@article {100,
	title = {The utility of nuclear ITS, a LEAFY homolog intron, and chloroplast atpB-rbcL spacer region data in phylogenetic analyses and species delimitation in Iso{\"e}tes},
	journal = {American Fern Journal},
	volume = {91},
	year = {2001},
	note = {Cited By (since 1996):46Export Date: 11 November 2013Source: Scopus},
	month = {2001///},
	pages = {166 - 177},
	abstract = {Despite its ancient origins, its worldwide distribution, and adaptation to diverse habitats, Iso{\"e}tes has a highly conserved morphology. This feature has made it difficult to resolve species and species relationships using morphological characters. In this paper, we report the utility of nucleotide sequences from the nuclear internal transcribed spacer (ITS) regions, chloroplast atpB/rbcL intergenic spacer region, and second intron of a LEAFY (LFY) homolog for identifying species relationships, delimiting basic diploid species, and determining hybrid origins. Variation in the ITS regions and atpB/rbcL spacer is most useful at the family level in Iso{\"e}tes and the LFY second intron is appropriate at the species and population level. The tree resulting from an analysis of the combined nuclear ITS and chloroplast atpB/rbcL spacer contains three major well supported clades (bootstrap >= 99\%): an Old-World/California clade (I. abyssinica, I. longissima, I. velata, I. nuttallii, and I. orcuttii), an Asian/Australian clade (I. taiwanensis, I. japonica, I. kirkii, and I. drummondii), and a poorly resolved clade consisting of nine North American species. To further resolve and delimit the North American species, a combination of the LEAFY second intron and ITS data was used. The resulting consensus tree has limited resolution, supporting the hypothesis that the North American species complex radiated rapidly. The combination of LFY and ITS data provided numerous characters, both substitutions and indels, that are useful in species delimitation and identification of cryptic species. ITS sequence data, through additive banding and sequence misalignment, is also useful in confirming interspecific hybrids and determining their parental origins.},
	url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-0040332183\&partnerID=40\&md5=e97f5c223e9a884b67c6347a0db81dd5},
	author = {Hoot, S.B. and Taylor, W.C.}
}
@article {80,
	title = {Phylogenetic relationships of Iso{\"e}tes (Iso{\"e}taceae) in China as revealed by nucleotide sequences of the nuclear ribosomal ITS region and the second intron of a LEAFY homolog},
	journal = {American Fern Journal},
	volume = {94},
	year = {2004},
	note = {Cited By (since 1996):17Export Date: 11 November 2013Source: Scopus},
	month = {2004///},
	pages = {196 - 205},
	abstract = {Iso{\"e}tes is an ancient lycopod lineage with a highly conserved morphology that provides few morphological characters to resolve the phylogeny of its species. Species appear to have evolved by divergence and allopolyploidy. The basic diploids I. hypsophila, I. taiwanensis, and I. yunguiensis and the tetraploid I. sinensis occur in China. Analysis of ITS sequences indicates that the Chinese Iso{\"e}tes species are part of an Australasian clade including I. brevicula from Western Australia and I. kirkii from New Zealand. Two distinct cloned sequences of the second intron of a LEAFY homolog were recovered from I. sinensis supporting the hypothesis that I. sinensis is an allotetraploid. One of the I. sinensis cloned sequences was similar to the I. taiwanensis sequence and the other cloned sequence was similar to the I. yunguiensis sequence identifying I. taiwanensis and I. yunguiensis as the likely parents of I. sinensis. Other cloned sequences recovered from I. sinensis were recombined parts of the two distinct sequences. Morphological evidence supporting an allotetraploid origin of I. sinensis is found in its larger microspore size and intermediate megaspore texture compared to I. taiwanensis, and I. yunguiensis.},
	url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-11444262662\&partnerID=40\&md5=7b7a2b568e139bee1b60bd62836ff6ef},
	author = {Taylor, W.C. and Lekschas, A.R. and Qing, F.W. and Liu, X. and Napier, N.S. and Hoot, S.B.}
}
@article {84,
	title = {Revealing unknown or extinct lineages within Iso{\"e}tes (Iso{\"e}taceae) using DNA sequences from hybrids},
	journal = {American Journal of Botany},
	volume = {91},
	year = {2004},
	note = {Cited By (since 1996):25Export Date: 11 November 2013Source: Scopus},
	month = {2004///},
	pages = {899 - 904},
	abstract = {Iso{\"e}tes, a heterosporous lycopod with a fossil record dating back to the Paleozoic, has numerous putative allopolyploids (resulting from hybridization events coupled with doubling of chromosome number). By using the highly variable nucleotide sequences from the second intron of a LFY homologue in Iso{\"e}tes, species could be delimited and hybrid origins determined. The data suggest that reticulate evolution is both common and complex within a more derived species complex of Iso{\"e}tes. Sequences of identifiable parentage and sequences that are unlike any diploid species known were recovered, leading to the conclusion that one or both of the putative parents have not yet been discovered or are extinct. A range of observations concerning allopolyploid speciation were categorized as follows: (1) verification of previous hypotheses regarding parentage (e.g., I. riparia, I. appalachiana), (2) determination that two morphologically distinct allotetraploid species can share the same parentage (I. azorica and I. acadiensis), (3) recognition of a cryptic allotetraploid species, indicated by the presence of different parental genomes (I. "appalachiana" from Florida), and (4) identification of allotetraploid species with one or two unknown parents (e.g., I. tuckermanii, I. acadiensis, I. azorica, and I. hyemalis). Some sequences from diploid species are remarkably uniform among populations (e.g., I. echinospora from various locations in North America, Iceland, and Wales), while others are variable at the subspecies level (e.g., northern and southern populations within I. engelmannii).},
	keywords = {Allopolyploidy, Hybrid origins, Isoetes, LEAFY intron},
	url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-11444256350\&partnerID=40\&md5=420a4ad06820ce82f60d7a70e7db9dec},
	author = {Hoot, S.B. and Napier, N.S. and Taylor, W.C.}
}
@book {59,
	title = {Phylogeny and biogeography of Iso{\"e}tes (Iso{\"e}taceae) based on nuclear and chloroplast DNA sequence data},
	series = {Systematic Botany},
	volume = {31},
	year = {2006},
	note = {Cited By (since 1996):14Export Date: 11 November 2013Source: Scopus},
	month = {2006///},
	pages = {449 - 460},
	abstract = {Despite its ancient origins, worldwide distribution, and adaptation to diverse habitats, Iso{\"e}tes species have a highly conserved morphology, making it difficult to resolve phylogenetic relationships using morphological characters. In this paper, we report the results from various analyses (maximum parsimony, maximum likelihood, and Bayesian inference) for Iso{\"e}tes species from around the world based on nucleotide sequences from the nuclear internal transcribed spacer (ITS) and chloroplast atpB/rbcL intergenic spacer regions. The trees resulting from our analyses of the combined data contain six major well-supported clades (bootstrap >= 90\%, posterior probabilities = 1.00): A clade with possible Gondwanan affinities (I. australis, I. coromandelina, I. panamensis, I. cubana, I. jamaicensis); a South African clade (I. capensis, I. toximontana, I. stellenbossiensis, I. stephansenii); a largely Northern Hemisphere clade (I. nuttallii, I. orcuttii, I. minima, I. dixitei, I. abyssinica, I. olympica, I. longissima, I. velata); an Asian/Australasian clade (I. drummondii, I. gunnii, I. pusilla, I. kirkii, I. muelleri, I. taiwanensis, I. japonica, I. yunguiensis, I. habbemensis); a Mediterranean clade (I. histrix and I. setacea); and a poorly resolved clade consisting of 12 new world species (American species complex). Our results are compared to past classifications and various biogeographical scenarios are explored. {\textcopyright} Copyright 2006 by the American Society of Plant Taxonomists.},
	keywords = {Biogeography, Isoetaceae, Isoetes, Phylogeny},
	url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-67650146436\&partnerID=40\&md5=c418d4b55db9dd7f2436a8d3189f1552},
	author = {Hoot, S.B. and Taylor, W.C. and Napier, N.S.}
}
@article {60,
	title = {Inferring the root of Iso{\"e}tes: Exploring alternatives in the absence of an acceptable outgroup},
	journal = {Systematic Botany},
	volume = {31},
	year = {2006},
	note = {Cited By (since 1996):11Export Date: 11 November 2013Source: Scopus},
	month = {2006///},
	pages = {258 - 270},
	abstract = {The ancient divergence between the lycopsid genus Iso{\"e}tes and its closest living relative (Selaginella) has resulted in considerable morphological and genetic disparity, yet within Iso{\"e}tes there is remarkable morphological and genetic uniformity. This has made it difficult to identify the phylogenetic root of the genus. In this study, we addressed this problem and characterized the early branching patterns within Iso{\"e}tes using an expanded set of taxa and three molecular markers. We assessed the saturation in the molecular data sets, tested for differences in evolutionary rate, determined the stability of the ingroup topology, and evaluated the applicability of the molecular clock. We then explored three alternative rooting approaches: outgroup, midpoint, and maximum likelihood under the assumption of a molecular clock. Attempts to infer the root of Iso{\"e}tes using the outgroup approach were severely hindered by the effects of saturation, but the results from midpoint rooting and the enforcement of the molecular clock were highly consistent among the data sets. We identify the root of Iso{\"e}tes to be located among three major, highly supported clades. {\textcopyright} Copyright 2006 by the American Society of Plant Taxonomists.},
	keywords = {Isoetaceae, Isoetes, Lycophyte, Midpoint rooting, Phylogenetic root, Relative rate comparisons},
	url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-33745493624\&partnerID=40\&md5=8d3abb9eb77572545e97747f1aaf51a5},
	author = {Schuettpelz, E. and Hoot, S.B.}
}
