-
1
-
-
79953304894
-
Multiplexedshotgun genotyping for rapid and efficient genetic mapping
-
Andolfatto P., Davison D., Erezyilmaz D., Hu T.T., Mast J., Sunayama-Morita T., Stern D.L. 2011.Multiplexedshotgun genotyping for rapid and efficient genetic mapping. Genome Res. 21:610-617.
-
(2011)
Genome Res.
, vol.21
, pp. 610-617
-
-
Andolfatto, P.1
Davison, D.2
Erezyilmaz, D.3
Hu, T.T.4
Mast, J.5
Sunayama-Morita, T.6
Stern, D.L.7
-
2
-
-
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
-
3
-
-
84921911596
-
New insights intoNewWorld biogeography:Anintegrated viewfromthe phylogeny of blackbirds, cardinals, sparrows, tanagers, warblers, and allies
-
Barker F.K., Burns K.J., Klicka J., Lanyon S.M., Lovette I.J. 2015. New insights intoNewWorld biogeography:Anintegrated viewfromthe phylogeny of blackbirds, cardinals, sparrows, tanagers, warblers, and allies. Auk 132:333-348.
-
(2015)
Auk
, vol.132
, pp. 333-348
-
-
Barker, F.K.1
Burns, K.J.2
Klicka, J.3
Lanyon, S.M.4
Lovette, I.J.5
-
4
-
-
84901305512
-
BEAST 2: A software platform for Bayesian evolutionary analysis
-
Bouckaert R., Heled J., Kühnert D., Vaughan T., Wu C.H., Xie D., et al. 2014. BEAST 2: a software platform for Bayesian evolutionary analysis. PLoS Comput. Biol. 10:e1003537.
-
(2014)
PLoS Comput. Biol.
, vol.10
, pp. e1003537
-
-
Bouckaert, R.1
Heled, J.2
Kühnert, D.3
Vaughan, T.4
Wu, C.H.5
Xie, D.6
-
5
-
-
84864697376
-
Inferring species trees directly from biallelic genetic markers: Bypassing gene trees in a full coalescent analysis
-
Bryant D., Bouckaert R., Felsenstein J., Rosenberg N.A., Roy Choudhury A. 2012. Inferring species trees directly from biallelic genetic markers: bypassing gene trees in a full coalescent analysis. Mol. Biol. Evol. 29:1917-1932.
-
(2012)
Mol. Biol. Evol.
, vol.29
, pp. 1917-1932
-
-
Bryant, D.1
Bouckaert, R.2
Felsenstein, J.3
Rosenberg, N.A.4
Roy Choudhury, A.5
-
6
-
-
0031869599
-
Molecular phylogenetics of the genus Piranga: Implications for biogeography and the evolution of morphology and behavior
-
Burns K.J. 1998. Molecular phylogenetics of the genus Piranga: Implications for biogeography and the evolution of morphology and behavior. Auk 115:621-634.
-
(1998)
Auk
, vol.115
, pp. 621-634
-
-
Burns, K.J.1
-
7
-
-
84886286947
-
Is RAD-seq suitable for phylogenetic inference? An in silico assessment and optimization
-
Cariou M., Duret L., Charlat S. 2013. Is RAD-seq suitable for phylogenetic inference? An in silico assessment and optimization. Ecol. Evol. 3:846-852.
-
(2013)
Ecol. Evol.
, vol.3
, pp. 846-852
-
-
Cariou, M.1
Duret, L.2
Charlat, S.3
-
8
-
-
84884299558
-
Stacks: Building and genotyping loci de novo from short-read sequences
-
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: Genes, Genomes, Genetics. 1:171-182.
-
(2011)
G3: Genes, Genomes, Genetics.
, Issue.1
, pp. 171-182
-
-
Catchen, J.M.1
Amores, A.2
Hohenlohe, P.3
Cresko, W.4
Postlethwait, J.H.5
-
9
-
-
84917697072
-
Quartet inference from SNP data under the coalescent model
-
Chifman J., Kubatko L. 2014. Quartet inference from SNP data under the coalescent model. Bioinformatics 30:3317-3324.
-
(2014)
Bioinformatics
, vol.30
, pp. 3317-3324
-
-
Chifman, J.1
Kubatko, L.2
-
10
-
-
84899556177
-
Empirical assessment of RAD sequencing for interspecific phylogeny
-
Cruaud A., Gautier M., Galan M., Foucaud J., Sauné L., Genson G., Dubois E., Nidelet S., Deuve T., Rasplus J.Y. 2014. Empirical assessment of RAD sequencing for interspecific phylogeny. Mol. Biol. Evol. 31:1272-1274.
-
(2014)
Mol. Biol. Evol.
, vol.31
, pp. 1272-1274
-
-
Cruaud, A.1
Gautier, M.2
Galan, M.3
Foucaud, J.4
Sauné, L.5
Genson, G.6
Dubois, E.7
Nidelet, S.8
Deuve, T.9
Rasplus, J.Y.10
-
11
-
-
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
-
12
-
-
84879162598
-
A phylogenomic perspective on the radiation of ray-finned fishes based upon targeted sequencing of ultraconserved elements (UCEs)
-
Faircloth B.C., Sorenson L., Santini F., Alfaro M.E. 2013. A phylogenomic perspective on the radiation of ray-finned fishes based upon targeted sequencing of ultraconserved elements (UCEs). PLoS One 8:e65923.
-
(2013)
PLoS One
, vol.8
, pp. e65923
-
-
Faircloth, B.C.1
Sorenson, L.2
Santini, F.3
Alfaro, M.E.4
-
13
-
-
84960093575
-
PHYLUCE is a software package for the analysis of conserved genomic loci
-
btv646
-
Faircloth B.C. 2015 PHYLUCE is a software package for the analysis of conserved genomic loci. Bioinformatics. btv646.
-
(2015)
Bioinformatics
-
-
Faircloth, B.C.1
-
14
-
-
84926468506
-
Target enrichment of ultraconserved elements from arthropods provides a genomic perspective on relationships among Hymenoptera
-
Faircloth B.C., Branstetter M.G., White N.D., Brady S.G. 2014. Target enrichment of ultraconserved elements from arthropods provides a genomic perspective on relationships among Hymenoptera. Mol. Ecol. Res. 15:489-501.
-
(2014)
Mol. Ecol. Res.
, vol.15
, pp. 489-501
-
-
Faircloth, B.C.1
Branstetter, M.G.2
White, N.D.3
Brady, S.G.4
-
15
-
-
77953509166
-
Bayesian analysis of molecular variance in pyrosequences quantifies population genetic structure across the genome of Lycaeides butterflies
-
Gompert Z., Forister M.L., Fordyce J.A., Nice C.C., Williamson R.J., Buerkle C.A. 2010. Bayesian analysis of molecular variance in pyrosequences quantifies population genetic structure across the genome of Lycaeides butterflies. Mol. Ecol. 19:2455-2473.
-
(2010)
Mol. Ecol.
, vol.19
, pp. 2455-2473
-
-
Gompert, Z.1
Forister, M.L.2
Fordyce, J.A.3
Nice, C.C.4
Williamson, R.J.5
Buerkle, C.A.6
-
16
-
-
79960264362
-
Full-length transcriptome assembly from RNA-Seq data without a reference genome
-
Grabherr M.G., Haas B.J., Yassour M., Levin J.Z., Thompson D.A., Amit I., Adiconis X., Fan L., Raychowdhury R., Zeng Q., Chen Z., Mauceli E., Hacohen N., Gnirke A., Rhind N., di Palma F., Birren B.W., Nusbaum C., Lindblad-Toh K., Friedman N., Regev A. 2011. Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat. Biotechnol. 29:644-652.
-
(2011)
Nat. Biotechnol.
, vol.29
, pp. 644-652
-
-
Grabherr, M.G.1
Haas, B.J.2
Yassour, M.3
Levin, J.Z.4
Thompson, D.A.5
Amit, I.6
Adiconis, X.7
Fan, L.8
Raychowdhury, R.9
Zeng, Q.10
Chen, Z.11
Mauceli, E.12
Hacohen, N.13
Gnirke, A.14
Rhind, N.15
Di Palma, F.16
Birren, B.W.17
Nusbaum, C.18
Lindblad-Toh, K.19
Friedman, N.20
Regev, A.21
more..
-
17
-
-
77950806408
-
New algorithms and methods to estimate maximumlikelihood phylogenies: Assessing the performance of PhyML 3.0
-
Guindon S., Dufayard J.F., Lefort V., Anisimova M., Hordijk W., Gascuel O. 2010. New algorithms and methods to estimate maximumlikelihood phylogenies: Assessing the performance of PhyML 3.0. Syst. Biol. 59:307-321.
-
(2010)
Syst. Biol.
, vol.59
, pp. 307-321
-
-
Guindon, S.1
Dufayard, J.F.2
Lefort, V.3
Anisimova, M.4
Hordijk, W.5
Gascuel, O.6
-
19
-
-
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
-
20
-
-
84979291210
-
Highland Hepatic-tanager (Piranga lutea)
-
del Hoyo J., Elliott A., Sargatal J., Christie D.A. de Juana E., editors Barcelona: Lynx Edicions. Retrieved from on 9 January 2016
-
Hilty S. 2016. Highland Hepatic-tanager (Piranga lutea). In: del Hoyo J., Elliott A., Sargatal J., Christie D.A. de Juana E., editors. Handbook of the birds of theworld alive. Barcelona: Lynx Edicions. Retrieved from http://www.hbw.com/node/61823 on 9 January 2016.
-
(2016)
Handbook of the Birds of Theworld Alive
-
-
Hilty, S.1
-
21
-
-
84964904973
-
Avoiding missing data biases in phylogenomic inference: An empirical study in the landfowl (Aves: Galliformes)
-
Hosner P.A., Faircloth B.C., Glenn T.C., Braun E.L., Kimball R.T. 2016. Avoiding missing data biases in phylogenomic inference: an empirical study in the landfowl (Aves: Galliformes). Mol. Biol. Evol. doi: 10.1093/molbev/msv347.
-
(2016)
Mol. Biol. Evol.
-
-
Hosner, P.A.1
Faircloth, B.C.2
Glenn, T.C.3
Braun, E.L.4
Kimball, R.T.5
-
22
-
-
84875619226
-
MAFFT multiple sequence alignment software version 7: Improvements in performance and usability
-
Katoh K., Standley D.M. 2013. MAFFT multiple sequence alignment software version 7: Improvements in performance and usability. Mol. Biol. Evol. 30:772-780.
-
(2013)
Mol. Biol. Evol.
, vol.30
, pp. 772-780
-
-
Katoh, K.1
Standley, D.M.2
-
23
-
-
36148966908
-
Defining a monophyletic Cardinalini: A molecular perspective
-
Klicka J., Burns K., Spellman G.M. 2007. Defining a monophyletic Cardinalini: A molecular perspective. Mol. Phylogenet. Evol. 45:1014-1032.
-
(2007)
Mol. Phylogenet. Evol.
, vol.45
, pp. 1014-1032
-
-
Klicka, J.1
Burns, K.2
Spellman, G.M.3
-
24
-
-
84888140829
-
How low can you go? the effects of mutation rate on the accuracy of species-tree estimation
-
Lanier H.C., Huang H., Knowles L.L. 2014. How low can you go? The effects of mutation rate on the accuracy of species-tree estimation. Mol. Phylogenet. Evol. 70:112-119.
-
(2014)
Mol. Phylogenet. Evol.
, vol.70
, pp. 112-119
-
-
Lanier, H.C.1
Huang, H.2
Knowles, L.L.3
-
25
-
-
84936771254
-
Phylogenomics of phrynosomatid lizards: Conflicting signals from sequence capture versus restriction site associated DNA sequencing
-
Leaché A.D., Chavez A.S., Jones L.N., Grummer J.A., Gottscho A.D., Linkem C.W. 2015. Phylogenomics of phrynosomatid lizards: Conflicting signals from sequence capture versus restriction site associated DNA sequencing. Genome Biol. Evol. 7:706-719.
-
(2015)
Genome Biol. Evol.
, Issue.7
, pp. 706-719
-
-
Leaché, A.D.1
Chavez, A.S.2
Jones, L.N.3
Grummer, J.A.4
Gottscho, A.D.5
Linkem, C.W.6
-
26
-
-
68049099068
-
Coalescent methods for estimating phylogenetic trees
-
Liu L., Yu L., Kubatko L., Pearl D.K., Edwards S.V. 2009. Coalescent methods for estimating phylogenetic trees. Mol. Phylogenet. Evol. 53:320-328.
-
(2009)
Mol. Phylogenet. Evol.
, Issue.53
, pp. 320-328
-
-
Liu, L.1
Yu, L.2
Kubatko, L.3
Pearl, D.K.4
Edwards, S.V.5
-
27
-
-
77957686501
-
A maximum pseudo-likelihood approach for estimating species trees under the coalescent model
-
Liu L., Yu L., Edwards S.V. 2010. A maximum pseudo-likelihood approach for estimating species trees under the coalescent model. BMC Evol. Biol. 10:302.
-
(2010)
BMC Evol. Biol.
, Issue.10
, pp. 302
-
-
Liu, L.1
Yu, L.2
Edwards, S.V.3
-
28
-
-
80051975928
-
Estimating species trees from unrooted gene trees
-
Liu L., Yu L. 2011. Estimating species trees from unrooted gene trees. Syst. Biol. 60:661-667.
-
(2011)
Syst. Biol.
, vol.60
, pp. 661-667
-
-
Liu, L.1
Yu, L.2
-
30
-
-
84935061240
-
Isolation by environment in Whitebreasted Nuthatches (Sitta carolinensis) of the Madrean Archipelago sky islands: A landscape genomics approach
-
Manthey J.D., Moyle R.G. 2015. Isolation by environment in WhitebreastedNuthatches (Sitta carolinensis) of the Madrean Archipelago sky islands: A landscape genomics approach. Mol. Ecol. 24: 3628-3638.
-
(2015)
Mol. Ecol.
, Issue.24
, pp. 3628-3638
-
-
Manthey, J.D.1
Moyle, R.G.2
-
31
-
-
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
-
32
-
-
84873860010
-
A phylogeny of birds based on over 1,500 loci collected by target enrichment and high-throughput sequencing
-
McCormack J.E., Harvey M.G., Faircloth B.C., Crawford N.G., Glenn T.C., Brumfield R.T. 2013. A phylogeny of birds based on over 1,500 loci collected by target enrichment and high-throughput sequencing. PLoS One 8:e54848.
-
(2013)
PLoS One
, vol.8
, pp. e54848
-
-
McCormack, J.E.1
Harvey, M.G.2
Faircloth, B.C.3
Crawford, N.G.4
Glenn, T.C.5
Brumfield, R.T.6
-
33
-
-
84979914560
-
Sequence capture of ultraconserved elements from bird museum specimens
-
McCormack J.E., Tsai W.L., Faircloth B.C. 2016. Sequence capture of ultraconserved elements from bird museum specimens. Mol. Ecol. Res. doi: 10.1111/1755-0998.12466.
-
(2016)
Mol. Ecol. Res.
-
-
McCormack, J.E.1
Tsai, W.L.2
Faircloth, B.C.3
-
34
-
-
33846874137
-
Rapid and cost-effective polymorphism identification and genotyping using restriction site associated DNA (RAD) markers
-
Miller M.R., Dunham J.P., Amores A., Cresko W.A., Johnson E.A. 2007. Rapid and cost-effective polymorphism identification and genotyping using restriction site associated DNA (RAD) markers. Genome Res. 17:240-248.
-
(2007)
Genome Res.
, vol.17
, pp. 240-248
-
-
Miller, M.R.1
Dunham, J.P.2
Amores, A.3
Cresko, W.A.4
Johnson, E.A.5
-
35
-
-
84907019380
-
ASTRAL: Genome-scale coalescent-based species tree estimation
-
Mirarab S., Reaz R., Bayzid M.S., Zimmermann T., Swenson M.S., Warnow T. 2014. ASTRAL: Genome-scale coalescent-based species tree estimation. Bioinformatics 30:i541-i548.
-
(2014)
Bioinformatics
, vol.30
, pp. i541-i548
-
-
Mirarab, S.1
Reaz, R.2
Bayzid, M.S.3
Zimmermann, T.4
Swenson, M.S.5
Warnow, T.6
-
36
-
-
39149141072
-
AWTY (are we there yet?): A system for graphical exploration of MCMC convergence in Bayesian phylogenetics
-
Nylander J.A., Wilgenbusch J.C., Warren D.L., Swofford D.L. 2008. AWTY (are we there yet?): a system for graphical exploration of MCMC convergence in Bayesian phylogenetics. Bioinformatics 24:581-583.
-
(2008)
Bioinformatics
, vol.24
, pp. 581-583
-
-
Nylander, J.A.1
Wilgenbusch, J.C.2
Warren, D.L.3
Swofford, D.L.4
-
37
-
-
0034118493
-
Inference of population structure using multilocus genotype data
-
Pritchard J.K., Stephens M., Donnelly P. 2000. Inference of population structure using multilocus genotype data. Genetics 155:945-959.
-
(2000)
Genetics
, vol.155
, pp. 945-959
-
-
Pritchard, J.K.1
Stephens, M.2
Donnelly, P.3
-
40
-
-
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
-
41
-
-
50949129519
-
Calculating bootstrap probabilities of phylogeny using multilocus sequence data
-
Seo T.K. 2008. Calculating bootstrap probabilities of phylogeny using multilocus sequence data. Mol. Biol. Evol. 25:960-971.
-
(2008)
Mol. Biol. Evol.
, vol.25
, pp. 960-971
-
-
Seo, T.K.1
-
42
-
-
33846099516
-
Intraspecific genetic analysis of the summer tanager Piranga rubra: Implications for species limits and conservation
-
Shepherd T.M., Burns K.J. 2007. Intraspecific genetic analysis of the summer tanager Piranga rubra: Implications for species limits and conservation. J. Avian Biol. 38:13-27.
-
(2007)
J. Avian Biol.
, vol.38
, pp. 13-27
-
-
Shepherd, T.M.1
Burns, K.J.2
-
43
-
-
84891531569
-
Target capture and massively 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. 2013. Target capture and massively parallel sequencing of ultraconserved elements for comparative studies at shallow evolutionary time scales. Syst. Biol. 63:83-95.
-
(2013)
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
-
44
-
-
84899553363
-
RAxML version 8: A tool for phylogenetic analysis and post-analysis of large phylogenies
-
Stamatakis A. 2014. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 30:1312-1313.
-
(2014)
Bioinformatics
, vol.30
, pp. 1312-1313
-
-
Stamatakis, A.1
-
46
-
-
85049838200
-
Phylogenetics: Theory and practice of phylogenetic systematics
-
2nd ed.
-
Wiley E.O., Lieberman B.S. 1981. Phylogenetics: Theory and practice of phylogenetic systematics. In: Species and speciation. 2nd ed. p. 23-65.
-
(1981)
Species and Speciation
, pp. 23-65
-
-
Wiley, E.O.1
Lieberman, B.S.2
-
47
-
-
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
|