Peer-reviewed Publications

PDFs can be found at ResearchGate and Academia.edu

Publications by Topic

DNA Alignment / Nucleotide Homology

  • Morrison DA, Morgan MJ, Kelchner SA (2015) Molecular homology and multiple sequence alignment: an analysis of concepts and practice. LAS Johnson Invited Review, Australian Systematic Botany 28:46-62  doi.org/10.1071/SB15001

  • Morgan MJ, Kelchner SA (2010) Inference of molecular homology and sequence alignment by direct optimization. Molecular Phylogenetics and Evolution 56: 305-31 doi.org/10.1016/j.ympev.2010.03.032

  • Kelchner SA (2009) Phylogenetic models and model selection for noncoding DNA. Plant Systematics and Evolution 282: 109-126 doi.org/10.1007/s00606-008-0071-6

  • Kelchner SA (2002) Group II introns as phylogenetic tools: structure, function, and evolutionary constraints. American Journal of Botany 89: 1651-1669  doi.org/10.3732/ajb.89.10.1651

  • Kelchner SA (2000) The evolution of non-coding chloroplast DNA and its application in plant systematics. Annals of the Missouri Botanical Garden 87: 482-498  doi.org/10.2307/2666142

  • Kelchner SA, Clark LG (1997) Molecular evolution and phylogenetic utility of the rpl16 intron in Chusquea and the Bambusoideae (Poaceae). Molecular Phylogenetics and Evolution 8: 385-397  doi.org/10.1006/mpev.1997.0432

  • Kelchner SA, Wendel JF (1996) Hairpins create minute inversions in non-coding regions of chloroplast DNA. Current Genetics 30: 259-262  doi.org/10.1007/s002940050130

Phylogenetic Models

Networks and Evolution

  • Bapteste E, van Iersel L, Janke A, Kelchner S, Kelk S, McInerney JO, Morrison DA, Nahkleh L, Steel M, Stougie L, Whitfield J (2013) Networks: expanding evolutionary thinking. Trends in Genetics 29: 439-441  doi.org/10.1016/j.tig.2013.05.007

  • Fisher AE, Clark LG, Kelchner SA (2014) Molecular phylogeny estimation of the bamboo genus Chusquea (Poaceae: Bambusoideae: Bambuseae) and description of two new bamboo subgenera. Systematic Botany 39:829–844  doi.org/10.1600/036364414X681554

  • Kelchner SA, Bamboo Phylogeny Group (2013) Higher level phylogenetic relationships within the bamboos (Poaceae: Bambusoideae) based on five plastid markers. Molecular Phylogenetics and Evolution 67: 404-413  doi.org/10.1016/j.ympev.2013.02.005

  • Fisher AE, Triplett J, Ho C-S, Schiller AD, Oltrogge KA, Schroeder ES, Kelchner SA, Clark LG (2009) Paraphyly in the bamboo subtribe Chusqueinae (Poaceae: Bambusoideae) and a revised infrageneric classification for Chusquea. Systematic Botany 34: 673-683  doi.org/10.1600/036364409790139790

  • Kelchner SA (2003) Phylogenetic structure, evolution, and biogeography of Myoporaceae. PhD Thesis, The Australian National University. 336 pp  [now classified as Myoporeae]

Group II Intron Structure and Evolution

  • Simon DM, Kelchner SA, Zimmerly S (2009) A broad-scale phylogenetic analysis of group II intron RNAs and intron-encoded reverse transcriptases. Molecular Biology and Evolution 26: 2795-2808  doi.org/10.1093/molbev/msp193

  • Duffy AM, Kelchner SA, Wolf PG (2009) Conservation of selection on matK following an ancient loss of its flanking intron. Gene 438: 17-25  doi.org/10.1016/j.gene.2009.02.006

  • Watts CD, Fisher AE, Shrum CD, Newbold WL, Hansen S, Liu C, Kelchner SA (2008) The D4 Set: primers that target highly variable intron loops in plant chloroplast genomes. Molecular Ecology Resources 8: 1344-1347  doi.org/10.1111/j.1755-0998.2008.02229.x

  • Kelchner SA (2002) Group II introns as phylogenetic tools: structure, function, and evolutionary constraints. American Journal of Botany 89: 1651-1669  doi.org/10.3732/ajb.89.10.1651

  • Kelchner SA, Clark LG (1997) Molecular evolution and phylogenetic utility of the rpl16 intron in Chusquea and the Bambusoideae (Poaceae). Molecular Phylogenetics and Evolution 8: 385-397  doi.org/10.1006/mpev.1997.0432

  • Kelchner SA, Wendel JF (1996) Hairpins create minute inversions in non-coding regions of chloroplast DNA. Current Genetics 30: 259-262  doi.org/10.1007/s002940050130

Bamboos

  • Canavan S, Richardson DM, Le Roux JJ, Kelchner SA, Wilson JRU (2021) The status of alien bamboos in South Africa. South African Journal of Botany 138: 33-40  doi.org/10.1016/j.sajb.2020.11.027

  • Fisher AE, Clark LG, Kelchner SA (2014) Molecular phylogeny estimation of the bamboo genus Chusquea (Poaceae: Bambusoideae: Bambuseae) and description of two new bamboo subgenera. Systematic Botany 39:829–844  doi.org/10.1600/036364414X681554

  • Kelchner SA, Bamboo Phylogeny Group (2013) Higher level phylogenetic relationships within the bamboos (Poaceae: Bambusoideae) based on five plastid markers. Molecular Phylogenetics and Evolution 67: 404-413  doi.org/10.1016/j.ympev.2013.02.005

  • Bamboo Phylogeny Group (2012b) An updated tribal and subtribal classification for the Bambusoideae (Poaceae). Bamboo Science & Culture 24: 1-10

  • Bamboo Phylogeny Group (2012a) An updated tribal and subtribal classification for the Bambusoideae (Poaceae). Pp. 3-27 in Gielis, J. and G. Potters (eds.), Proceedings of the 9th World Bamboo Congress, 10-12 April 2012, Antwerp, Belgium

  • Fisher AE, Triplett J, Ho C-S, Schiller AD, Oltrogge KA, Schroeder ES, Kelchner SA, Clark LG (2009) Paraphyly in the bamboo subtribe Chusqueinae (Poaceae: Bambusoideae) and a revised infrageneric classification for Chusquea. Systematic Botany 34: 673-683  doi.org/10.1600/036364409790139790

  • Bamboo Phylogeny Group (2006) The Bamboo Phylogeny Project. Bamboo Science & Culture 27: 11-14

  • Kelchner SA, Clark LG (1997) Molecular evolution and phylogenetic utility of the rpl16 intron in Chusquea and the Bambusoideae (Poaceae). Molecular Phylogenetics and Evolution 8: 385-397  doi.org/10.1006/mpev.1997.0432

Plant Genomics

  • Burke SV, Wysocki WP, Zuloaga F, Craine J, Pires JC, Edger P, Mayfield-Jones D, Clark LG, Kelchner SA, Duvall MR (2016) Evolutionary relationships in panicoid grasses based on plastome phylogenomics (Panicoideae; Poaceae). BMC Plant Biology 16:140  doi.org/10.1186/s12870-016-0823-3

  • Duvall MR, Coumbus JT, Fisher AE, Ingram AL, Wysocki WP, Burke SV, Clark LG, Kelchner SA (2016) Phylogenomics and plastome evolution of the chloridoid grasses (Chloridoideae; Poaceae). International Journal of Plant Sciences 177:235-246  doi.org/10.1086/684526

  • Cotton JL, Wysocki WP, Clark LG, Kelchner SA, Pires JC, Edger PP, Mayfield DR, Duvall MR (2015) Resolving deep relationships of PACMAD grasses; a phylogenomic approach. BMC Plant Biology 15:178  doi.org/10.1186/s12870-015-0563-9

  • Saarela JM, Wysocki WP, Barrett C, Soreng RJ, Davis JI, Clark LC, Kelchner SA, Pires JC, Edger PP, Mayfield DR, Duvall MR (2015) Plastid phylogenomics of the cool-season grass subfamily: clarification of relationships among early-diverging tribes. Annals of Botany Plants 7:plv046-27  doi.org/10.1093/aobpla/plv046

  • Wysocki WP, Clark LG, Kelchner SA, Burke SV, Pires JC, Edger PP, Mayfield DR, Triplett JK, Columbus JT, Ingram AL, Duvall, MR (2014) A multi-step comparison of short-read full plastome sequence assembly methods. Taxon 63:899-910  doi.org/10.12705/634.5

Systematics

  • Burke SV, Wysocki WP, Zuloaga F, Craine J, Pires JC, Edger P, Mayfield-Jones D, Clark LG, Kelchner SA, Duvall MR (2016) Evolutionary relationships in panicoid grasses based on plastome phylogenomics (Panicoideae; Poaceae). BMC Plant Biology 16:140  doi.org/10.1186/s12870-016-0823-3

  • Duvall MR, Coumbus JT, Fisher AE, Ingram AL, Wysocki WP, Burke SV, Clark LG, Kelchner SA (2016) Phylogenomics and plastome evolution of the chloridoid grasses (Chloridoideae; Poaceae). International Journal of Plant Sciences 177:235-246  doi.org/10.1086/684526

  • Cotton JL, Wysocki WP, Clark LG, Kelchner SA, Pires JC, Edger PP, Mayfield DR, Duvall MR (2015) Resolving deep relationships of PACMAD grasses; a phylogenomic approach. BMC Plant Biology 15:178  doi.org/10.1186/s12870-015-0563-9

  • Saarela JM, Wysocki WP, Barrett C, Soreng RJ, Davis JI, Clark LC, Kelchner SA, Pires JC, Edger PP, Mayfield DR, Duvall MR (2015) Plastid phylogenomics of the cool-season grass subfamily: clarification of relationships among early-diverging tribes. Annals of Botany Plants 7:plv046-27  doi.org/10.1093/aobpla/plv046

  • Fisher AE, Clark LG, Kelchner SA (2014) Molecular phylogeny estimation of the bamboo genus Chusquea (Poaceae: Bambusoideae: Bambuseae) and description of two new bamboo subgenera. Systematic Botany 39:829–844  doi.org/10.1600/036364414X681554

  • Kelchner SA, Bamboo Phylogeny Group (2013) Higher level phylogenetic relationships within the bamboos (Poaceae: Bambusoideae) based on five plastid markers. Molecular Phylogenetics and Evolution 67: 404-413  doi.org/10.1016/j.ympev.2013.02.005

  • Bamboo Phylogeny Group (2012b) An updated tribal and subtribal classification for the Bambusoideae (Poaceae). Bamboo Science & Culture 24: 1-10

  • Bamboo Phylogeny Group (2012a) An updated tribal and subtribal classification for the Bambusoideae (Poaceae). Pp. 3-27 in Gielis, J. and G. Potters (eds.), Proceedings of the 9th World Bamboo Congress, 10-12 April 2012, Antwerp, Belgium

  • Fisher AE, Triplett J, Ho C-S, Schiller AD, Oltrogge KA, Schroeder ES, Kelchner SA, Clark LG (2009) Paraphyly in the bamboo subtribe Chusqueinae (Poaceae: Bambusoideae) and a revised infrageneric classification for Chusquea. Systematic Botany 34: 673-683  doi.org/10.1600/036364409790139790

  • Tank DC, Beardsley PM, Kelchner SA, Olmstead RG (2006) Review of the systematics of Scrophulariaceae s.l. and its current disposition. LAS Johnson Invited Review No. 7, Australian Systematic Botany 19: 289-307  10.1071/SB05009

  • Trueman JWH, Pfeil BE, Kelchner SA, Yeates DK (2004) Did stick insects really regain their wings? Systematic Entomology 29: 138-139  doi.org/10.1111/j.0307-6970.2004.00251.x

  • Kelchner SA (2003) Phylogenetic structure, evolution, and biogeography of Myoporaceae. PhD Thesis, The Australian National University. 336 pp  [now classified as Myoporeae]

  • Bayer RJ, Puttock CF, Kelchner SA (2000) Phylogeny of South African Gnaphalieae (Asteraceae) based on two non-coding chloroplast sequences. American Journal of Botany 87: 259-272  doi.org/10.2307/2656914

  • Kelchner SA, Clark LG (1997) Molecular evolution and phylogenetic utility of the rpl16 intron in Chusquea and the Bambusoideae (Poaceae). Molecular Phylogenetics and Evolution 8: 385-397  doi.org/10.1006/mpev.1997.0432

Bird Behavior

  • Kelchner SA (1992) American robins’ use of old nests as cues for nest-site selection in central Iowa. Iowa Bird Life 62: 32-34

Book Reviews