-
1
-
-
84872519378
-
Hybridization and speciation
-
Abbott RJ, et al. 2013. Hybridization and speciation. J Evol Biol. 26: 229-246.
-
(2013)
J Evol Biol.
, vol.26
, pp. 229-246
-
-
Abbott, R.J.1
-
2
-
-
0025183708
-
Basic local alignment search tool
-
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. 1990. Basic local alignment search tool. J Mol Biol. 215:403-410.
-
(1990)
J Mol Biol.
, vol.215
, pp. 403-410
-
-
Altschul, S.F.1
Gish, W.2
Miller, W.3
Myers, E.W.4
Lipman, D.J.5
-
3
-
-
54149092976
-
Multiple paleopolyploidizations during the evolution of the Compositae reveal parallel patterns of duplicate gene retention after millions of years
-
Barker MS, et al. 2008. Multiple paleopolyploidizations during the evolution of the Compositae reveal parallel patterns of duplicate gene retention after millions of years. Mol Biol Evol. 25:2445-2455.
-
(2008)
Mol Biol Evol.
, vol.25
, pp. 2445-2455
-
-
Barker, M.S.1
-
4
-
-
0001677717
-
Controlling the false discovery rate: A practical and powerful approach to multiple testing
-
Benjamini Y, Hochberg Y. 1995. Controlling the false discovery rate: a practical and powerful approach to multiple testing. J R Stat Soc Ser B. 57:289-300.
-
(1995)
J R Stat Soc ser B.
, vol.57
, pp. 289-300
-
-
Benjamini, Y.1
Hochberg, Y.2
-
5
-
-
84855335503
-
Geological evolution of a complex basaltic stratovolcano: Mount Etna, Italy
-
Branca S, Coltelli M, Groppelli G. 2011. Geological evolution of a complex basaltic stratovolcano: Mount Etna, Italy. Ital J Geosci (Boll Soc Geol It). 130:306-317.
-
(2011)
Ital J Geosci (Boll Soc Geol It).
, vol.130
, pp. 306-317
-
-
Branca, S.1
Coltelli, M.2
Groppelli, G.3
-
6
-
-
67650938423
-
Adaptation and selection in the Senecio (Asteraceae) hybrid zone on Mount Etna, Sicily
-
Brennan AC, Bridle JR,Wang A-L, Hiscock SJ, Abbott RJ. 2009. Adaptation and selection in the Senecio (Asteraceae) hybrid zone on Mount Etna, Sicily. New Phytol. 183:702-717.
-
(2009)
New Phytol.
, vol.183
, pp. 702-717
-
-
Brennan, A.C.1
Bridle Jrwang, A.-L.2
Hiscock, S.J.3
Abbott, R.J.4
-
7
-
-
74049108922
-
BLAST+: Architecture and applications
-
Camacho C, et al. 2009. BLAST+: architecture and applications. BMC Bioinformatics 10:421.
-
(2009)
BMC Bioinformatics
, vol.10
, pp. 421
-
-
Camacho, C.1
-
8
-
-
16244399208
-
Pollen competition among two species of Senecio (Asteraceae) that form a hybrid zone on Mt. Etna, Sicily
-
Chapman MA, Forbes DG, Abbott RJ. 2005. Pollen competition among two species of Senecio (Asteraceae) that form a hybrid zone on Mt. Etna, Sicily. Am J Bot. 92:730-735.
-
(2005)
Am J Bot.
, vol.92
, pp. 730-735
-
-
Chapman, M.A.1
Forbes, D.G.2
Abbott, R.J.3
-
9
-
-
0035543309
-
Molecular phylogeography, reticulation, and lineage sorting in Mediterranean Senecio sect Senecio (Asteraceae)
-
Comes HP, Abbott RJ. 2001. Molecular phylogeography, reticulation, and lineage sorting in Mediterranean Senecio sect. Senecio (Asteraceae). Evolution 55:1943-1962.
-
(2001)
Evolution
, vol.55
, pp. 1943-1962
-
-
Comes, H.P.1
Abbott, R.J.2
-
10
-
-
24644503098
-
Blast2GO: A universal tool for annotation, visualization and analysis in functional genomics research
-
Conesa A, et al. 2005. Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics 21: 3674-3676.
-
(2005)
Bioinformatics
, vol.21
, pp. 3674-3676
-
-
Conesa, A.1
-
11
-
-
19344363466
-
Preferential duplication of conserved proteins in eukaryotic genomes
-
Davis JC, Petrov DA. 2004. Preferential duplication of conserved proteins in eukaryotic genomes. PLoS Biol. 2:55.
-
(2004)
PLoS Biol.
, vol.2
, pp. 55
-
-
Davis, J.C.1
Petrov, D.A.2
-
12
-
-
84855317886
-
Ar-40/Ar-39 isotopic dating of Etna volcanic succession
-
De Beni E, Branca S, Coltelli M, Groppelli G, Wijbrans JR. 2011. Ar-40/Ar-39 isotopic dating of Etna volcanic succession. Ital J Geosci (Boll Soc Geol It). 130:292-305.
-
(2011)
Ital J Geosci (Boll Soc Geol It)
, vol.130
, pp. 292-305
-
-
De Beni, E.1
Branca, S.2
Coltelli, M.3
Groppelli, G.4
Wijbrans, J.R.5
-
13
-
-
80053918503
-
Do interactions between plant and soil biota change with elevation? A study on Fagus sylvatica
-
Defossez E, et al. 2011. Do interactions between plant and soil biota change with elevation? A study on Fagus sylvatica. Biol Lett. 7: 699-701.
-
(2011)
Biol Lett.
, vol.7
, pp. 699-701
-
-
Defossez, E.1
-
14
-
-
79954605059
-
The complete chloroplast genome of 17 individuals of pest species Jacobaea vulgaris: SKIPs, microsatellites and barcoding markers for population and phylogenetic studies
-
Doorduin L, et al. 2011. The complete chloroplast genome of 17 individuals of pest species Jacobaea vulgaris: SKIPs, microsatellites and barcoding markers for population and phylogenetic studies. DNA Res. 18: 93-105.
-
(2011)
DNA Res.
, vol.18
, pp. 93-105
-
-
Doorduin, L.1
-
15
-
-
26444621352
-
Why highly expressed proteins evolve slowly
-
Drummond DA, Bloom JD, Adami C, Wilke CO, Arnold FH. 2005. Why highly expressed proteins evolve slowly. Proc Natl Acad Sci U S A. 102: 14338-14343.
-
(2005)
Proc Natl Acad Sci U S A.
, vol.102
, pp. 14338-14343
-
-
Drummond, D.A.1
Bloom, J.D.2
Adami, C.3
Wilke, C.O.4
Arnold, F.H.5
-
16
-
-
79959300621
-
Applications of next generation sequencing in molecular ecology of non-model organisms
-
Ekblom R, Galindo J. 2011. Applications of next generation sequencing in molecular ecology of non-model organisms. Heredity 107:1-15.
-
(2011)
Heredity
, vol.107
, pp. 1-15
-
-
Ekblom, R.1
Galindo, J.2
-
17
-
-
0030888864
-
Correlated rates of synonymous site evolution across plant genomes
-
Eyre-Walker A, Gaut BS. 1997. Correlated rates of synonymous site evolution across plant genomes. Mol Biol Evol. 14:455-460.
-
(1997)
Mol Biol Evol.
, vol.14
, pp. 455-460
-
-
Eyre-Walker, A.1
Gaut, B.S.2
-
18
-
-
75949124473
-
Processing and population genetic analysis of multigenic datasets with ProSeq3 software
-
Filatov DA. 2009. Processing and population genetic analysis of multigenic datasets with ProSeq3 software. Bioinformatics 25:3189-3190.
-
(2009)
Bioinformatics
, vol.25
, pp. 3189-3190
-
-
Filatov, D.A.1
-
19
-
-
84863496231
-
Butterfly genome reveals promiscuous exchange of mimicry adaptations among species
-
Heliconius Genome Consortium
-
Heliconius Genome Consortium. 2012. Butterfly genome reveals promiscuous exchange of mimicry adaptations among species. Nature 487: 94-98.
-
(2012)
Nature
, vol.487
, pp. 94-98
-
-
-
20
-
-
30344467525
-
Recent, allopatric, homoploid hybrid speciation: The origin of Senecio squalidus (Asteraceae) in the British Isles from a hybrid zone on Mount Etna, Sicily
-
James JK, Abbott RJ. 2005. Recent, allopatric, homoploid hybrid speciation: the origin of Senecio squalidus (Asteraceae) in the British Isles from a hybrid zone on Mount Etna, Sicily. Evolution 59:2533-2547.
-
(2005)
Evolution
, vol.59
, pp. 2533-2547
-
-
James, J.K.1
Abbott, R.J.2
-
21
-
-
84859462157
-
The genomic basis of adaptive evolution in threespine sticklebacks
-
Jones FC, et al. 2012. The genomic basis of adaptive evolution in threespine sticklebacks. Nature 484:55-61.
-
(2012)
Nature
, vol.484
, pp. 55-61
-
-
Jones, F.C.1
-
22
-
-
8744268628
-
Duplicated genes evolve slower than singletons despite the initial rate increase
-
Jordan IK,Wolf YI, Koonin EV. 2004. Duplicated genes evolve slower than singletons despite the initial rate increase. BMC Evol Biol. 4:22.
-
(2004)
BMC Evol Biol.
, vol.4
, pp. 22
-
-
Jordan Ikwolf, Y.I.1
Koonin, E.V.2
-
23
-
-
80052313163
-
Are there laws of genome evolution?
-
Koonin EV. 2011. Are there laws of genome evolution? PLoS Comput Biol. 7:e1002173.
-
(2011)
PLoS Comput Biol.
, vol.7
-
-
Koonin, E.V.1
-
24
-
-
33748980210
-
Evolutionary systems biology: Links between gene evolution and function
-
Koonin EV, Wolf YI. 2006. Evolutionary systems biology: links between gene evolution and function. Curr Opin Biotech. 17:481-487.
-
(2006)
Curr Opin Biotech.
, vol.17
, pp. 481-487
-
-
Koonin, E.V.1
Wolf, Y.I.2
-
25
-
-
36248950165
-
The use of "altitude" in ecological research
-
Körner C. 2007. The use of "altitude" in ecological research. Trends Ecol Evol. 22:569-574.
-
(2007)
Trends Ecol Evol.
, vol.22
, pp. 569-574
-
-
Körner, C.1
-
26
-
-
63949083912
-
Amplification-free Illumina sequencing-library preparation facilitates improved mapping and assembly of (G plus C)-biased genomes
-
Kozarewa I, et al. 2009. Amplification-free Illumina sequencing-library preparation facilitates improved mapping and assembly of (G plus C)-biased genomes. Nat Methods. 6:291-295.
-
(2009)
Nat Methods.
, vol.6
, pp. 291-295
-
-
Kozarewa, I.1
-
27
-
-
68549104404
-
The sequence alignment/map format and SAMtools
-
Li H, et al. 2009. The Sequence Alignment/Map format and SAMtools. Bioinformatics 25:2078-2079.
-
(2009)
Bioinformatics
, vol.25
, pp. 2078-2079
-
-
Li, H.1
-
28
-
-
84863337847
-
Phylogenomic analysis of transcriptome data elucidates co-occurrence of a paleopolyploid event and the origin of bimodal karyotypes in Agavoideae (Asparagaceae)
-
McKain MR, et al. 2012. Phylogenomic analysis of transcriptome data elucidates co-occurrence of a paleopolyploid event and the origin of bimodal karyotypes in Agavoideae (Asparagaceae). Am J Bot. 99: 397-406.
-
(2012)
Am J Bot.
, vol.99
, pp. 397-406
-
-
McKain, M.R.1
-
29
-
-
14744269229
-
The evolutionary dynamics of plant duplicate genes
-
Moore RC, Purugganan MD. 2005. The evolutionary dynamics of plant duplicate genes. Curr Opin Plant Biol. 8:122-128.
-
(2005)
Curr Opin Plant Biol.
, vol.8
, pp. 122-128
-
-
Moore, R.C.1
Purugganan, M.D.2
-
30
-
-
84885058809
-
Recent ecological selection on regulatory divergence is shaping clinal variation in Senecio on Mount Etna
-
Advance Access published June 21, 2013, doi: 10.1111/evo.12157
-
Muir G, Osborne OG, Sarasa J, Hiscock SJ, Filatov DA. Forthcoming 2013. Recent ecological selection on regulatory divergence is shaping clinal variation in Senecio on Mount Etna. Evolution. Advance Access published June 21, 2013, doi: 10.1111/evo.12157.
-
(2013)
Evolution
-
-
Muir, G.1
Osborne, O.G.2
Sarasa, J.3
Hiscock, S.J.4
Filatov, D.A.5
-
31
-
-
0031972161
-
Likelihood models for detecting positively selected amino acid sites and applications to the HIV-1 envelope gene
-
Nielsen R, Yang ZH. 1998. Likelihood models for detecting positively selected amino acid sites and applications to the HIV-1 envelope gene. Genetics 148:929-936.
-
(1998)
Genetics
, vol.148
, pp. 929-936
-
-
Nielsen, R.1
Zh, Y.2
-
32
-
-
58749092473
-
Divergent selection and heterogeneous genomic divergence
-
Nosil P, Funk DJ, Ortiz-Barrientos D. 2009. Divergent selection and heterogeneous genomic divergence. Mol Ecol. 18:375-402.
-
(2009)
Mol Ecol.
, vol.18
, pp. 375-402
-
-
Nosil, P.1
Funk, D.J.2
Ortiz-Barrientos, D.3
-
34
-
-
43049100301
-
The value of sampling anomalous taxa in phylogenetic studies: Major clades of the Asteraceae revealed
-
Panero JL, Funk VA. 2008. The value of sampling anomalous taxa in phylogenetic studies: major clades of the Asteraceae revealed. Mol Phylogenet Evol. 47:757-782.
-
(2008)
Mol Phylogenet Evol.
, vol.47
, pp. 757-782
-
-
Panero, J.L.1
Funk, V.A.2
-
35
-
-
78149383270
-
Divergence with gene flow: Models and data
-
Pinho C, Hey J. 2010. Divergence with gene flow: models and data. Annu Rev Ecol Evol Syst. 41:215-230.
-
(2010)
Annu Rev Ecol Evol Syst.
, vol.41
, pp. 215-230
-
-
Pinho, C.1
Hey, J.2
-
36
-
-
62849096845
-
Harnessing genomics for evolutionary insights
-
Rokas A, Abbot P. 2009. Harnessing genomics for evolutionary insights. Trends Ecol Evol. 24:192-200.
-
(2009)
Trends Ecol Evol.
, vol.24
, pp. 192-200
-
-
Rokas, A.1
Abbot, P.2
-
37
-
-
84869188877
-
Exogenous selection shapes germination behaviour and seedling traits of populations at different altitudes in a Senecio hybrid zone
-
Ross RIC, Agren JA, Pannell JR. 2012. Exogenous selection shapes germination behaviour and seedling traits of populations at different altitudes in a Senecio hybrid zone. Ann Bot. 110:1439-1447.
-
(2012)
Ann Bot.
, vol.110
, pp. 1439-1447
-
-
Ross, R.I.C.1
Agren, J.A.2
Pannell, J.R.3
-
38
-
-
33644907774
-
The effect of multifunctionality on the rate of evolution in yeast
-
SalathéM, Ackermann M, Bonhoeffer S. 2006. The effect of multifunctionality on the rate of evolution in yeast. Mol Biol Evol. 23:721-722.
-
(2006)
Mol Biol Evol.
, vol.23
, pp. 721-722
-
-
Salathé, M.1
Ackermann, M.2
Bonhoeffer, S.3
-
39
-
-
1642375725
-
Hybridization and adaptive radiation
-
Seehausen O. 2004. Hybridization and adaptive radiation. Trends Ecol Evol. 19:198-207.
-
(2004)
Trends Ecol Evol.
, vol.19
, pp. 198-207
-
-
Seehausen, O.1
-
40
-
-
84859114543
-
Genomic determinants of protein evolution and polymorphism in Arabidopsis
-
Slotte T, et al. 2011. Genomic determinants of protein evolution and polymorphism in Arabidopsis. Genome Biol Evol. 3:1210-1219.
-
(2011)
Genome Biol Evol.
, vol.3
, pp. 1210-1219
-
-
Slotte, T.1
-
41
-
-
47749146161
-
Molecular demographic history of the annual sunflowers Helianthus annuus and H. Petiolaris-large effective population sizes and rates of long-term gene flow
-
Strasburg JL, Rieseberg LH. 2008. Molecular demographic history of the annual sunflowers Helianthus annuus and H. petiolaris-large effective population sizes and rates of long-term gene flow. Evolution 62:1936-1950.
-
(2008)
Evolution
, vol.62
, pp. 1936-1950
-
-
Strasburg, J.L.1
Rieseberg, L.H.2
-
42
-
-
78649294100
-
Optimization of de novo transcriptome assembly from next-generation sequencing data
-
Surget-Groba Y, Montoya-Burgos JI. 2010. Optimization of de novo transcriptome assembly from next-generation sequencing data. Genome Res. 20:1432-1440.
-
(2010)
Genome Res.
, vol.20
, pp. 1432-1440
-
-
Surget-Groba, Y.1
Montoya-Burgos, J.I.2
-
43
-
-
38549144806
-
The Arabidopsis Information Resource (TAIR): Gene structure and function annotation
-
Swarbreck D, et al. 2008. The Arabidopsis Information Resource (TAIR): gene structure and function annotation. Nucleic Acids Res. 36: 1009-1014.
-
(2008)
Nucleic Acids Res.
, vol.36
, pp. 1009-1014
-
-
Swarbreck, D.1
-
44
-
-
0027453388
-
Simple methods for testing the molecular evolutionary clock hypothesis
-
Tajima F. 1993. Simple methods for testing the molecular evolutionary clock hypothesis. Genetics 135:599-607.
-
(1993)
Genetics
, vol.135
, pp. 599-607
-
-
Tajima, F.1
-
45
-
-
79957613599
-
MEGA5: Molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods
-
Tamura K, et al. 2011. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol. 28:2731-2739.
-
(2011)
Mol Biol Evol.
, vol.28
, pp. 2731-2739
-
-
Tamura, K.1
-
46
-
-
0023462635
-
Rates of nucleotide substitution vary greatly among plant mitochondrial, chloroplast, and nuclear DNAs
-
Wolfe KH, Li WH, Sharp PM. 1987. Rates of nucleotide substitution vary greatly among plant mitochondrial, chloroplast, and nuclear DNAs. Proc Natl Acad Sci U S A. 84:9054-9058.
-
(1987)
Proc Natl Acad Sci U S A.
, vol.84
, pp. 9054-9058
-
-
Wolfe, K.H.1
Li, W.H.2
Sharp, P.M.3
-
47
-
-
0035677674
-
The genic view of the process of speciation
-
Wu CI. 2001. The genic view of the process of speciation. J Evol Biol. 14: 851-865.
-
(2001)
J Evol Biol.
, vol.14
, pp. 851-865
-
-
Wu, C.I.1
-
48
-
-
0036961518
-
Likelihood and Bayes estimation of ancestral population sizes in hominoids using data from multiple loci
-
Yang ZH. 2002. Likelihood and Bayes estimation of ancestral population sizes in hominoids using data from multiple loci. Genetics 162: 1811-1823.
-
(2002)
Genetics
, vol.162
, pp. 1811-1823
-
-
Zh, Y.1
-
49
-
-
34547803197
-
PAML 4: Phylogenetic analysis by maximum likelihood
-
Yang ZH. 2007. PAML 4: phylogenetic analysis by maximum likelihood. Mol Biol Evol. 24:1586-1591.
-
(2007)
Mol Biol Evol.
, vol.24
, pp. 1586-1591
-
-
Zh, Y.1
-
50
-
-
77957905707
-
A likelihood ratio test of speciation with gene flow using genomic sequence data
-
Yang ZH. 2010. A likelihood ratio test of speciation with gene flow using genomic sequence data. Genome Biol Evol. 2:200-211.
-
(2010)
Genome Biol Evol.
, vol.2
, pp. 200-211
-
-
Yang, Z.H.1
-
51
-
-
79961064486
-
Factors that contribute to variation in evolutionary rate among Arabidopsis genes
-
Yang L, Gaut BS. 2011. Factors that contribute to variation in evolutionary rate among Arabidopsis genes. Mol Biol Evol. 28: 2359-2369.
-
(2011)
Mol Biol Evol.
, vol.28
, pp. 2359-2369
-
-
Yang, L.1
Gaut, B.S.2
-
52
-
-
0036270185
-
Codon-substitution models for detecting molecular adaptation at individual sites along specific lineages
-
Yang ZH, Nielsen R. 2002. Codon-substitution models for detecting molecular adaptation at individual sites along specific lineages. Mol Biol Evol. 19:908-917.
-
(2002)
Mol Biol Evol.
, vol.19
, pp. 908-917
-
-
Yang, Z.H.1
Nielsen, R.2
-
53
-
-
0034097381
-
Codon-substitution models for heterogeneous selection pressure at amino acid sites
-
Yang ZH, Nielsen R, Goldman N, Pedersen AMK. 2000. Codon-substitution models for heterogeneous selection pressure at amino acid sites. Genetics 155:431-449.
-
(2000)
Genetics
, vol.155
, pp. 431-449
-
-
Yang, Z.H.1
Nielsen, R.2
Goldman, N.3
Pedersen, A.M.K.4
-
54
-
-
16344378246
-
Bayes empirical Bayes inference of amino acid sites under positive selection
-
Yang ZH, Wong WSW, Nielsen R. 2005. Bayes empirical Bayes inference of amino acid sites under positive selection. Mol Biol Evol. 22: 1107-1118.
-
(2005)
Mol Biol Evol.
, vol.22
, pp. 1107-1118
-
-
Yang, Z.H.1
Wong, W.S.W.2
Nielsen, R.3
-
55
-
-
27844439855
-
Evaluation of an improved branch-site likelihood method for detecting positive selection at the molecular level
-
Zhang J, Nielsen R, Yang ZH. 2005. Evaluation of an improved branch-site likelihood method for detecting positive selection at the molecular level. Mol Biol Evol. 22:2472-2479.
-
(2005)
Mol Biol Evol.
, vol.22
, pp. 2472-2479
-
-
Zhang, J.1
Nielsen, R.2
Zh, Y.3
|