-
1
-
-
0024379002
-
Newly arisen DNA repeats in primate phylogeny
-
2480599, ().:
-
Ryan SC, Dugaiczyk A, (1989) Newly arisen DNA repeats in primate phylogeny. Proc Natl Acad Sci U S A86: 9360–9364. 2480599
-
(1989)
Proc Natl Acad Sci U S A
, vol.86
, pp. 9360-9364
-
-
Ryan, S.C.1
Dugaiczyk, A.2
-
2
-
-
0030794201
-
Molecular evidence from retroposons that whales form a clade within even-toed ungulates
-
9262399, . ().:
-
Shimamura M, Yasue H, Ohshima K, Abe H, Kato H, et al. (1997) Molecular evidence from retroposons that whales form a clade within even-toed ungulates. Nature388: 666–670. 9262399
-
(1997)
Nature
, vol.388
, pp. 666-670
-
-
Shimamura, M.1
Yasue, H.2
Ohshima, K.3
Abe, H.4
Kato, H.5
-
3
-
-
84962125835
-
Exploring Massive Incomplete Lineage Sorting in Arctoids (Laurasiatheria, Carnivora)
-
26337548, . ().:
-
Doronina L, Churakov G, Shi J, Brosius J, Baertsch R, et al. (2015) Exploring Massive Incomplete Lineage Sorting in Arctoids (Laurasiatheria, Carnivora). Mol Biol Evol32: 3194–3204. doi: 10.1093/molbev/msv18826337548
-
(2015)
Mol Biol Evol
, vol.32
, pp. 3194-3204
-
-
Doronina, L.1
Churakov, G.2
Shi, J.3
Brosius, J.4
Baertsch, R.5
-
4
-
-
33847180610
-
SINEs of a nearly perfect character
-
17345674, ().:
-
Ray DA, Xing J, Salem AH, Batzer MA, (2006) SINEs of a nearly perfect character. Syst Biol55: 928–935. 17345674
-
(2006)
Syst Biol
, vol.55
, pp. 928-935
-
-
Ray, D.A.1
Xing, J.2
Salem, A.H.3
Batzer, M.A.4
-
5
-
-
24344509193
-
Genomic deletions and precise removal of transposable elements mediated by short identical DNA segments in primates
-
16140992, ().:
-
van de Lagemaat LN, Gagnier L, Medstrand P, Mager DL, (2005) Genomic deletions and precise removal of transposable elements mediated by short identical DNA segments in primates. Genome Res15: 1243–1249. 16140992
-
(2005)
Genome Res
, vol.15
, pp. 1243-1249
-
-
van de Lagemaat, L.N.1
Gagnier, L.2
Medstrand, P.3
Mager, D.L.4
-
6
-
-
0033964296
-
SINE insertions: powerful tools for molecular systematics
-
10655034, ().:
-
Shedlock AM, Okada N, (2000) SINE insertions: powerful tools for molecular systematics. Bioessays22: 148–160. 10655034
-
(2000)
Bioessays
, vol.22
, pp. 148-160
-
-
Shedlock, A.M.1
Okada, N.2
-
7
-
-
67649134834
-
Primate phylogenomics: developing numerous nuclear non-coding, non-repetitive markers for ecological and phylogenetic applications and analysis of evolutionary rate variation
-
19470178, ()
-
Peng Z, Elango N, Wildman DE, Yi SV, (2009) Primate phylogenomics: developing numerous nuclear non-coding, non-repetitive markers for ecological and phylogenetic applications and analysis of evolutionary rate variation. BMC Genomics10: 247. doi: 10.1186/1471-2164-10-24719470178
-
(2009)
BMC Genomics
, vol.10
, pp. 247
-
-
Peng, Z.1
Elango, N.2
Wildman, D.E.3
Yi, S.V.4
-
8
-
-
67049159696
-
Natural selection and phylogenetic analysis
-
19470454, ().:
-
Edwards SV, (2009) Natural selection and phylogenetic analysis. Proc Natl Acad Sci U S A106: 8799–8800. doi: 10.1073/pnas.090410310619470454
-
(2009)
Proc Natl Acad Sci U S A
, vol.106
, pp. 8799-8800
-
-
Edwards, S.V.1
-
9
-
-
0015259854
-
The effective number of a population with overlapping generations: a correction and further discussion
-
().:
-
Crow JF, Kimura M, (1972) The effective number of a population with overlapping generations: a correction and further discussion. Am J Hum Genet24: 1–10.
-
(1972)
Am J Hum Genet
, vol.24
, pp. 1-10
-
-
Crow, J.F.1
Kimura, M.2
-
10
-
-
33645227457
-
Self-synthesizing DNA transposons in eukaryotes
-
16537396, ().:
-
Kapitonov VV, Jurka J, (2006) Self-synthesizing DNA transposons in eukaryotes. Proc Natl Acad Sci U S A103: 4540–4545. 16537396
-
(2006)
Proc Natl Acad Sci U S A
, vol.103
, pp. 4540-4545
-
-
Kapitonov, V.V.1
Jurka, J.2
-
11
-
-
84877763626
-
Retrophylogenomics place tarsiers on the evolutionary branch of anthropoids
-
23629008, . ()
-
Hartig G, Churakov G, Warren WC, Brosius J, Makalowski W, et al. (2013) Retrophylogenomics place tarsiers on the evolutionary branch of anthropoids. Sci Rep3: 1756. doi: 10.1038/srep0175623629008
-
(2013)
Sci Rep
, vol.3
, pp. 1756
-
-
Hartig, G.1
Churakov, G.2
Warren, W.C.3
Brosius, J.4
Makalowski, W.5
-
12
-
-
84913585432
-
Lineage sorting in apes
-
25251849, ().:
-
Mailund T, Munch K, Schierup MH, (2014) Lineage sorting in apes. Annu Rev Genet48: 519–535. doi: 10.1146/annurev-genet-120213-09253225251849
-
(2014)
Annu Rev Genet
, vol.48
, pp. 519-535
-
-
Mailund, T.1
Munch, K.2
Schierup, M.H.3
-
14
-
-
77957686501
-
A maximum pseudo-likelihood approach for estimating species trees under the coalescent model
-
20937096, ()
-
Liu L, Yu L, Edwards SV, (2010) A maximum pseudo-likelihood approach for estimating species trees under the coalescent model. BMC Evol Biol10: 302. doi: 10.1186/1471-2148-10-30220937096
-
(2010)
BMC Evol Biol
, vol.10
, pp. 302
-
-
Liu, L.1
Yu, L.2
Edwards, S.V.3
-
15
-
-
66049159777
-
Mosaic retroposon insertion patterns in placental mammals
-
19261842, . ().:
-
Churakov G, Kriegs JO, Baertsch R, Zemann A, Brosius J, et al. (2009) Mosaic retroposon insertion patterns in placental mammals. Genome Res19: 868–875. doi: 10.1101/gr.090647.10819261842
-
(2009)
Genome Res
, vol.19
, pp. 868-875
-
-
Churakov, G.1
Kriegs, J.O.2
Baertsch, R.3
Zemann, A.4
Brosius, J.5
-
16
-
-
65249116423
-
Retroposon analysis and recent geological data suggest near-simultaneous divergence of the three superorders of mammals
-
19286970, ().:
-
Nishihara H, Maruyama S, Okada N, (2009) Retroposon analysis and recent geological data suggest near-simultaneous divergence of the three superorders of mammals. Proc Natl Acad Sci U S A106: 5235–5240. doi: 10.1073/pnas.080929710619286970
-
(2009)
Proc Natl Acad Sci U S A
, vol.106
, pp. 5235-5240
-
-
Nishihara, H.1
Maruyama, S.2
Okada, N.3
-
17
-
-
77952827905
-
Rodent evolution: back to the root
-
20100942, . ().:
-
Churakov G, Sadasivuni MK, Rosenbloom KR, Huchon D, Brosius J, et al. (2010) Rodent evolution: back to the root. Mol Biol Evol27: 1315–1326. doi: 10.1093/molbev/msq01920100942
-
(2010)
Mol Biol Evol
, vol.27
, pp. 1315-1326
-
-
Churakov, G.1
Sadasivuni, M.K.2
Rosenbloom, K.R.3
Huchon, D.4
Brosius, J.5
-
18
-
-
0031055331
-
Sequence patterns indicate an enzymatic involvement in integration of mammalian retroposons
-
9050872, ().:
-
Jurka J, (1997) Sequence patterns indicate an enzymatic involvement in integration of mammalian retroposons. Proc Natl Acad Sci U S A94: 1872–1877. 9050872
-
(1997)
Proc Natl Acad Sci U S A
, vol.94
, pp. 1872-1877
-
-
Jurka, J.1
-
19
-
-
84866948626
-
Activity of ancient RTE retroposons during the evolution of cows, spiral-horned antelopes, and Nilgais (Bovinae)
-
22688946, ().:
-
Nilsson MA, Klassert D, Bertelsen MF, Hallstrom BM, Janke A, (2012) Activity of ancient RTE retroposons during the evolution of cows, spiral-horned antelopes, and Nilgais (Bovinae). Mol Biol Evol29: 2885–2888. 22688946
-
(2012)
Mol Biol Evol
, vol.29
, pp. 2885-2888
-
-
Nilsson, M.A.1
Klassert, D.2
Bertelsen, M.F.3
Hallstrom, B.M.4
Janke, A.5
-
20
-
-
0026031181
-
Inferences of species phylogeny in relation to segregation of ancient polymorphisms
-
2004713, ().:
-
Wu CI, (1991) Inferences of species phylogeny in relation to segregation of ancient polymorphisms. Genetics127: 429–435. 2004713
-
(1991)
Genetics
, vol.127
, pp. 429-435
-
-
Wu, C.I.1
-
21
-
-
0001017871
-
Solution of a Process of Random Genetic Drift with a Continuous Model
-
16589632, ().:
-
Kimura M, (1955) Solution of a Process of Random Genetic Drift with a Continuous Model. Proc Natl Acad Sci U S A41: 144–150. 16589632
-
(1955)
Proc Natl Acad Sci U S A
, vol.41
, pp. 144-150
-
-
Kimura, M.1
-
22
-
-
0026747106
-
Gene trees, species trees and the segregation of ancestral alleles
-
1644284, ().:
-
Hudson RR, (1992) Gene trees, species trees and the segregation of ancestral alleles. Genetics131: 509–513. 1644284
-
(1992)
Genetics
, vol.131
, pp. 509-513
-
-
Hudson, R.R.1
-
23
-
-
70450277249
-
Identifying hybridization events in the presence of coalescence via model selection
-
20525602, ().:
-
Kubatko LS, (2009) Identifying hybridization events in the presence of coalescence via model selection. Syst Biol58: 478–488. doi: 10.1093/sysbio/syp05520525602
-
(2009)
Syst Biol
, vol.58
, pp. 478-488
-
-
Kubatko, L.S.1
-
24
-
-
58249136809
-
Detecting hybrid speciation in the presence of incomplete lineage sorting using gene tree incongruence: a model
-
19038278, ().:
-
Meng C, Kubatko LS, (2009) Detecting hybrid speciation in the presence of incomplete lineage sorting using gene tree incongruence: a model. Theor Popul Biol75: 35–45. doi: 10.1016/j.tpb.2008.10.00419038278
-
(2009)
Theor Popul Biol
, vol.75
, pp. 35-45
-
-
Meng, C.1
Kubatko, L.S.2
-
25
-
-
79953097998
-
Nuclear versus mitochondrial DNA: evidence for hybridization in colobine monkeys
-
21435245, . ()
-
Roos C, Zinner D, Kubatko LS, Schwarz C, Yang M, et al. (2011) Nuclear versus mitochondrial DNA: evidence for hybridization in colobine monkeys. BMC Evol Biol11: 77. doi: 10.1186/1471-2148-11-7721435245
-
(2011)
BMC Evol Biol
, vol.11
, pp. 77
-
-
Roos, C.1
Zinner, D.2
Kubatko, L.S.3
Schwarz, C.4
Yang, M.5
-
26
-
-
0035752767
-
A phylogenetic foundation for comparative mammalian genomics
-
11791233, ().:
-
Waddell PJ, Kishino H, Ota R, (2001) A phylogenetic foundation for comparative mammalian genomics. Genome Inform12: 141–154. 11791233
-
(2001)
Genome Inform
, vol.12
, pp. 141-154
-
-
Waddell, P.J.1
Kishino, H.2
Ota, R.3
-
27
-
-
4544222472
-
SINEs of speciation: tracking lineages with retroposons
-
16701320, ().:
-
Shedlock AM, Takahashi K, Okada N, (2004) SINEs of speciation: tracking lineages with retroposons. Trends Ecol Evol19: 545–553. 16701320
-
(2004)
Trends Ecol Evol
, vol.19
, pp. 545-553
-
-
Shedlock, A.M.1
Takahashi, K.2
Okada, N.3
-
28
-
-
0035108258
-
SINE insertions in cladistic analyses and the phylogenetic affiliations of Tarsius bancanus to other primates
-
11156996, ().:
-
Schmitz J, Ohme M, Zischler H, (2001) SINE insertions in cladistic analyses and the phylogenetic affiliations of Tarsius bancanus to other primates. Genetics157: 777–784. 11156996
-
(2001)
Genetics
, vol.157
, pp. 777-784
-
-
Schmitz, J.1
Ohme, M.2
Zischler, H.3
-
29
-
-
84861358284
-
Retroposon insertion patterns of neoavian birds: strong evidence for an extensive incomplete lineage sorting era
-
22319163, . ().:
-
Matzke A, Churakov G, Berkes P, Arms EM, Kelsey D, et al. (2012) Retroposon insertion patterns of neoavian birds: strong evidence for an extensive incomplete lineage sorting era. Mol Biol Evol29: 1497–1501. doi: 10.1093/molbev/msr31922319163
-
(2012)
Mol Biol Evol
, vol.29
, pp. 1497-1501
-
-
Matzke, A.1
Churakov, G.2
Berkes, P.3
Arms, E.M.4
Kelsey, D.5
-
30
-
-
84940641284
-
The Dynamics of Incomplete Lineage Sorting across the Ancient Adaptive Radiation of Neoavian Birds
-
26284513, ()
-
Suh A, Smeds L, Ellegren H, (2015) The Dynamics of Incomplete Lineage Sorting across the Ancient Adaptive Radiation of Neoavian Birds. PLoS Biol13: e1002224. doi: 10.1371/journal.pbio.100222426284513
-
(2015)
PLoS Biol
, vol.13
, pp. 1002224
-
-
Suh, A.1
Smeds, L.2
Ellegren, H.3
-
31
-
-
84942086916
-
Ancient traces of tailless retropseudogenes in therian genomes
-
25724209, ().:
-
Noll A, Raabe CA, Churakov G, Brosius J, Schmitz J, (2015) Ancient traces of tailless retropseudogenes in therian genomes. Genome Biol Evol7: 889–900. doi: 10.1093/gbe/evv04025724209
-
(2015)
Genome Biol Evol
, vol.7
, pp. 889-900
-
-
Noll, A.1
Raabe, C.A.2
Churakov, G.3
Brosius, J.4
Schmitz, J.5
-
32
-
-
84962103456
-
-
Chang W, Cheng J, Allaire JJ, Xie Y, Mac-Pherson J (2015) shiny: Web Application Framework for
-
Chang W, Cheng J, Allaire JJ, Xie Y, Mac-Pherson J (2015) shiny: Web Application Framework for R.
-
-
-
-
33
-
-
84962061333
-
-
R.Core.Team (2014) R: A Language and Environment for Statistical Computin
-
R.Core.Team (2014) R: A Language and Environment for Statistical Computing.
-
-
-
-
34
-
-
0033621101
-
Phylogenetic relationships among cetartiodactyls based on insertions of short and long interpersed elements: hippopotamuses are the closest extant relatives of whales
-
10468596, ().:
-
Nikaido M, Rooney AP, Okada N, (1999) Phylogenetic relationships among cetartiodactyls based on insertions of short and long interpersed elements: hippopotamuses are the closest extant relatives of whales. Proc Natl Acad Sci U S A96: 10261–10266. 10468596
-
(1999)
Proc Natl Acad Sci U S A
, vol.96
, pp. 10261-10266
-
-
Nikaido, M.1
Rooney, A.P.2
Okada, N.3
-
35
-
-
80052392767
-
Mesozoic retroposons reveal parrots as the closest living relatives of passerine birds
-
21863010, . ()
-
Suh A, Paus M, Kiefmann M, Churakov G, Franke FA, et al. (2011) Mesozoic retroposons reveal parrots as the closest living relatives of passerine birds. Nat Commun2: 443. doi: 10.1038/ncomms144821863010
-
(2011)
Nat Commun
, vol.2
, pp. 443
-
-
Suh, A.1
Paus, M.2
Kiefmann, M.3
Churakov, G.4
Franke, F.A.5
-
36
-
-
0034750288
-
Phylogenetic relationships and ancient incomplete lineage sorting among cichlid fishes in Lake Tanganyika as revealed by analysis of the insertion of retroposons
-
11606702, ().:
-
Takahashi K, Terai Y, Nishida M, Okada N, (2001) Phylogenetic relationships and ancient incomplete lineage sorting among cichlid fishes in Lake Tanganyika as revealed by analysis of the insertion of retroposons. Mol Biol Evol18: 2057–2066. 11606702
-
(2001)
Mol Biol Evol
, vol.18
, pp. 2057-2066
-
-
Takahashi, K.1
Terai, Y.2
Nishida, M.3
Okada, N.4
-
37
-
-
34147192150
-
Extensive morphological convergence and rapid radiation in the evolutionary history of the family Geoemydidae (old world pond turtles) revealed by SINE insertion analysis
-
17345673, . ().:
-
Sasaki T, Yasukawa Y, Takahashi K, Miura S, Shedlock AM, et al. (2006) Extensive morphological convergence and rapid radiation in the evolutionary history of the family Geoemydidae (old world pond turtles) revealed by SINE insertion analysis. Syst Biol55: 912–927. 17345673
-
(2006)
Syst Biol
, vol.55
, pp. 912-927
-
-
Sasaki, T.1
Yasukawa, Y.2
Takahashi, K.3
Miura, S.4
Shedlock, A.M.5
-
38
-
-
33646255212
-
Retroposed elements as archives for the evolutionary history of placental mammals
-
16515367, . ()
-
Kriegs JO, Churakov G, Kiefmann M, Jordan U, Brosius J, et al. (2006) Retroposed elements as archives for the evolutionary history of placental mammals. PLoS Biol4: e91. 16515367
-
(2006)
PLoS Biol
, vol.4
, pp. 91
-
-
Kriegs, J.O.1
Churakov, G.2
Kiefmann, M.3
Jordan, U.4
Brosius, J.5
-
39
-
-
84979859184
-
Targeted Capture of Phylogenetically Informative Ves SINE Insertions in Genus Myotis
-
26014613, . ().:
-
Platt RN, 2ndZhang Y, Witherspoon DJ, Xing J, Suh A, et al. (2015) Targeted Capture of Phylogenetically Informative Ves SINE Insertions in Genus Myotis. Genome Biol Evol7: 1664–1675. doi: 10.1093/gbe/evv09926014613
-
(2015)
Genome Biol Evol
, vol.7
, pp. 1664-1675
-
-
Platt, R.N.1
Zhang, Y.2
Witherspoon, D.J.3
Xing, J.4
Suh, A.5
-
40
-
-
84857422378
-
Updating the evolutionary history of Carnivora (Mammalia): a new species-level supertree complete with divergence time estimates
-
22369503, ()
-
Nyakatura K, Bininda-Emonds OR, (2012) Updating the evolutionary history of Carnivora (Mammalia): a new species-level supertree complete with divergence time estimates. BMC Biol10: 12. doi: 10.1186/1741-7007-10-1222369503
-
(2012)
BMC Biol
, vol.10
, pp. 12
-
-
Nyakatura, K.1
Bininda-Emonds, O.R.2
-
41
-
-
77953128894
-
Pattern and timing of diversification of the mammalian order Carnivora inferred from multiple nuclear gene sequences
-
20138220, . ().:
-
Eizirik E, Murphy WJ, Koepfli KP, Johnson WE, Dragoo JW, et al. (2010) Pattern and timing of diversification of the mammalian order Carnivora inferred from multiple nuclear gene sequences. Mol Phylogenet Evol56: 49–63. doi: 10.1016/j.ympev.2010.01.03320138220
-
(2010)
Mol Phylogenet Evol
, vol.56
, pp. 49-63
-
-
Eizirik, E.1
Murphy, W.J.2
Koepfli, K.P.3
Johnson, W.E.4
Dragoo, J.W.5
-
43
-
-
84860109324
-
MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space
-
. ().:
-
Ronquist F, Teslenko M, van der Mark P, Ayres DL, Darling A, et al. (2002) MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space. Syst Biol61: 539–542.
-
(2002)
Syst Biol
, vol.61
, pp. 539-542
-
-
Ronquist, F.1
Teslenko, M.2
van der Mark, P.3
Ayres, D.L.4
Darling, A.5
-
45
-
-
84883530606
-
Impact of marker ascertainment bias on genomic selection accuracy and estimates of genetic diversity
-
24040295, ()
-
Heslot N, Rutkoski J, Poland J, Jannink JL, Sorrells ME, (2013) Impact of marker ascertainment bias on genomic selection accuracy and estimates of genetic diversity. PLoS One8: e74612. doi: 10.1371/journal.pone.007461224040295
-
(2013)
PLoS One
, vol.8
, pp. 74612
-
-
Heslot, N.1
Rutkoski, J.2
Poland, J.3
Jannink, J.L.4
Sorrells, M.E.5
-
46
-
-
43449123631
-
Genome analysis of the platypus reveals unique signatures of evolution
-
18464734, . ().:
-
Warren WC, Hillier LW, Marshall Graves JA, Birney E, Ponting CP, et al. (2008) Genome analysis of the platypus reveals unique signatures of evolution. Nature453: 175–183. doi: 10.1038/nature0693618464734
-
(2008)
Nature
, vol.453
, pp. 175-183
-
-
Warren, W.C.1
Hillier, L.W.2
Marshall, G.J.A.3
Birney, E.4
Ponting, C.P.5
|