-
1
-
-
84878449439
-
RADseq underestimates diversity and introduces genealogical biases due to nonrandom haplotype sampling
-
Arnold B., Corbett-Detig R.B., Hartl D., Bomblies K. 2013. RADseq underestimates diversity and introduces genealogical biases due to nonrandom haplotype sampling. Mol. Ecol. 22:3179-3190.
-
(2013)
Mol. Ecol
, vol.22
, pp. 3179-3190
-
-
Arnold, B.1
Corbett-Detig, R.B.2
Hartl, D.3
Bomblies, K.4
-
2
-
-
54449098752
-
Rapid SNP discovery and genetic mapping using sequenced RAD markers
-
Baird N.A., Etter P.D., Atwood T.S., Currey M.C., Shiver A.L., Lewis Z.A., Selker E.U., Cresko W.A., Johnson E.A. 2008. Rapid SNP discovery and genetic mapping using sequenced RAD markers. PLoS One 3:e3376.
-
(2008)
PLoS One
, vol.3
, pp. e3376
-
-
Baird, N.A.1
Etter, P.D.2
Atwood, T.S.3
Currey, M.C.4
Shiver, A.L.5
Lewis, Z.A.6
Selker, E.U.7
Cresko, W.A.8
Johnson, E.A.9
-
3
-
-
0036931408
-
The (Super)tree of life: Procedures, problems, and prospects
-
Bininda-Emonds O.R.P., Gittleman J.L., Steel M.A. 2002. The (Super)tree of life: procedures, problems, and prospects. Annu. Rev. Ecol. Syst. 33:265-289.
-
(2002)
Annu. Rev. Ecol. Syst
, vol.33
, pp. 265-289
-
-
Bininda-Emonds, O.R.P.1
Gittleman, J.L.2
Steel, M.A.3
-
4
-
-
84878464979
-
Population genomics based on low coverage sequencing: How low should we go?
-
Buerkle C.A., Gompert Z. 2013. Population genomics based on low coverage sequencing: how low should we go? Mol. Ecol. 22:3028-3035.
-
(2013)
Mol Ecol
, vol.22
, pp. 3028-3035
-
-
Buerkle, C.A.1
Gompert, Z.2
-
5
-
-
84884299558
-
-
Catchen J.M., Amores A., Hohenlohe P., Cresko W., Postlethwait J.H. 2011. Stacks: building and genotyping loci de novo from short-read sequences. G3 1:171-182.
-
(2011)
Stacks: Building and Genotyping Loci de Novo from Short-read Sequences
, vol.3
, Issue.1
, pp. 171-182
-
-
Catchen, J.M.1
Amores, A.2
Hohenlohe, P.3
Cresko, W.4
Postlethwait, J.H.5
-
6
-
-
0029096506
-
Sampling properties of DNA sequence data in phylogenetic analysis
-
Cummings M.P., Otto S.P., Wakeley J. 1995. Sampling properties of DNA sequence data in phylogenetic analysis. Mol. Biol. Evol. 12:814-822.
-
(1995)
Mol. Biol. Evol
, vol.12
, pp. 814-822
-
-
Cummings, M.P.1
Otto, S.P.2
Wakeley, J.3
-
7
-
-
84881616406
-
Inferring phylogeny and introgression using RADseq data: An example from flowering plants (Pedicularis: Orobanchaceae
-
Eaton D.A.R., Ree R.H. 2013. Inferring phylogeny and introgression using RADseq data: An example from flowering plants (Pedicularis: Orobanchaceae). Syst. Biol. 62:689-706.
-
(2013)
Syst. Biol
, vol.62
, pp. 689-706
-
-
Eaton, D.A.R.1
Ree, R.H.2
-
8
-
-
77958007159
-
Resolving postglacial phylogeography using high-Throughput sequencing
-
Emerson K.J., Merz C.R., Catchen J.M., Hohenlohe P.A., Cresko W.A., Bradshaw W.E., Holzapfel C.M. 2010. Resolving postglacial phylogeography using high-Throughput sequencing. Proc. Natl Acad. Sci. U. S. A. 107:16196-16200.
-
(2010)
Proc. Natl Acad. Sci. U. S. A
, vol.107
, pp. 16196-16200
-
-
Emerson, K.J.1
Merz, C.R.2
Catchen, J.M.3
Hohenlohe, P.A.4
Cresko, W.A.5
Bradshaw, W.E.6
Holzapfel, C.M.7
-
9
-
-
84859548731
-
Ultraconserved elements anchor thousands of genetic markers spanning multiple evolutionary timescales
-
Faircloth B.C., McCormack J.E., Crawford N.G., Harvey M.G., Brumfield R.T., Glenn T.C. 2012. Ultraconserved elements anchor thousands of genetic markers spanning multiple evolutionary timescales. Syst. Biol. 61:717-726.
-
(2012)
Syst. Biol
, vol.61
, pp. 717-726
-
-
Faircloth, B.C.1
McCormack, J.E.2
Crawford, N.G.3
Harvey, M.G.4
Brumfield, R.T.5
Glenn, T.C.6
-
10
-
-
33748204460
-
Molecular phylogeny of the Arctoidea (Carnivora): Effect of missing data on supertree and supermatrix analyses of multiple gene data sets
-
Fulton T.L., Strobeck C. 2006. Molecular phylogeny of the Arctoidea (Carnivora): effect of missing data on supertree and supermatrix analyses of multiple gene data sets. Mol. Phylogenet. Evol. 41:165-181.
-
(2006)
Mol. Phylogenet. Evol
, vol.41
, pp. 165-181
-
-
Fulton, T.L.1
Strobeck, C.2
-
11
-
-
77958059433
-
Sources of error for species-Tree estimation: Impact of mutational and coalescent effects on acuracy and implications for choosing among different methods
-
Huang H., He Q., Kubatko L.S., Knowles L.L. 2010. Sources of error for species-Tree estimation: impact of mutational and coalescent effects on acuracy and implications for choosing among different methods. Syst. Biol. 59:573-583.
-
(2010)
Syst. Biol
, vol.59
, pp. 573-583
-
-
Huang, H.1
He, Q.2
Kubatko, L.S.3
Knowles, L.L.4
-
12
-
-
77249086587
-
Bayesian inference of species trees from multilocus data
-
Heled J., DrummondA.J. 2010. Bayesian inference of species trees from multilocus data. Mol. Biol. Evol. 27:570-580.
-
(2010)
Mol. Biol. Evol
, vol.27
, pp. 570-580
-
-
Heled, J.1
Drummond, A.J.2
-
13
-
-
79959221246
-
PRGMATIC: An efficient pipeline for collating genome-enriched second-generation sequencing data using a provisional-reference genome
-
Hird S.M., Brumfield R.T., Carstens B.C. 2011. PRGMATIC: An efficient pipeline for collating genome-enriched second-generation sequencing data using a provisional-reference genome. Mol. Ecol. Resour. 11:743-748.
-
(2011)
Mol. Ecol. Resour
, vol.11
, pp. 743-748
-
-
Hird, S.M.1
Brumfield, R.T.2
Carstens, B.C.3
-
14
-
-
84884589326
-
Effects of missing data on species tree estimation under the coalescent
-
Hovmöller R., Knowles L.L., Kubatko L.S. 2013. Effects of missing data on species tree estimation under the coalescent. Mol. Phylogenet. Evol. 69:1057-1062.
-
(2013)
Mol. Phylogenet. Evol
, vol.69
, pp. 1057-1062
-
-
Hovmöller, R.1
Knowles, L.L.2
Kubatko, L.S.3
-
15
-
-
0036184745
-
Generating samples under a wright-fisher neutral model of genetic variation
-
Hudson R.R. 2002. Generating samples under a wright-fisher neutral model of genetic variation. Bioinformatics 18:337-338.
-
(2002)
Bioinformatics
, vol.18
, pp. 337-338
-
-
Hudson, R.R.1
-
16
-
-
84866147332
-
Full modeling versus summarizing gene-Tree uncertainty:method choice and species-Tree accuracy
-
Knowles L.L., Lanier H., Klimov P.B., He Q. 2012. Full modeling versus summarizing gene-Tree uncertainty:method choice and species-Tree accuracy. Mol. Phylogenet. Evol. 65:501-509.
-
(2012)
Mol. Phylogenet. Evol
, vol.65
, pp. 501-509
-
-
Knowles, L.L.1
Lanier, H.2
Klimov, P.B.3
He, Q.4
-
17
-
-
62349130698
-
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
-
Langmead B., Trapnell C., Pop M., Salzberg S.L. 2009. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 10:R25.
-
(2009)
Genome Biol
, vol.10
, pp. R25
-
-
Langmead, B.1
Trapnell, C.2
Pop, M.3
Salzberg, S.L.4
-
18
-
-
84865266483
-
Anchored hybrid enrichment for massively high-Throughput phylogenomics
-
Lemmon A.R., Emme S.A., Lemmon E.M. 2012. Anchored hybrid enrichment for massively high-Throughput phylogenomics. Syst. Biol. 61:727-744.
-
(2012)
Syst. Biol
, vol.61
, pp. 727-744
-
-
Lemmon, A.R.1
Emme, S.A.2
Lemmon, E.M.3
-
19
-
-
0031504952
-
Gene trees in species trees
-
Maddison W.P. 1997. Gene trees in species trees. Syst. Biol. 46:523-536.
-
(1997)
Syst. Biol
, vol.46
, pp. 523-536
-
-
Maddison, W.P.1
-
20
-
-
33644606488
-
Inferring phylogeny despite incomplete lineage sorting
-
Maddison W.P., Knowles L.L. 2006. Inferring phylogeny despite incomplete lineage sorting. Syst. Biol. 55:21-30.
-
(2006)
Syst. Biol
, vol.55
, pp. 21-30
-
-
Maddison, W.P.1
Knowles, L.L.2
-
22
-
-
83655201166
-
Next-generation sequencing reveals phylogeographic structure and a species tree for recent bird divergences
-
McCormack J.E., Maley J.M., Hird S.M., Derryberry E.P., Graves G.R., Brumfield R.T. 2012. Next-generation sequencing reveals phylogeographic structure and a species tree for recent bird divergences. Mol. Phylogenet. Evol. 62:397-406.
-
(2012)
Mol. Phylogenet. Evol
, vol.62
, pp. 397-406
-
-
McCormack, J.E.1
Maley, J.M.2
Hird, S.M.3
Derryberry, E.P.4
Graves, G.R.5
Brumfield, R.T.6
-
24
-
-
0023822631
-
Relationships between gene trees and species trees
-
Pamilo P., Ne M. 1988. Relationships between gene trees and species trees. Mol. Biol. Evol. 5:568-583.
-
(1988)
Mol. Biol. Evol
, vol.5
, pp. 568-583
-
-
Pamilo, P.1
Ne, M.2
-
25
-
-
0030928378
-
Seq-gen: An application for the monte carlo simulation of DNA sequence evolution along phylogenetic trees
-
Rambaut A., Grassly N.C. 1997. Seq-gen: An application for the monte carlo simulation of DNA sequence evolution along phylogenetic trees. Comput. Appl. Biosci. 13:235-238.
-
(1997)
Comput. Appl. Biosci
, vol.13
, pp. 235-238
-
-
Rambaut, A.1
Grassly, N.C.2
-
26
-
-
0030889065
-
Differences inDNA methylation patterns are detectable during the dimorphic transition of fungi by amplification of restriction polymorphisms
-
Reyna-Lopez G.E., Simpson J., Ruiz-Herrera J. 1997. Differences inDNA methylation patterns are detectable during the dimorphic transition of fungi by amplification of restriction polymorphisms. Mol. Gen. Genet. 253:703-710.
-
(1997)
Mol. Gen. Genet
, vol.253
, pp. 703-710
-
-
Reyna-Lopez, G.E.1
Simpson, J.2
Ruiz-Herrera, J.3
-
27
-
-
0019424782
-
Comparison of phylogenetic trees
-
Robinson D.F., Foulds L.R. 1981. Comparison of phylogenetic trees. Math. Biosci. 53:131-147.
-
(1981)
Math. Biosci
, vol.53
, pp. 131-147
-
-
Robinson, D.F.1
Foulds, L.R.2
-
28
-
-
84871842306
-
Impact of missing data on phylogenies inferred from empirical phylogenomic data sets
-
Roure B., Baurain D., Philippe H. 2013. Impact of missing data on phylogenies inferred from empirical phylogenomic data sets. Mol. Biol. Evol. 30:197-214.
-
(2013)
Mol. Biol. Evol
, vol.30
, pp. 197-214
-
-
Roure, B.1
Baurain, D.2
Philippe, H.3
-
29
-
-
84859516080
-
Inferring phylogenies from RAD sequence data
-
Rubin B.E., Ree R.H., Moreau C.S. 2012. Inferring phylogenies from RAD sequence data. PLoS One 7:e33394.
-
(2012)
PLoS One
, vol.7
, pp. e33394
-
-
Rubin, B.E.1
Ree, R.H.2
Moreau, C.S.3
-
30
-
-
84891531569
-
Target capture and massivel parallel sequencing of ultraconserved elements for comparative studies at shallow evolutionary time scales
-
Smith B.T., Harvey M.G., Faircloth B.C., Glenn T.C., Brumfield R.T. 2014. Target capture and massivel parallel sequencing of ultraconserved elements for comparative studies at shallow evolutionary time scales. Syst. Biol. 63:83-95.
-
(2014)
Syst. Biol
, vol.63
, pp. 83-95
-
-
Smith, B.T.1
Harvey, M.G.2
Faircloth, B.C.3
Glenn, T.C.4
Brumfield, R.T.5
-
31
-
-
50249100595
-
A rapid bootstrap algorithm for the RAxML web servers
-
Stamatakis A., Hoover P., Rougemont J. 2008. A rapid bootstrap algorithm for the RAxML web servers. Syst. Biol. 57: 758-771.
-
(2008)
Syst. Biol
, vol.57
, pp. 758-771
-
-
Stamatakis, A.1
Hoover, P.2
Rougemont, J.3
-
32
-
-
0024713112
-
Gene genealogy in 3 related populations-consistency probability between gene and population trees
-
Takahata N. 1989. Gene genealogy in 3 related populations-consistency probability between gene and population trees. Genetics 122:957-966.
-
(1989)
Genetics
, vol.122
, pp. 957-966
-
-
Takahata, N.1
-
33
-
-
3242795999
-
An assessment of accuracy error, and conflict with support values from genome-scale phylogenetic data 21 1534 2004
-
Taylor D.J., Piel W.H. 2004. An assessment of accuracy, error, and conflict with support values from genome-scale phylogenetic data (Vol. 21, p. 1534, 2004). Mol. Biol. Evol. 21:1812-1812.
-
(2004)
Mol. Biol. Evol
, vol.21
, pp. 1812
-
-
Taylor, D.J.1
Piel, W.H.2
-
34
-
-
84872480881
-
Genome-wide RAD sequence data provide unprecedented resolution of species boundaries and relationships in the Lake Victoria cichlid adaptive radiation
-
Wagner C.E., Keller I., Wittwer S., Selz O.M., Mwaiko S., Greuter L., Sivasundar A., Seehausen O. 2013. Genome-wide RAD sequence data provide unprecedented resolution of species boundaries and relationships in the Lake Victoria cichlid adaptive radiation. Mol. Ecol. 22:787-798.
-
(2013)
Mol. Ecol
, vol.22
, pp. 787-798
-
-
Wagner, C.E.1
Keller, I.2
Wittwer, S.3
Selz, O.M.4
Mwaiko, S.5
Greuter, L.6
Sivasundar, A.7
Seehausen, O.8
-
35
-
-
84881616937
-
Identification of SNP markers for inferring phylogeny in temperate bamboos (Poaceae: Bambusoideae) usingRADsequencing
-
Wang X.Q., Zhao L., Eaton D.A., Li D.Z., Guo Z.H. 2013. Identification of SNP markers for inferring phylogeny in temperate bamboos (Poaceae: Bambusoideae) usingRADsequencing. Mol. Ecol.Resour. 13:938-945.
-
(2013)
Mol. Ecol.Resour
, vol.13
, pp. 938-945
-
-
Wang, X.Q.1
Zhao, L.2
Eaton, D.A.3
Li, D.Z.4
Guo, Z.H.5
-
36
-
-
0042905752
-
Missing data, incomplete taxa, and phylogenetic accuracy
-
Wiens J.J. 2003. Missing data, incomplete taxa, and phylogenetic accuracy. Syst. Biol. 52:528-538.
-
(2003)
Syst. Biol
, vol.52
, pp. 528-538
-
-
Wiens, J.J.1
-
37
-
-
31344471014
-
Missing data and the design of phylogenetic analyses
-
Wiens J.J. 2006. Missing data and the design of phylogenetic analyses. J. Biomed. Inform. 39:34-42.
-
(2006)
J. Biomed. Inform
, vol.39
, pp. 34-42
-
-
Wiens, J.J.1
-
38
-
-
0029498439
-
Coping with missing entries in phylogenetic inference using parsimony
-
Wilkinson M. 1995. Coping with missing entries in phylogenetic inference using parsimony. Syst. Biol. 44:501-514.
-
(1995)
Syst. Biol
, vol.44
, pp. 501-514
-
-
Wilkinson, M.1
-
39
-
-
80955136714
-
Algorithms for MDC-based multilocus phylogeny inference: Beyond rooted binary gene trees on single alleles
-
Yu Y., Warnow T., Nakhleh L. 2011. Algorithms for MDC-based multilocus phylogeny inference: beyond rooted binary gene trees on single alleles. J. Comput. Biol. 18:1543-1559.
-
(2011)
J. Comput. Biol
, vol.18
, pp. 1543-1559
-
-
Yu, Y.1
Warnow, T.2
Nakhleh, L.3
-
40
-
-
84865263760
-
Deep phylogeographic structure and environmental differentiation in the carnivorous plant Sarracenia alata
-
Zellmer A.J., Hanes M.M., Hird S.M., Carstens B.C. 2012. Deep phylogeographic structure and environmental differentiation in the carnivorous plant Sarracenia alata. Syst. Biol. 61:763-777.
-
(2012)
Syst. Biol
, vol.61
, pp. 763-777
-
-
Zellmer, A.J.1
Hanes, M.M.2
Hird, S.M.3
Carstens, B.C.4
|