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Two major obstacles to quantifying biodiversity are reticulate evolution and the evolution of genetically distinct but morphologically overlapping cryptic species. The Spiranthes cernua species complex (Orchidaceae) has defied satisfactory species delineation, often described as intractable, due to morphological variability within species, overall morphological similarity between species, possible cryptic speciation, and suspected hybridization. Weutilized low copy nuclear, nuclear ribosomal, and chloroplast molecular phylogenetic datasets, in addition to expansive field and herbarium research, to clarify long-standing questions regarding species boundaries within the S. cernua species complex. Our results justify: 1) narrowing the concept of S. cernua; 2) the description of a new cryptic species, Spiranthes arcisepala; 3) the description of a new geographically restricted species of cryptic and ancient hybrid origin, Spiranthes niklasii (S. cernua × S. ovalis); 4) a new combination for a biogeographically specific cryptic species of ancient hybrid origin, Spiranthes incurva (S. cernua×S. magnicamporum); and 5) the description of a new localized hybrid, Spiranthes ×kapnosperia (S. cernua × S. ochroleuca). We also propose formal synonymization of federally endangered Spiranthes parksii under S. cernua s. s. Our research clarifies species boundaries within this challenging group, and is the first to use molecular phylogenetic data to support hybridization as an evolutionary force within the S. cernua species complex.

Hybrid speciation is relatively common in plants compared to other well-studied groups. Polyploidy and apomixis are strongly associated with hybrid speciation, presumably due to the opportunities they provide for both reestablishing reproductive function in hybrids with incomplete chromosomal homology and creating rapid reproductive isolation in sympatry. Boechera, a species-rich genus closely related to Arabidopsis, is a particularly fertile ground for the study of hybrid speciation. Thirty-eight apomictic triploid hybrid species are currently recognized in Boechera. Recent research has shown that apomictic diploid hybrids, although very rare in angiosperms, are common in Boechera. Given this complexity, focused studies of individual species complexes are critical to understanding speciation and diagnosing biodiversity in Boechera. Here we analyze DNA sequences from seven nuclear loci and multilocus genotypes from 15 microsatellite markers in a group of closely related taxa formerly included in ...

Polyploidy, hybridization, and agamospory have been considered important mechanisms in fern speciation. By integrating the methods of cytology, molecular phylogeny, and morphology, we examined the origins of polyploid species in the Pteris cretica group, which comprises five agamosporous taxa and six sexual species. Phylogenetic analysis was conducted using both cpDNA (rbcL and trnV-trnM) and a low-copy nuclear gene (gapCp). The combined results of cytology and the phylogenetic trees suggested that the sexual diploid P. kidoi had played a central role in the diversification of polyploid species in the P. cretica group. Some triploid clones of agamosporous P. cretica var. cretica originated through hybridization between the diploid cytotype of P. cretica var. cretica and the sexual diploid P. kidoi. The sexual polyploid species, P. henryi, P. multifida, P. ryukyuensis, and P. yamatensis, and the hexaploid race of P. deltodon have arisen through allopolyploidization between their respective ancestr...

Boechera (Brassicaceae) is a diverse genus of ±70 sexual diploid species and numerous apomictic hybrids concentrated in western North America. It is the largest genus in tribe Boechereae, which also includes seven other small genera. Boechera is closely related to Arabidopsis and is becoming a model genus for diverse studies, focusing particularly on apomixis and hybrid speciation. As part of an ongoing effort to clarify the taxonomy of the group, we present phylogenetic analyses of Boechereae, including all genera of the tribe and most of the sexual diploid species of Boechera. Ten loci are used, including two plastid loci, nrDNA ITS, and seven low-copy nuclear loci. These analyses indicate that Boechera, as currently circumscribed, is polyphyletic, comprising three main clades. Eastern North American species previously assigned to Boechera form a distinct clade with the Asian taxon Borodinia macrophylla and are herein transferred to the genus Borodinia, resulting in seven new combinations (Boro...

Polymnia johnbeckii , a new, narrowly endemic species, is distinct in its combination of highly dissected leaves, hirsute herbage, and relatively large, showy heads. It is known from two populations in Marion County, Tennessee, and should be considered a rare species at both the state and federal level. A chromosome count indicates that P. johnbeckii is diploid. Although standard cladogenesis is the null hypothesis for the origin of this diploid species, evidence supporting an alternative scenario of homoploid hybrid speciation is discussed.

The relationships and taxonomy of the genus Thysanocarpus (Brassicaceae) are reassessed based on molecular phylogenetic analyses of nuclear ribosomal (ITS) and chloroplast (trnh-F) sequences and a critical re-examination of morphology and nomenclatural types. Based on these results, Thysanocarpus is well-supported as a member of tribe Thelypodieae, but no illuminating phylogenetic structure is found within the tribe. The independent origin of similar fruit morphology in Thysanocarpus and Athysanus is confirmed. Within Thysanocarpus,seven species are recognized: T. conchuliferus, T. curvipes, T. desertorum, T. erectus, T. laciniatus, T. radians, and T. rigidus comb. nov. Thysanocarpus laciniatus is found to have originated through hybridization. However, T. desertorum and T. rigidus, which have previously been included within T. laciniatus (as T. laciniatus var. hitchcockii and T. laciniatus var. rigidus,respectively), do not share that species' hybrid origin and are distinct both phylogenetically and morphologically. Within T. curvipes,five subspecies are recognized: T. curvipes subsp. amplectens comb. nov., T. curvipes subsp. curvipes, T. curvipes subsp. elegans comb. nov., T. curvipes subsp. longistylus comb. nov., and T. curvipes subsp. eradiatus comb. nov. Thysanocarpus curvipes subsp. elegans and T. curvipes subsp. longistylus form clades in ITS and/or trnL-F cladograms as well as showing morphological distinction. The remaining three subspecies are recognized based on a combination of morphology and geography.

Phylogenetic analyses of chloroplast trnK intron and nuclear ribosomal ITS DNA sequences yield signie cant improvements in our understanding of relationships, character evolution, and biogeography in Viburnum (Adoxaceae). We cone rm that most of the ten traditionally recognized sections are monophyletic. The most striking exception is Odontotinus , which is divided into: (i) a purple-fruited New World clade within which the Latin American section Oreinotinus is nested, and (ii) an Old World, mostly red-fruited clade that is closely related to V. cylindricum (section Megalotinus ) and the New World, purple-fruited V. acerifolium . We identify three major supra-sectional groupings: (i) a clade consisting of the Odonto- tinus-Oreinotinus -Megalotinus complex,the circum-boreal section Opulus, andtheEurasiansection Tinus,(ii)acladecontaining the Old World section Viburnum, the New World section Lentago, and, with less support, section Pseudotinus , and (iii) aclade containing the Asian sections Tomentosa and Solenotinus . Two species are not clearly allied to any of these supra-sectional clades: V. urceolatum , a Taiwanese/Japanese species traditionally placed in section Viburnum, and V. clemensiae , a Bornean species previously assigned to section Solenotinus . The placement of the root also remains uncertain, but probably does not fall within any of the three major supra-sectional clades. Knowledge of relationships within sections is useful in clarifying historical biogeography and the evolution of sterile e owers and fruit color. The one case of cone ict between datasets high- lights a possible instance of homoploid hybrid speciation.

Alcohol dehydrogenase (Adh) genes were amplified with PCR, cloned, and sequenced for five putative hybrid species of the genus Paeonia (Paeoniaceae): P sinjiangensis, P arietina, P humilis, P officinalis, and P parnassica. Two to three diverged types of sequences were found at each of the AdhiA and Adh2 loci for each species. Parsimony analyses of these sequences together with previously obtained Adh sequences of non-hybrid species of Paeonia indicated that two major types of Adh sequences of each of the five species were phylogenetically separated on the AdhiA and Adh2 trees. Along with nrDNA and cpDNA phylogenies, it is most parsimonious to hypothesize that these diverged sequences represent alleles derived from different parents through hybrid speciation. The approach of separating parental alleles of a nuclear gene in a hybrid genome and reconstructing phylogenies of these alleles offers a solution to the long standing methodological difficulty of reconstructing reticulate evolution. Phylogenies of plant nuclear genes, however, may be con- founded by dynamic evolutionary processes of the gene families, such as gene duplication/ deletion, gene conversion, and recombination. Thus, a strong hypothesis of hybrid speciation should rely on the congruence of multiple gene phylogenies as well as the congruence between gene phylogenies and other lines of evidence.

Solanum chacoense is a highly variable wild potato species widely distributed from central Bolivia to central Argentina, from sea level to over 3,000 m in the Andes. Upland populations of S. chacoense were thought to have arisen from introgression of lowland populations with S. microdontum. Our study uses morphological data, molecular data from singleto low-copy nuclear DNA restriction fragment length polymorphisms (RFLP's), and random amplified polymorphic DNA (RAPD's) to reinvestigate this hypothesis. The data do not support introgression but show relative equal divergence of upland and lowland populations from S. microdontum. These results suggest that other hybridization hypotheses need to be reexamined in sect. Petota. However, the similarity of many taxa in the group and alternative explanations of morphological or molecular intermediacy will complicate conclusions of hybridization. Solanum L. sect. Petota Dumort., the potato and its wild relatives, includes 232 species (Hawkes 1990). An alternative classification (Child 1990), supported by morphological and chloroplast DNA (cpDNA) data (Spooner et al. 1993) removes the eight non-tuberous species to sect. Etuberosum (Bukasov and Kameraz) A. Child, sect. Juglandifolium (Rydb.) A. Child, and sect. Lycopersicum (Mill.) Wettst. The remaining 224 tuberous species occur from the southwestern United States to south central Chile, with the greatest diversity of species in Peru and Bolivia. Species occur from sea level to over 4,500 m, but most occur between 2,000 and 3,500 m. Most members of sect. Petota are diploids (2n=24), but a few are triploid, tetraploid, pentaploid, or hexaploid (Correll 1962; Hawkes 1990). Section Petota is taxonomically complex. There is much disagreement regarding species boundaries, affiliation of species to series, rank of infraspecific taxa, and hypotheses of hybridization (Spooner and van den Berg 1992a). Diploid and polyploid hybrid speciation and introgressive hybridization are hypothesized to be common and important evolutionary mechanisms in sect. Petota (Ugent 1970; Hawkes 1978, 1990). Approximately 12% (26) of the 224 species in sect. Petota have been hypothesized to have arisen by hybrid speciation (listed in Spooner and van den Berg 1992b). In addition, local hybridization not leading to widespread introgression or speciation is believed to be common. Hawkes and Hjerting (1969, 1989) provided extensive lists of such putative occasional hybrids. Some species in sect. Petota have strong interspecific reproductive isolating mechanisms. One mechanism is governed by a process involving ratios of maternal/paternal effective ploidy in the endosperm, and evidenced by endosperm breakdown (Endosperm Balance Number, EBN; Hanneman 1994). In addition, some interspecific crosses within EBN levels are inhibited by stylar barriers (Abdalla and Hermsen 1972; Fritz and Hanneman 1989). However, most diploid species, especially those in South America, can artificially be hybridized to form viable interspecific progeny, although some may show reduced fertility in subsequent generations (Hawkes 1990). Often, different species occur sympatrically, providing the opportunity for natural hybridization (Hawkes 1978, 1990). Solanum chacoense Bitter was the first wild potato species investigated for introgressive hybridization in sect. Petota (Hawkes 1962). The latest comprehensive taxonomic revision (Hawkes 1990) and a subsequent review of evolution in sect. Petota (Hawkes 1994) continue to cite S. chacoense as one of the better-documented examples of introgressive hybridization in the group. A recent review of introgression in plants, however, cites S. chacoense as an example of an introgression hypothesis where alternative explanations were not adequately pursued (Rieseberg and Wendel 1993). Solanum chacoense grows from central Bolivia south to central Argentina, Brazil, and Paraguay, and from the Atlantic coast to the Andes, up to 3,700 m. It covers an area 1,700 km north-south by 1,500 km east-west (Hawkes 1962), and is one of the most widely distributed wild potato species.

Restriction-site variation of chloroplast DNA was used to assess hypotheses of diploid hybrid speciation in Penstemon sect. Peltanthera where P. spectabilis is a putative stabilized hybrid of P. centranthifolius and P. grinnellii, and P. clevelandii is a purported hybrid derivative of P. centranthifolius and P. spectabilis. Based on restriction-site mapping, cpDNA haplotypes were determined for hy- pothesized parental species and P. spectabilis and P. clevelandii. The distribution of nuclear and organellar DNA markers among populations of P. spectabilis and P. clevelandii were evaluated to determine whether the observed patterns result from diploid hybrid speciation, or from introgres- sion. Nuclear markers of P. centranthifolius were found in several populations of P. grinnellii, P. spectabilis, and P. clevelandii; whereas chloroplast haplotypes of P. centranthifolius were found in only two populations of P. grinnellii. We suggest that the patterns of introgression observed for sect. Peltanthera result predominantly from pollen-mediated gene flow, with hummingbirds the most likely vector. A comparison of the phylogenetic trees based on cpDNA vs. nuclear restriction data reveals that at least one chloroplast-capture event has occurred in Penstemon sect. Peltanthera.