI = {10.1093/gbe/evu051},
url = {https://www.ncbi.nlm.nih.gov/pubmed/24610837},
year = {2014},
type = {Journal Article}
}
@article{RN828,
author = {Sandve, S. R. and Rohlfs, R. V. and Hvidsten, T. R.},
title = {Subfunctionalization versus neofunctionalization after whole-genome duplication},
journal = {Nat Genet},
volume = {50},
number = {7},
pages = {908-909},
ISSN = {1546-1718},
DOI = {10.1038/s41588-018-0162-4},
url = {https://www.ncbi.nlm.nih.gov/pubmed/29955176},
year = {2018},
type = {Journal Article}
}
@article{RN802,
author = {Schliep, K. P.},
title = {phangorn: phylogenetic analysis in R},
journal = {Bioinformatics},
volume = {27},
number = {4},
pages = {592-3},
ISSN = {1367-4811},
DOI = {10.1093/bioinformatics/btq706},
url = {https://www.ncbi.nlm.nih.gov/pubmed/21169378},
year = {2011},
type = {Journal Article}
}
@article{RN775,
author = {Sipos, B. and Massingham, T. and Jordan, G. E. and Goldman, N.},
title = {PhyloSim - Monte Carlo simulation of sequence evolution in the R statistical computing environment},
journal = {BMC Bioinformatics},
volume = {12},
pages = {104},
ISSN = {1471-2105},
DOI = {10.1186/1471-2105-12-104},
url = {https://www.ncbi.nlm.nih.gov/pubmed/21504561},
year = {2011},
type = {Journal Article}
}
@article{RN812,
author = {Sipos, B. and Massingham, T. and Jordan, G. E. and Goldman, N.},
title = {PhyloSim - Monte Carlo simulation of sequence evolution in the R statistical computing environment},
journal = {BMC Bioinformatics},
volume = {12},
pages = {104},
ISSN = {1471-2105},
DOI = {10.1186/1471-2105-12-104},
url = {https://www.ncbi.nlm.nih.gov/pubmed/21504561},
year = {2011},
type = {Journal Article}
}
@article{RN776,
author = {Stadler, T.},
title = {Simulating trees with a fixed number of extant species},
journal = {Syst Biol},
volume = {60},
number = {5},
pages = {676-84},
ISSN = {1076-836X},
DOI = {10.1093/sysbio/syr029},
url = {https://www.ncbi.nlm.nih.gov/pubmed/21482552},
year = {2011},
type = {Journal Article}
}
@article{RN771,
author = {Studer, R. A. and Robinson-Rechavi, M.},
title = {How confident can we be that orthologs are similar, but paralogs differ?},
journal = {Trends Genet},
volume = {25},
number = {5},
pages = {210-6},
ISSN = {0168-9525},
DOI = {10.1016/j.tig.2009.03.004},
url = {https://www.ncbi.nlm.nih.gov/pubmed/19368988},
year = {2009},
type = {Journal Article}
}
@article{RN799,
author = {Thomas, P. D. and Wood, V. and Mungall, C. J. and Lewis, S. E. and Blake, J. A. and Consortium, Gene Ontology},
title = {On the Use of Gene Ontology Annotations to Assess Functional Similarity among Orthologs and Paralogs: A Short Report},
journal = {PLoS Comput Biol},
volume = {8},
number = {2},
pages = {e1002386},
ISSN = {1553-7358},
DOI = {10.1371/journal.pcbi.1002386},
url = {https://www.ncbi.nlm.nih.gov/pubmed/22359495},
year = {2012},
type = {Journal Article}
}
@article{RN215,
author = {Yanai, I. and Benjamin, H. and Shmoish, M. and Chalifa-Caspi, V. and Shklar, M. and Ophir, R. and Bar-Even, A. and Horn-Saban, S. and Safran, M. and Domany, E. and Lancet, D. and Shmueli, O.},
title = {Genome-wide midrange transcription profiles reveal expression level relationships in human tissue specification},
journal = {Bioinformatics},
volume = {21},
number = {5},
pages = {650-659},
ISSN = {1367-4803},
DOI = {10.1093/bioinformatics/bti042},
url = {<Go to ISI>://WOS:000227241200012},
year = {2005},
type = {Journal Article}
}
@article{RN806,
author = {Yu, Guangchuang. and Smith, David. and Zhu, Huachen. and Guan, Yi. and Lam, Tommy Tsan-Yu.},
title = {ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data.},
journal = {Methods in Ecology and Evolution},
volume = {8},
number = {1},
pages = {28-36},
DOI = {10.1111/2041-210X.12628},
year = {2017},
type = {Journal Article}
}
@Manual{Rcore,
title = {R: A Language and Environment for Statistical Computing},
author = {{R Core Team}},
organization = {R Foundation for Statistical Computing},
address = {Vienna, Austria},
year = {2018},
url = {https://www.R-project.org/},
}
@article{RN837,
author = {Eisen, J. A. and Wu, M.},
title = {Phylogenetic analysis and gene functional predictions: phylogenomics in action},
journal = {Theor Popul Biol},
volume = {61},
number = {4},
pages = {481-7},
ISSN = {0040-5809},
url = {https://www.ncbi.nlm.nih.gov/pubmed/12167367},
year = {2002},
type = {Journal Article}
}
@article{RN836,
author = {Cooper, N. and Thomas, G. H. and Venditti, C. and Meade, A. and Freckleton, R. P.},
title = {A cautionary note on the use of Ornstein Uhlenbeck models in macroevolutionary studies},
journal = {Biol J Linn Soc Lond},
volume = {118},
number = {1},
pages = {64-77},
ISSN = {0024-4066},
DOI = {10.1111/bij.12701},
url = {https://www.ncbi.nlm.nih.gov/pubmed/27478249},
year = {2016},
type = {Journal Article}
}
@article{RN841,
author = {Chen, J. and Swofford, R. and Johnson, J. and Cummings, B. B. and Rogel, N. and Lindblad-Toh, K. and Haerty, W. and Palma, F. D. and Regev, A.},
title = {A quantitative framework for characterizing the evolutionary history of mammalian gene expression},
journal = {Genome Res},
volume = {29},
number = {1},
pages = {53-63},
ISSN = {1549-5469},
DOI = {10.1101/gr.237636.118},
url = {https://www.ncbi.nlm.nih.gov/pubmed/30552105},
year = {2019},
type = {Journal Article}
}