-
1
-
-
0842322955
-
Species-level paraphyly and polyphyly: Frequency, causes, and consequences, with insights from animal mitochondrial DNA
-
Funk DJ, Omland KE (2003) Species-level paraphyly and polyphyly: frequency, causes, and consequences, with insights from animal mitochondrial DNA. Annu Rev Ecol Evol Syst 34:397-423.
-
(2003)
Annu Rev Ecol Evol Syst
, vol.34
, pp. 397-423
-
-
Funk, D.J.1
Omland, K.E.2
-
2
-
-
58249100073
-
Is a new and general theory of molecular systematics emerging?
-
Edwards SV (2009) Is a new and general theory of molecular systematics emerging? Evolution 63:1-19.
-
(2009)
Evolution
, vol.63
, pp. 1-19
-
-
Edwards, S.V.1
-
3
-
-
84888626247
-
High-throughput genomic data in systematics and phylogenetics
-
Lemmon EM, Lemmon AR (2013) High-throughput genomic data in systematics and phylogenetics. Annu Rev Ecol Evol Syst 44:99-121.
-
(2013)
Annu Rev Ecol Evol Syst
, vol.44
, pp. 99-121
-
-
Lemmon, E.M.1
Lemmon, A.R.2
-
4
-
-
84865248393
-
The promises and pitfalls of next-generation sequencing data in phylogeography
-
Carstens B, Lemmon AR, Lemmon EM (2012) The promises and pitfalls of next-generation sequencing data in phylogeography. Syst Biol 61:713-715.
-
(2012)
Syst Biol
, vol.61
, pp. 713-715
-
-
Carstens, B.1
Lemmon, A.R.2
Lemmon, E.M.3
-
5
-
-
33847302458
-
Inconsistency of phylogenetic estimates from concatenated data under coalescence
-
Kubatko LS, Degnan JH (2007) Inconsistency of phylogenetic estimates from concatenated data under coalescence. Syst Biol 56:17-24.
-
(2007)
Syst Biol
, vol.56
, pp. 17-24
-
-
Kubatko, L.S.1
Degnan, J.H.2
-
6
-
-
34347256397
-
High-resolution species trees without concatenation
-
Edwards SV, Liu L, Pearl DK (2007) High-resolution species trees without concatenation. Proc Natl Acad Sci USA 104:5936-5941.
-
(2007)
Proc Natl Acad Sci USA
, vol.104
, pp. 5936-5941
-
-
Edwards, S.V.1
Liu, L.2
Pearl, D.K.3
-
7
-
-
84861373817
-
Concatenation and concordance in the reconstruction of mouse lemur phylogeny: An empirical demonstration of the effect of allele sampling in phylogenetics
-
Weisrock DW, Smith SD, Chan LM, Biebouw K, Kappeler PM, et al.. (2012) Concatenation and concordance in the reconstruction of mouse lemur phylogeny: an empirical demonstration of the effect of allele sampling in phylogenetics. Mol Biol Evol 29:1615-1630.
-
(2012)
Mol Biol Evol
, vol.29
, pp. 1615-1630
-
-
Weisrock, D.W.1
Smith, S.D.2
Chan, L.M.3
Biebouw, K.4
Kappeler, P.M.5
-
8
-
-
84897908606
-
Ignoring heterozygous sites biases phylogenomic estimates of divergence times: Implications for the evolutionary history of Microtus voles
-
Lischer H e L, Excoffier L, Heckel G (2014) Ignoring heterozygous sites biases phylogenomic estimates of divergence times: implications for the evolutionary history of Microtus voles. Mol Biol Evol 31:817-831.
-
(2014)
Mol Biol Evol
, vol.31
, pp. 817-831
-
-
Lischer, H.E.L.1
Excoffier, L.2
Heckel, G.3
-
9
-
-
33846839390
-
Bayesian estimation of concordance among gene trees
-
Ané C, Larget B, Baum DA, Smith SD, Rokas A (2007) Bayesian estimation of concordance among gene trees. Mol Biol Evol 24:412-426.
-
(2007)
Mol Biol Evol
, vol.24
, pp. 412-426
-
-
Ané, C.1
Larget, B.2
Baum, D.A.3
Smith, S.D.4
Rokas, A.5
-
10
-
-
33846839295
-
Concordance trees, concordance factors, and the exploration of reticulate genealogy
-
Baum DA (2007) Concordance trees, concordance factors, and the exploration of reticulate genealogy. Taxon 56:417-426.
-
(2007)
Taxon
, vol.56
, pp. 417-426
-
-
Baum, D.A.1
-
11
-
-
65649131928
-
Gene tree discordance, phylogenetic inference and the multispecies coalescent
-
Degnan JH, Rosenberg NA (2009) Gene tree discordance, phylogenetic inference and the multispecies coalescent. Trends Ecol Evol 24:332-340.
-
(2009)
Trends Ecol Evol
, vol.24
, pp. 332-340
-
-
Degnan, J.H.1
Rosenberg, N.A.2
-
12
-
-
84888140829
-
How low can you go? The effects of mutation rate on the accuracy of species-tree estimation
-
Lanier HC, Huang H, Knowles LL (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
-
13
-
-
79951561454
-
The accuracy of species tree estimation under simulation: A comparison of methods
-
Leaché AD, Rannala B (2011) The accuracy of species tree estimation under simulation: a comparison of methods. Syst Biol 60:126-137.
-
(2011)
Syst Biol
, vol.60
, pp. 126-137
-
-
Leaché, A.D.1
Rannala, B.2
-
14
-
-
84887319003
-
The influence of gene flow on species tree estimation: A simulation study
-
Leaché AD, Harris RB, Rannala B, Yang Z (2014) The influence of gene flow on species tree estimation: a simulation study. Syst Biol 63:17-30.
-
(2014)
Syst Biol
, vol.63
, pp. 17-30
-
-
Leaché, A.D.1
Harris, R.B.2
Rannala, B.3
Yang, Z.4
-
15
-
-
84904966117
-
Bears in a Forest of Gene Trees: Phylogenetic Inference Is Complicated by Incomplete Lineage Sorting and Gene Flow
-
Kutschera VE, Bidon T, Hailer F, Rodi JL, Fain SR, et al.. (2014) Bears in a Forest of Gene Trees: Phylogenetic Inference Is Complicated by Incomplete Lineage Sorting and Gene Flow. Mol Biol Evol 31:2004-2017.
-
(2014)
Mol Biol Evol
, vol.31
, pp. 2004-2017
-
-
Kutschera, V.E.1
Bidon, T.2
Hailer, F.3
Rodi, J.L.4
Fain, S.R.5
-
16
-
-
40549084970
-
The phylogeny of crested newts (Triturus cristatus superspecies): Nuclear and mitochondrial genetic characters suggest a hard polytomy, in line with the paleogeography of the centre of origin
-
Arntzen JW, Espregueira Themudo G, Wielstra B (2007) The phylogeny of crested newts (Triturus cristatus superspecies): nuclear and mitochondrial genetic characters suggest a hard polytomy, in line with the paleogeography of the centre of origin. Contrib Zool 76:261-278.
-
(2007)
Contrib Zool
, vol.76
, pp. 261-278
-
-
Arntzen, J.W.1
Espregueira Themudo, G.2
Wielstra, B.3
-
17
-
-
77954722261
-
Where to draw the line? A nuclear genetic perspective on proposed range boundaries of the crested newts Triturus karelinii and T. Arntzeni
-
Arntzen JW, Wielstra B (2010) Where to draw the line? A nuclear genetic perspective on proposed range boundaries of the crested newts Triturus karelinii and T. arntzeni. Amphibia-Reptilia 31:311-322.
-
(2010)
Amphibia-reptilia
, vol.31
, pp. 311-322
-
-
Arntzen, J.W.1
Wielstra, B.2
-
18
-
-
53249153509
-
Triturus cristatus Superspecies - Kammolch-Artenkreis (Triturus cristatus (Laurenti, 1768) - Nördlicher Kammolch, Triturus carnifex (Laurenti, 1768) - Italienischer Kammolch, Triturus dobrogicus (Kiritzescu, 1903) - Donau-Kammolch, Triturus karelinii (Strauch, 1870) - Südlicher Kammolch)
-
Grossenbacher K, Thiesmeier B, editors, Wiebelsheim: Aula-Verlag
-
Arntzen JW (2003) Triturus cristatus Superspecies - Kammolch-Artenkreis (Triturus cristatus (Laurenti, 1768) - Nördlicher Kammolch, Triturus carnifex (Laurenti, 1768) - Italienischer Kammolch, Triturus dobrogicus (Kiritzescu, 1903) - Donau-Kammolch, Triturus karelinii (Strauch, 1870) - Südlicher Kammolch). In: Grossenbacher K, Thiesmeier B, editors. Handbuch der Reptilien und Amphibien Europas Schwanzlurche IIA. Wiebelsheim: Aula-Verlag. pp. 421-514.
-
(2003)
Handbuch der Reptilien und Amphibien Europas Schwanzlurche IIA
, pp. 421-514
-
-
Arntzen, J.W.1
-
19
-
-
79958285525
-
Unraveling the rapid radiation of crested newts (Triturus cristatus superspecies) using complete mitogenomic sequences
-
Wielstra B, Arntzen JW (2011) Unraveling the rapid radiation of crested newts (Triturus cristatus superspecies) using complete mitogenomic sequences. BMC Evol Biol 11:162.
-
(2011)
BMC Evol Biol
, vol.11
, pp. 162
-
-
Wielstra, B.1
Arntzen, J.W.2
-
20
-
-
84873718216
-
A multimarker phylogeography of crested newts (Triturus cristatus superspecies) reveals cryptic species
-
Wielstra B, Baird AB, Arntzen JW (2013) A multimarker phylogeography of crested newts (Triturus cristatus superspecies) reveals cryptic species. Mol Phylogenet Evol 67:167-175.
-
(2013)
Mol Phylogenet Evol
, vol.67
, pp. 167-175
-
-
Wielstra, B.1
Baird, A.B.2
Arntzen, J.W.3
-
21
-
-
65649096520
-
Multiple nuclear and mitochondrial genes resolve the branching order of a rapid radiation of crested newts (Triturus, Salamandridae)
-
Espregueira Themudo G, Wielstra B, Arntzen JW (2009) Multiple nuclear and mitochondrial genes resolve the branching order of a rapid radiation of crested newts (Triturus, Salamandridae). Mol Phylogenet Evol 52:321-328.
-
(2009)
Mol Phylogenet Evol
, vol.52
, pp. 321-328
-
-
Espregueira Themudo, G.1
Wielstra, B.2
Arntzen, J.W.3
-
22
-
-
1642285792
-
The incomplete natural history of mitochondria
-
Ballard J W O, Whitlock MC (2004) The incomplete natural history of mitochondria. Mol Ecol 13:729-744.
-
(2004)
Mol Ecol
, vol.13
, pp. 729-744
-
-
Ballard, J.W.O.1
Whitlock, M.C.2
-
23
-
-
77958059433
-
Sources of error inherent in species-tree estimation: Impact of mutational and coalescent effects on accuracy and implications for choosing among different methods
-
Huang H, He Q, Kubatko LS, Knowles LL (2010) Sources of error inherent in species-tree estimation: impact of mutational and coalescent effects on accuracy 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
-
24
-
-
84875063013
-
Tracing glacial refugia of Triturus newts based on mitochondrial DNA phylogeography and species distribution modeling
-
Wielstra B, Crnobrnja-Isailović J, Litvinchuk SN, Reijnen BT, Skidmore AK, et al.. (2013) Tracing glacial refugia of Triturus newts based on mitochondrial DNA phylogeography and species distribution modeling. Front Zool 10:13.
-
(2013)
Front Zool
, vol.10
, pp. 13
-
-
Wielstra, B.1
Crnobrnja-Isailović, J.2
Litvinchuk, S.N.3
Reijnen, B.T.4
Skidmore, A.K.5
-
25
-
-
0032805966
-
Marking and tissue sampling effects on body condition and survival in the newt Triturus cristatus
-
Arntzen JW, Smithson A, Oldham RS (1999) Marking and tissue sampling effects on body condition and survival in the newt Triturus cristatus. Journal of Herpetology 33:567-576.
-
(1999)
Journal of Herpetology
, vol.33
, pp. 567-576
-
-
Arntzen, J.W.1
Smithson, A.2
Oldham, R.S.3
-
26
-
-
84879774396
-
A revised taxonomy of crested newts in the Triturus karelinii group (Amphibia: Caudata: Salamandridae), with the description of a new species
-
Wielstra B, Litvinchuk SN, Naumov B, Tzankov N, Arntzen JW (2013) A revised taxonomy of crested newts in the Triturus karelinii group (Amphibia: Caudata: Salamandridae), with the description of a new species. Zootaxa 3682:441-453.
-
(2013)
Zootaxa
, vol.3682
, pp. 441-453
-
-
Wielstra, B.1
Litvinchuk, S.N.2
Naumov, B.3
Tzankov, N.4
Arntzen, J.W.5
-
27
-
-
84899701187
-
Exploring the effect of asymmetric mitochondrial DNA introgression on estimating niche divergence in morphologically cryptic species
-
Wielstra B, Arntzen JW (2014) Exploring the effect of asymmetric mitochondrial DNA introgression on estimating niche divergence in morphologically cryptic species. PLoS ONE 9:e95504.
-
(2014)
PLoS ONE
, vol.9
, pp. e95504
-
-
Wielstra, B.1
Arntzen, J.W.2
-
28
-
-
84905974425
-
Parallel tagged amplicon sequencing of transcriptome-based genetic markers for Triturus newts with the Ion Torrent next-generation sequencing platform
-
Wielstra B, Duijm E, Lagler P, Lammers Y, Meilink W R M, et al.. (2014) Parallel tagged amplicon sequencing of transcriptome-based genetic markers for Triturus newts with the Ion Torrent next-generation sequencing platform. Mol Ecol Resour 14:1080-1089.
-
(2014)
Mol Ecol Resour
, vol.14
, pp. 1080-1089
-
-
Wielstra, B.1
Duijm, E.2
Lagler, P.3
Lammers, Y.4
Meilink, W.R.M.5
-
29
-
-
84897654018
-
Alternative reproductive tactics and sexbiased gene expression: The study of the bulb mite transcriptome
-
Stuglik MT, Babik W, Radwan J (2014) Alternative reproductive tactics and sexbiased gene expression: the study of the bulb mite transcriptome. Ecology and Evolution 4:623-632.
-
(2014)
Ecology and Evolution
, vol.4
, pp. 623-632
-
-
Stuglik, M.T.1
Babik, W.2
Radwan, J.3
-
30
-
-
84894283962
-
Development, validation and high throughput analysis of sequence markers in non-model species
-
Zieliń Ski P, Stuglik MT, Dudek K, Konczal M, Babik W (2014) Development, validation and high throughput analysis of sequence markers in non-model species. Mol Ecol Resour 14:352-360.
-
(2014)
Mol Ecol Resour
, vol.14
, pp. 352-360
-
-
Ski, P.Z.1
Stuglik, M.T.2
Dudek, K.3
Konczal, M.4
Babik, W.5
-
31
-
-
46049108350
-
BatchPrimer3: A high throughput web application for PCR and sequencing primer design
-
You F, Huo N, Gu Y, Luo M-c, Ma Y, et al.. (2008) BatchPrimer3: a high throughput web application for PCR and sequencing primer design. BMC Bioinformatics 9:253.
-
(2008)
BMC Bioinformatics
, vol.9
, pp. 253
-
-
You, F.1
Huo, N.2
Gu, Y.3
Luo, M.-C.4
Ma, Y.5
-
33
-
-
67449163699
-
The effect of ambiguous data on phylogenetic estimates obtained by maximum likelihood and Bayesian inference
-
Lemmon AR, Brown JM, Stanger-Hall K, Lemmon EM (2009) The effect of ambiguous data on phylogenetic estimates obtained by maximum likelihood and Bayesian inference. Syst Biol 58:130-145.
-
(2009)
Syst Biol
, vol.58
, pp. 130-145
-
-
Lemmon, A.R.1
Brown, J.M.2
Stanger-Hall, K.3
Lemmon, E.M.4
-
34
-
-
65649117685
-
DnaSP v5: A software for comprehensive analysis of DNA polymorphism data
-
Librado P, Rozas J (2009) DnaSP v5: a software for comprehensive analysis of DNA polymorphism data. Bioinformatics 25:1451-1452.
-
(2009)
Bioinformatics
, vol.25
, pp. 1451-1452
-
-
Librado, P.1
Rozas, J.2
-
35
-
-
62349132559
-
Enhanced Bayesian modelling in BAPS software for learning genetic structures of populations
-
Corander J, Marttinen P, Siren J, Tang J (2008) Enhanced Bayesian modelling in BAPS software for learning genetic structures of populations. BMC Bioinformatics 9:539.
-
(2008)
BMC Bioinformatics
, vol.9
, pp. 539
-
-
Corander, J.1
Marttinen, P.2
Siren, J.3
Tang, J.4
-
36
-
-
1342331102
-
DISTRUCT: A program for the graphical display of population structure
-
Rosenberg NA (2004) DISTRUCT: a program for the graphical display of population structure. Mol Ecol Notes 4:137-138.
-
(2004)
Mol Ecol Notes
, vol.4
, pp. 137-138
-
-
Rosenberg, N.A.1
-
37
-
-
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.. (2012) MrBayes 3.2: Efficient Bayesian phylogenetic inference and model choice across a large model space. Syst Biol.
-
(2012)
Syst Biol
-
-
Ronquist, F.1
Teslenko, M.2
Van Der Mark, P.3
Ayres, D.L.4
Darling, A.5
-
39
-
-
78149256307
-
BUCKy: Gene tree/species tree reconciliation with Bayesian concordance analysis
-
Larget BR, Kotha SK, Dewey CN, Ané C (2010) BUCKy: gene tree/species tree reconciliation with Bayesian concordance analysis. Bioinformatics 26:2910-2911.
-
(2010)
Bioinformatics
, vol.26
, pp. 2910-2911
-
-
Larget, B.R.1
Kotha, S.K.2
Dewey, C.N.3
Ané, C.4
-
40
-
-
77249086587
-
Bayesian inference of species trees from multilocus data
-
Heled J, Drummond AJ (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
-
42
-
-
52149099649
-
Multilocus phylogenetics of a rapid radiation in the genus Thomomys (Rodentia: Geomyidae)
-
Belfiore NM, Liu L, Moritz C (2008) Multilocus phylogenetics of a rapid radiation in the genus Thomomys (Rodentia: Geomyidae). Syst Biol 57:294-310.
-
(2008)
Syst Biol
, vol.57
, pp. 294-310
-
-
Belfiore, N.M.1
Liu, L.2
Moritz, C.3
-
43
-
-
85027956222
-
The modality of nine Triturus newt hybrid zones, assessed with nuclear, mitochondrial and morphological data
-
Arntzen JW, Wielstra B, Wallis GP (2014) The modality of nine Triturus newt hybrid zones, assessed with nuclear, mitochondrial and morphological data. Biol J Linn Soc 113:604-622.
-
(2014)
Biol J Linn Soc
, vol.113
, pp. 604-622
-
-
Arntzen, J.W.1
Wielstra, B.2
Wallis, G.P.3
-
44
-
-
84865514429
-
Postglacial species displacement in Triturus newts deduced from asymmetrically introgressed mitochondrial DNA and ecological niche models
-
Wielstra B, Arntzen JW (2012) Postglacial species displacement in Triturus newts deduced from asymmetrically introgressed mitochondrial DNA and ecological niche models. BMC Evol Biol 12:161.
-
(2012)
BMC Evol Biol
, vol.12
, pp. 161
-
-
Wielstra, B.1
Arntzen, J.W.2
-
45
-
-
0026311951
-
Restricted gene flow in a moving hybrid zone of the newts Triturus cristatus and T. Marmoratus in western France
-
Arntzen JW, Wallis GP (1991) Restricted gene flow in a moving hybrid zone of the newts Triturus cristatus and T. marmoratus in western France. Evolution 45:805-826.
-
(1991)
Evolution
, vol.45
, pp. 805-826
-
-
Arntzen, J.W.1
Wallis, G.P.2
-
46
-
-
45249121769
-
Environmental parameters that determine species geographical range limits as a matter of time and space
-
Arntzen JW, Espregueira Themudo G (2008) Environmental parameters that determine species geographical range limits as a matter of time and space. J Biogeogr 35:1177-1186.
-
(2008)
J Biogeogr
, vol.35
, pp. 1177-1186
-
-
Arntzen, J.W.1
Espregueira Themudo, G.2
-
47
-
-
78149386517
-
Phylogenetic insights on adaptive radiation
-
Glor RE (2010) Phylogenetic insights on adaptive radiation. Annu Rev Ecol Evol Syst 41:251-270.
-
(2010)
Annu Rev Ecol Evol Syst
, vol.41
, pp. 251-270
-
-
Glor, R.E.1
-
49
-
-
84879418928
-
Species tree reconstruction of a poorly resolved clade of salamanders (Ambystomatidae) using multiple nuclear loci
-
Williams JS, Niedzwiecki JH, Weisrock DW (2013) Species tree reconstruction of a poorly resolved clade of salamanders (Ambystomatidae) using multiple nuclear loci. Mol Phylogenet Evol 68:671-682.
-
(2013)
Mol Phylogenet Evol
, vol.68
, pp. 671-682
-
-
Williams, J.S.1
Niedzwiecki, J.H.2
Weisrock, D.W.3
-
50
-
-
56549103832
-
Does gene flow destroy phylogenetic signal? The performance of three methods for estimating species phylogenies in the presence of gene flow
-
Eckert AJ, Carstens BC (2008) Does gene flow destroy phylogenetic signal? The performance of three methods for estimating species phylogenies in the presence of gene flow. Mol Phylogenet Evol 49:832-842.
-
(2008)
Mol Phylogenet Evol
, vol.49
, pp. 832-842
-
-
Eckert, A.J.1
Carstens, B.C.2
|