-
1
-
-
33745128392
-
Conservation options for the Baiji: Time for realism?
-
Yang, G., Bruford, M. W., Wei, F. & Zhou, K. Conservation options for the Baiji: time for realism? Conserv Biol. 20, 620-622 (2006).
-
(2006)
Conserv Biol
, vol.20
, pp. 620-622
-
-
Yang, G.1
Bruford, M.W.2
Wei, F.3
Zhou, K.4
-
2
-
-
35548965566
-
First human-caused extinction of a cetacean species?
-
Turvey, S. T. et al. First human-caused extinction of a cetacean species? Biol. Lett. 3, 537-540 (2007).
-
(2007)
Biol Lett
, vol.3
, pp. 537-540
-
-
Turvey, S.T.1
-
3
-
-
84889240539
-
-
Montgelard, C., Douzery, E. & Michaux, J. Reproductive Biology and Phylogeny of Cetacea, Whales, Porpoises and Dolphins (Science Publishers, Inc. Enfield, New Hampshire, 2007).
-
(2007)
Reproductive Biology and Phylogeny of Cetacea, Whales, Porpoises and Dolphins (Science Publishers, Inc. Enfield, New Hampshire
-
-
Montgelard, C.1
Douzery, E.2
Michaux, J.3
-
4
-
-
34250637228
-
Anatomical adaptations of aquatic mammals
-
Reidenberg, J. Anatomical adaptations of aquatic mammals. Anat. Rec. A 290, 507-513 (2007).
-
(2007)
Anat. Rec
, vol.290
, pp. 507-513
-
-
Reidenberg, J.1
-
5
-
-
80052730828
-
Phylogenomic analyses and improved resolution of Cetartiodactyla
-
Zhou, X., Xu, S., Yang, Y., Zhou, K. & Yang, G. Phylogenomic analyses and improved resolution of Cetartiodactyla. Mol. Phylogenet. Evol. 61, 255-264 (2012).
-
(2012)
Mol. Phylogenet. Evol
, vol.61
, pp. 255-264
-
-
Zhou, X.1
Xu, S.2
Yang, Y.3
Zhou, K.4
Yang, G.5
-
6
-
-
20144366003
-
The genomes of Oryza sativa: A history of duplications
-
Yu, J. et al. The genomes of Oryza sativa: a history of duplications. PLoS Biol. 3, e38 (2005).
-
(2005)
PLoS Biol
, vol.3
-
-
Yu, J.1
-
7
-
-
84864398778
-
The yak genome and adaptation to life at high altitude
-
Qiu, Q. et al. The yak genome and adaptation to life at high altitude. Nat. Genet. 44, 946-949 (2012).
-
(2012)
Nat. Genet
, vol.44
, pp. 946-949
-
-
Qiu, Q.1
-
9
-
-
0030442757
-
Determinants of rate variation in mammalian DNA sequence evolution
-
Bromham, L., Rambaut, A. & Harvey, P. H. Determinants of rate variation in mammalian DNA sequence evolution. J. Mol. Evol. 43, 610-621 (1996).
-
(1996)
J. Mol. Evol
, vol.43
, pp. 610-621
-
-
Bromham, L.1
Rambaut, A.2
Harvey, P.H.3
-
10
-
-
22944437097
-
Molecular clocks: Four decades of evolution
-
Kumar, S. Molecular clocks: four decades of evolution. Nat. Rev. Genet. 6, 654-662 (2005).
-
(2005)
Nat. Rev. Genet
, vol.6
, pp. 654-662
-
-
Kumar, S.1
-
11
-
-
73349099032
-
Big and slow: Phylogenetic estimates of molecular evolution in baleen whales (suborder mysticeti)
-
Jackson, J. A. et al. Big and slow: phylogenetic estimates of molecular evolution in baleen whales (suborder mysticeti).Mol. Biol. Evol. 26, 2427-2440 (2009).
-
(2009)
Mol Biol. Evol
, vol.26
, pp. 2427-2440
-
-
Jackson, J.A.1
-
12
-
-
73949117816
-
Phylogenomic analyses reveal convergent patterns of adaptive evolution in elephant and human ancestries
-
Goodman, M. et al. Phylogenomic analyses reveal convergent patterns of adaptive evolution in elephant and human ancestries. Proc. Natl Acad. Sci. USA 106, 20824-20829 (2009).
-
(2009)
Proc. Natl Acad. Sci. USA
, vol.106
, pp. 20824-20829
-
-
Goodman, M.1
-
14
-
-
80054760378
-
Variation in the mutation rate across mammalian genomes
-
Hodgkinson, A. & Eyre-Walker, A. Variation in the mutation rate across mammalian genomes. Nat. Rev. Genet. 12, 756-766 (2011).
-
(2011)
Nat. Rev. Genet
, vol.12
, pp. 756-766
-
-
Hodgkinson, A.1
Eyre-Walker, A.2
-
15
-
-
0027308854
-
Body size, metabolic rate, generation time and the molecular clock
-
Martin, A. P. & Palumbi, S. R. Body size, metabolic rate, generation time and the molecular clock. Proc. Natl Acad. Sci. USA 90, 4087-4091 (1993).
-
(1993)
Proc. Natl Acad. Sci. USA
, vol.90
, pp. 4087-4091
-
-
Martin, A.P.1
Palumbi, S.R.2
-
16
-
-
34547803197
-
Paml 4: Phylogenetic analysis by maximum likelihood
-
Yang, Z. PAML 4: phylogenetic analysis by maximum likelihood. Mol. Biol. Evol. 24, 1586-1591 (2007).
-
(2007)
Mol. Biol. Evol
, vol.24
, pp. 1586-1591
-
-
Yang, Z.1
-
17
-
-
50849122974
-
Patterns of positive selection in six mammalian genomes
-
Kosiol, C. et al. Patterns of positive selection in six mammalian genomes. PLoS. Genet. 4, e1000144 (2008).
-
(2008)
PLoS. Genet
, vol.4
-
-
Kosiol, C.1
-
18
-
-
84864959956
-
Dolphin genome provides evidence for adaptive evolution of nervous system genes and a molecular rate slowdown
-
McGowen, M. R., Grossman, L. I. & Wildman, D. E. Dolphin genome provides evidence for adaptive evolution of nervous system genes and a molecular rate slowdown. Proc. Biol. Sci. 279, 3643-3651 (2012).
-
(2012)
Proc. Biol. Sci.
, vol.279
, pp. 3643-3651
-
-
McGowen, M.R.1
Grossman, L.I.2
Wildman, D.E.3
-
19
-
-
84876512828
-
Genome-wide scans for candidate genes involved to the aquatic adaptation of dolphins
-
Sun, Y. B. et al. Genome-Wide Scans for Candidate Genes Involved to the Aquatic Adaptation of Dolphins. Genome Biol Evol 5, 130-139 (2012).
-
(2012)
Genome Biol Evol
, vol.5
, pp. 130-139
-
-
Sun, Y.B.1
-
20
-
-
44949208286
-
The role of the DNA damage response pathways in brain development and microcephaly: Insight from human disorders
-
ODriscoll, M. & Jeggo, P. A. The role of the DNA damage response pathways in brain development and microcephaly: insight from human disorders. DNA Repair (Amst.) 7, 1039-1050 (2008).
-
(2008)
DNA Repair (Amst.)
, vol.7
, pp. 1039-1050
-
-
Odriscoll, M.1
Jeggo, P.A.2
-
21
-
-
58549092574
-
DNA repair deficiency and neurological disease
-
McKinnon, P. J. DNA repair deficiency and neurological disease. Nat. Rev. Neurosci. 10, 100-112 (2009).
-
(2009)
Nat. Rev. Neurosci
, vol.10
, pp. 100-112
-
-
McKinnon, P.J.1
-
22
-
-
0022534918
-
Rates of DNA sequence evolution differ between taxonomic groups
-
Britten, R. J. Rates of DNA sequence evolution differ between taxonomic groups. Science 231, 1393-1398 (1986).
-
(1986)
Science
, vol.231
, pp. 1393-1398
-
-
Britten, R.J.1
-
23
-
-
84889256413
-
The eye of Pontoporia blainvillei and Inia boliviensis and some remarks on the problem of regressive evolution of eye in Platanistoidea
-
Pillieri, G. The eye of Pontoporia blainvillei and Inia boliviensis and some remarks on the problem of regressive evolution of eye in Platanistoidea. Invest. Cetacea 11, 58-108 (1977).
-
(1977)
Invest. Cetacea
, vol.11
, pp. 58-108
-
-
Pillieri, G.1
-
24
-
-
84876864107
-
Rod monochromacy and the coevolution of cetacean retinal opsins
-
Meredith, R. W., Gatesy, J., Emerling, C. A., York, V. M. & Springer, M. S. Rod monochromacy and the coevolution of cetacean retinal opsins. PLoS Genet. 9, e1003432 (2013).
-
(2013)
PLoS Genet
, vol.9
-
-
Meredith, R.W.1
Gatesy, J.2
Emerling, C.A.3
York, M.V.4
Springer, M.S.5
-
25
-
-
0037424990
-
Genetic evidence for the ancestral loss of shortwavelength-sensitive cone pigments in mysticete and odontocete cetaceans
-
Levenson, D. H. & Dizon, A. Genetic evidence for the ancestral loss of shortwavelength-sensitive cone pigments in mysticete and odontocete cetaceans. Proc. Biol. Sci. 270, 673-679 (2003).
-
(2003)
Proc. Biol. Sci
, vol.270
, pp. 673-679
-
-
Levenson, D.H.1
Dizon, A.2
-
26
-
-
74549224446
-
Convergent sequence evolution between echolocating bats and dolphins
-
Liu, Y. et al. Convergent sequence evolution between echolocating bats and dolphins. Curr. Biol. 20, R53-R54 (2010).
-
(2010)
Curr. Biol
, vol.20
-
-
Liu, Y.1
-
27
-
-
78049285239
-
Cetaceans on a molecular fast track to ultrasonic hearing
-
Liu, Y., Rossiter, S. J., Han, X., Cotton, J. A. & Zhang, S. Cetaceans on a molecular fast track to ultrasonic hearing. Curr. Biol. 20, 1834-1839 (2010).
-
(2010)
Curr. Biol
, vol.20
, pp. 1834-1839
-
-
Liu, Y.1
Rossiter, S.J.2
Han, X.3
Cotton, J.A.4
Zhang, S.5
-
28
-
-
84864063616
-
Parallel evolution of auditory genes for echolocation in bats and toothed whales
-
Shen, Y. Y., Liang, L., Li, G. S., Murphy, R. W. & Zhang, Y. P. Parallel evolution of auditory genes for echolocation in bats and toothed whales. PLoS Genet. 8, e1002788 (2012).
-
(2012)
PLoS Genet
, vol.8
-
-
Shen, Y.Y.1
Liang, L.2
Li, G.S.3
Murphy, R.W.4
Zhang, Y.P.5
-
29
-
-
84859934504
-
Parallel signatures of sequence evolution among hearing genes in echolocating mammals: An emerging model of genetic convergence
-
Davies, K. T., Cotton, J. A., Kirwan, J. D., Teeling, E. C. & Rossiter, S. J. Parallel signatures of sequence evolution among hearing genes in echolocating mammals: an emerging model of genetic convergence. Heredity 108, 480-489 (2012).
-
(2012)
Heredity
, vol.108
, pp. 480-489
-
-
Davies, K.T.1
Cotton, J.A.2
Kirwan, J.D.3
Teeling, E.C.4
Rossiter, S.J.5
-
30
-
-
84859450268
-
Major taste loss in carnivorous mammals
-
Jiang, P. et al. Major taste loss in carnivorous mammals. Proc Natl Acad Sci USA 109, 4956-4961 (2012).
-
(2012)
Proc Natl Acad Sci USA
, vol.109
, pp. 4956-4961
-
-
Jiang, P.1
-
31
-
-
74949117308
-
Ecological adaptation determines functional mammalian olfactory subgenomes
-
Hayden, S. et al. Ecological adaptation determines functional mammalian olfactory subgenomes. Genome Res. 20, 1-9 (2010).
-
(2010)
Genome Res
, vol.20
, pp. 1-9
-
-
Hayden, S.1
-
32
-
-
56549101000
-
The vestigial olfactory receptor subgenome of odontocete whales: Phylogenetic congruence between gene-tree reconciliation and supermatrix methods
-
McGowen, M. R., Clark, C. & Gatesy, J. The vestigial olfactory receptor subgenome of odontocete whales: phylogenetic congruence between gene-tree reconciliation and supermatrix methods. Syst. Biol. 57, 574-590 (2008).
-
(2008)
Syst. Biol
, vol.57
, pp. 574-590
-
-
McGowen, M.R.1
Clark, C.2
Gatesy, J.3
-
33
-
-
84889247977
-
-
second ed. Perrin, W. F., Wursig, B. & Thewissen, J. G M. (Eds.) Elsevier
-
Oelschlager, H. H. A. & Oelschlager, J. S. Brain. In: Encyclopedia of Marine Mammals second ed. Perrin, W. F., Wursig, B. & Thewissen, J. G. M. (Eds.) (Elsevier, 2008).
-
(2008)
Brain. In: Encyclopedia of Marine Mammals
-
-
Oelschlager, H.H.A.1
Oelschlager, J.S.2
-
34
-
-
84655167913
-
Evolutionary changes of the importance of olfaction in cetaceans based on the olfactory marker protein gene
-
Kishida, T. & Thewissen, J. G. Evolutionary changes of the importance of olfaction in cetaceans based on the olfactory marker protein gene. Gene 492, 349-353 (2012).
-
(2012)
Gene
, vol.492
, pp. 349-353
-
-
Kishida, T.1
Thewissen, J.G.2
-
35
-
-
75149155568
-
The sequence and de novo assembly of the giant panda genome
-
Li, R. et al. The sequence and de novo assembly of the giant panda genome. Nature 463, 311-317 (2010).
-
(2010)
Nature
, vol.463
, pp. 311-317
-
-
Li, R.1
-
36
-
-
84871986062
-
Whole-genome sequencing of giant pandas provides insights into demographic history and local adaptation
-
Zhao, S. et al. Whole-genome sequencing of giant pandas provides insights into demographic history and local adaptation. Nat. Genet. 45, 67-71 (2013).
-
(2013)
Nat. Genet
, vol.45
, pp. 67-71
-
-
Zhao, S.1
-
37
-
-
80855165387
-
Genome sequencing reveals insights into physiology and longevity of the naked mole rat
-
Kim, E. B. et al. Genome sequencing reveals insights into physiology and longevity of the naked mole rat. Nature 479, 223-227 (2011).
-
(2011)
Nature
, vol.479
, pp. 223-227
-
-
Kim, E.B.1
-
38
-
-
79960914105
-
Inference of human population history from individual whole genome sequences
-
Li, H. & Durbin, R. Inference of human population history from individual whole genome sequences. Nature 475, 493-496 (2011).
-
(2011)
Nature
, vol.475
, pp. 493-496
-
-
Li, H.1
Durbin, R.2
-
39
-
-
0035957736
-
Trends, rhythms, and aberrations in global climate 65 Ma to present
-
Zachos, J., Pagani, M., Sloan, L., Thomas, E. & Billups., K. Trends, rhythms, and aberrations in global climate 65 Ma to present. Science 292, 686-693 (2001).
-
(2001)
Science
, vol.292
, pp. 686-693
-
-
Zachos, J.1
Pagani, M.2
Sloan, L.3
Thomas, E.4
Billups, K.5
-
40
-
-
0033559367
-
Molecular biomarker record of sea surface temperature and climatic change in the South China Sea during the last 140,000 years
-
Pelejero, C., Grimalt, J. O., Sarnthein, M., Wang, L. & Flores, J. A. Molecular biomarker record of sea surface temperature and climatic change in the South China Sea during the last 140,000 years. Mar. Geol. 156, 109-121 (1999).
-
(1999)
Mar. Geol
, vol.156
, pp. 109-121
-
-
Pelejero, C.1
Grimalt, J.O.2
Sarnthein, M.3
Wang, L.4
Flores, J.A.5
-
41
-
-
28144453198
-
The Phanerozoic record of global sea-level change
-
Miller, K. G. et al. The Phanerozoic record of global sea-level change. Science 310, 1293-1298 (2005).
-
(2005)
Science
, vol.310
, pp. 1293-1298
-
-
Miller, K.G.1
-
42
-
-
0000799466
-
Sedimentary processes in the Yangtze Delta since late Pleistocene
-
Li, C. X. Sedimentary processes in the Yangtze Delta since late Pleistocene. Coll Ocean Works 7, 116-126 (1984).
-
(1984)
Coll Ocean Works
, vol.7
, pp. 116-126
-
-
Li, C.X.1
-
43
-
-
75649124547
-
De novo assembly of human genomes with massively parallel short read sequencing
-
Li, R. et al. De novo assembly of human genomes with massively parallel short read sequencing. Genome Res. 20, 265-272 (2010).
-
(2010)
Genome Res
, vol.20
, pp. 265-272
-
-
Li, R.1
-
44
-
-
23844525077
-
Repbase Update, a database of eukaryotic repetitive elements
-
Jurka, J. et al. Repbase Update, a database of eukaryotic repetitive elements. Cytogenet. Genome Res. 110, 462-467 (2005).
-
(2005)
Cytogenet. Genome Res
, vol.110
, pp. 462-467
-
-
Jurka, J.1
-
45
-
-
0033555906
-
Tandem repeats finder: A program to analyze DNA sequences
-
Benson, G. Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Res. 27, 573-580 (1999).
-
(1999)
Nucleic Acids Res
, vol.27
, pp. 573-580
-
-
Benson, G.1
-
46
-
-
33846659488
-
Composition-based statistics and translated nucleotide searches: Improving the TBLASTN module of BLAST
-
Gertz, E. M., Yu, Y. K., Agarwala, R., Schaffer, A. A. & Altschul, S. F. Composition-based statistics and translated nucleotide searches: improving the TBLASTN module of BLAST. BMC Boil. 4, 41, 2006).
-
(2006)
BMC Boil
, vol.4
, pp. 41
-
-
Gertz, E.M.1
Yu, Y.K.2
Agarwala, R.3
Schaffer, A.A.4
Altschul, S.F.5
-
47
-
-
2442713832
-
-
Birney, E., Clamp, M. & Durbin, R. GeneWise and Genomewise. Genome Res. 14, 988-995 (2004).
-
(2004)
GeneWise and Genomewise. Genome Res
, vol.14
, pp. 988-995
-
-
Birney, E.1
Clamp, M.2
Durbin, R.3
-
48
-
-
33747830848
-
AUGUSTUS: Ab initio prediction of alternative transcripts
-
Stanke, M. et al. AUGUSTUS: ab initio prediction of alternative transcripts. Nucleic Acids Res. 34, W435-W439 (2006).
-
(2006)
Nucleic Acids Res
, vol.34
-
-
Stanke, M.1
-
49
-
-
0034065724
-
Ab initio gene finding in Drosophila genomic DNA
-
Salamov, A. A. & Solovyev, V. V. Ab initio gene finding in Drosophila genomic DNA. Genome Res. 10, 516-522 (2000).
-
(2000)
Genome Res
, vol.10
, pp. 516-522
-
-
Salamov, A.A.1
Solovyev, V.V.2
-
50
-
-
8844252293
-
Tigrscan and glimmerhmm: Two open source ab initio eukaryotic gene-finders
-
Majoros, W. H., Pertea, M. & Salzberg, S. L. TigrScan and GlimmerHMM: two open source ab initio eukaryotic gene-finders. Bioinformatics 20, 2878-2879 (2004).
-
(2004)
Bioinformatics
, vol.20
, pp. 2878-2879
-
-
Majoros, W.H.1
Pertea, M.2
Salzberg, S.L.3
-
51
-
-
34147180390
-
Creating a honey bee consensus gene set
-
Elsik, C. G. et al. Creating a honey bee consensus gene set. Genome Boil. 8, R13 (2007).
-
(2007)
Genome Boil
, vol.8
-
-
Elsik, C.G.1
-
52
-
-
0033982936
-
Kegg: Kyoto encyclopedia of genes and genomes
-
Kanehisa, M. & Goto, S. KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Res. 28, 27-30 (2000).
-
(2000)
Nucleic Acids Res
, vol.28
, pp. 27-30
-
-
Kanehisa, M.1
Goto, S.2
-
53
-
-
0033957834
-
The swiss-prot protein sequence database and its supplement trembl in 2000
-
Bairoch, A. & Apweiler, R. The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000. Nucleic Acids Res. 28, 45-48 (2000).
-
(2000)
Nucleic Acids Res
, vol.28
, pp. 45-48
-
-
Bairoch, A.1
Apweiler, R.2
-
54
-
-
0037255072
-
The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003
-
Boeckmann, B. et al. The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003. Nucleic Acids Res. 31, 365-370 (2003).
-
(2003)
Nucleic Acids Res
, vol.31
, pp. 365-370
-
-
Boeckmann, B.1
-
55
-
-
0034800374
-
Interproscan-an integration platform for the signature-recognition methods in InterPro
-
Zdobnov, E. M. & Apweiler, R. InterProScan-an integration platform for the signature-recognition methods in InterPro. Bioinformatics 17, 847-848 (2001).
-
(2001)
Bioinformatics
, vol.17
, pp. 847-848
-
-
Zdobnov, E.M.1
Apweiler, R.2
-
56
-
-
0034849408
-
Mrbayes: Bayesian inference of phylogenetic trees
-
Huelsenbeck, J. P. & Ronquist, F. MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics 17, 754-755 (2001).
-
(2001)
Bioinformatics
, vol.17
, pp. 754-755
-
-
Huelsenbeck, J.P.1
Ronquist, F.2
-
57
-
-
84864453108
-
Jmodeltest 2: More models, new heuristics and parallel computing
-
Darriba, D., Taboada, G. L., Doallo, R. & Posada, D. jModelTest 2: more models, new heuristics and parallel computing. Nat. methods 9, 772 (2012).
-
(2012)
Nat. Methods
, vol.9
, pp. 772
-
-
Darriba, D.1
Taboada, G.L.2
Doallo, R.3
Posada, D.4
-
58
-
-
0034044313
-
Estimating the rate of molecular evolution: Incorporating noncontemporaneous sequences into maximum likelihood phylogenies
-
Rambaut, A. Estimating the rate of molecular evolution: incorporating noncontemporaneous sequences into maximum likelihood phylogenies. Bioinformatics 16, 395-399 (2000).
-
(2000)
Bioinformatics
, vol.16
, pp. 395-399
-
-
Rambaut, A.1
-
59
-
-
27844439855
-
Evaluation of an improved branch-site likelihood method for detecting positive selection at the molecular level
-
Zhang, J., Nielsen, R. & Yang, Z. Evaluation of an improved branch-site likelihood method for detecting positive selection at the molecular level. Mol. Biol. Evol. 22, 2472-2479 (2005).
-
(2005)
Mol. Biol. Evol
, vol.22
, pp. 2472-2479
-
-
Zhang, J.1
Nielsen, R.2
Yang, Z.3
-
60
-
-
66449114324
-
SNP detection for massively parallel whole-genome resequencing
-
Li, R. et al. SNP detection for massively parallel whole-genome resequencing. Genome Res. 19, 1124-1132 (2009). China
-
(2009)
Genome Res
, vol.19
, pp. 1124-1132
-
-
Li, R.1
|