Backbone phylogeny of Lepisorus (Polypodiaceae) and a novel infrageneric classification based on the total evidence from plastid and morphological data

The fern genus Lepisorus represents one of the most complicated and controversial lineages in Polypodiaceae, with about 80 species which have been classified into several separate genera, and is notorious for its taxonomic difficulty. Despite progress in recent phylogenetic studies of the family Polypodiaceae involving Lepisorus and its allies, the deep phylogenetic relationship within this group of ferns is still unresolved, and no formal infrageneric classification has been proposed. This contribution presents the most comprehensive phylogenetic analysis of the genus, with 72% species sampled, using a total-evidence approach based on eight plastid markers and ≤25 morphological characters for each species. The analyses resolve the backbone relationship and yield the most robust phylogenetic framework to date. Congruent with previous studies but with new findings, the results herein show that Lepisorus is monophyletic when Neolepisorus, Lemmaphyllum, Tricholepidium, Neocheiropteris and Lepidomicrosorium are included, as well as Lepisorus jakonensis and Paragramma. Furthermore, 17 well-resolved clades are found in the phylogenetic topology, which can be characterized by morphological synapomorphies from traits of rhizome scales, laminae, sori and paraphyses. Based on molecular and morphological evidence, a new infrageneric classification system of Lepisorus is proposed which subdivided Lepisorus into 17 sections.     

Axial skeleton of Cebupithecia sarmientoi (Pitheciinae,Platyrrhini) from the middle miocene of La Venta,Colombia

The axial skeleton of Cebupithecia sarmientoi is described and analyzed for its functional and phylogenetic implications. The vertebrae of the holotype of C. sarmientoi (UCMP 38762) most closely resemble those of the extant pitheciine genus Pithecia and display features associated with adaptations for clinging and leaping as in that genus. Cebupithecia has a relatively long non-prehensile tail, which is most similar in absolute dimensions and proportions to Pithecia monachus. It also shares with P. monachus a distinctive morphology of the thoracic vertebrae, specifically the presence of a bony pillar spanning the vertebral lamina and body, caudal to the pedicle, herein designated the vinculum laminum. It is proposed that many of these features are shared primitive retentions from the last common ancestor of the Cebupithecia-pitheciine clade.     

Miniatures,morphology and molecules: Paedocypris and its phylogenetic position (Teleostei,Cypriniformes)

We review the morphological and molecular evidence that Mayden & Chen recently used to infer that the developmentally truncated fish genus Paedocypris is not a member of the teleost order Cypriniformes or carp‐like fishes, but is ‘the basal sister group to all Cypriniformes’. This hypothesis contradicts several previous studies that used molecular sequence data or morphological characters. A review of the morphological characters that Mayden & Chen discussed and mapped onto their ‘simplified tree’ shows that these, analysed alone, rather support a close relationship of the cyprinids Sundadanio, Danionella, and Paedocypris. We also present four additional analyses of morphological data, which all contradict Mayden & Chen's result. Despite its highly reductive skeleton, posing a serious problem when analysing its phylogenetic position with skeletal characters, the presence in Paedocypris of the basioccipital masticatory plate is compelling evidence that it is a member of the Cyprinoidei (Cyprinidae plus Psilorhynchidae). Our reanalysis and exploration of their molecular sequence data shows that only a single gene, EGR3, of the six nuclear genes analysed by Mayden & Chen, is responsible for the position of Paedocypris as ‘the basal sister group to all Cypriniformes’. Three independent methods to visualize and analyse phylogenetic signal and conflict of data sets (phylogenetic networks, splits analysis methods or SAMS, and site‐wise likelihood analyses) reveal a high level of character conflict and noise in Mayden & Chen's data set. The ‘basal’ position of Paedocypris seems to be the outcome of the interplay of two long‐branch effects. We apply the same analytical methods to the data set from Rüber et al.'s molecular analysis of the phylogenetic position of Paedocypris and discuss our findings. We conclude that none of the molecular data sets compiled to date can establish the phylogenetic position of Paedocypris with confidence. Morphological data suggest that Paedocypris and Danionella are sister genera, and that their closest relative is Sundadanio, although the position of these three miniatures among cyprinoids is still unclear. © 2014 The Linnean Society of London     

Cladistic tests of monophyly and relationships of biostratigraphically significant conodonts using multielement skeletal data –Lochriea homopunctatus and the genus Lochriea

Abstract: Since the 1960s, huge progress has been made in reconstructing the multielement skeletons of conodont species and developing a biologically defensible taxonomy. Nevertheless, a widespread prejudice remains that certain parts of the conodont skeleton, particularly the P₁ elements, are more informative than others with regard to taxonomy and evolutionary relationships. Here, we test these views. A new partial multielement reconstruction of the skeleton of the biostratigraphically significant conodont originally described as Gnathodus commutatus homopunctatus allows us to conduct a cladistic test of the alternative hypotheses of phylogenetic placement of this species. Our analysis also provides the first test of the hypothesis that Lochriea– species of which are markers for global correlation – is monophyletic and tests hypotheses concerning the origins of the genus. Our results demonstrate that homopunctatus is a species of Lochriea and that the genus is monophyletic. The widely held view that Lochriea arose from a species of Bispathodus is not supported. Our results show that it is difficult to predict a priori which parts of the conodont skeleton carry phylogenetic signal, and provide strong support for the hypothesis that similarity in the morphology of conodont P₁ elements alone is not a reliable guide to relationships and taxonomic groupings of conodont species. This is because P₁ elements with similar morphologies are convergently acquired in multiple conodont clades, because reliance on the characters of only one of the six or seven morphologically distinct elements of the conodont skeleton ignores phylogenetically significant data and because P₁ elements can lack characters that might seem to be diagnostic of a genus. Conodonts are no different to other organisms: ignoring data that have the potential to be phylogenetically informative is unlikely to produce the most reliable hypotheses of evolutionary relationships. We suggest that other biostratigraphically significant hypotheses of relationship between conodont taxa that are based on P₁ elements alone should be subject to cladistic testing.     

Phylogenetic analysis of bovine pestiviruses: testing the evolution of clinical symptoms

This study presents a phylogenetic analysis of 115 bovine pestiviruses. A sequence data set from the 5′ untranslated genomic region was analyzed with maximum parsimony, bootstrapping and parsimony jackknifing. We tested for the proposed classifications of the group and analyzed the evolution of the symptoms associated with Pestivirus infections in bovines. Based on the historical framework provided by our phylogenetic trees, we also characterized the extent and importance of contamination caused in biologicals by the virus. Our phylogenetic analyses showed that the previously defined genotypes are monophyletic, except for genotype 1a. Based on our cladograms, we propose the existence of more than 12 monophyletic groups within the species BVDV 1. The mapping of clinical symptoms suggests that the emergence of some genotypes could have been driven by a change in the pathogenic process. Enteric Problems appear to be ancestral, while Reproductive and Respiratory Problems arise with the emergence of genotypes 1b, 1d and the herein‐proposed genotype Arg 1. The distribution of contaminant strains on the cladograms shows that pestiviral contamination is a common process, and also suggests that a contaminated product might be a vehicle for virus dispersion. Implications for virus evolution, virus taxonomy, veterinary medicine and biotechnology are discussed.     

To be or not to be a valid genus: the systematic position of Ophyra R.‐D. revised (Diptera: Muscidae)

Ophyra Robineau‐Desvoidy is one of the better‐studied genera of the family Muscidae (Diptera). The larvae of species of this genus feed on highly decomposed organic matter of various origins, and may reveal predatory behaviour as they mature. These feeding habits, combined with the widespread distribution and close association with human dwellings of some species, give the genus commercial and medico‐legal importance. However, the systematic position of Ophyra has been a matter of debate for many years. Ophyra has been considered by muscid workers to be either a valid genus or a junior synonym of Hydrotaea Robineau‐Desvoidy. A lack of agreement about the systematic position of Ophyra has led to serious errors, particularly in the applied literature. Recent molecular and morphological studies provided contradictory information on the validity of the genus and its subfamilial classification. We revise the systematic position of Ophyra herein by means of molecular phylogenetic reconstruction. Our results are incongruent with opinions on the systematic position of Ophyra based on previously published molecular phylogenies, although they correspond with the concept of the genus based on adult morphology. All analyses of the concatenated dataset revealed Ophyra as monophyletic and placed within a paraphyletic Azeliini. Depending on the phylogenetic approach, Ophyra was placed within either a monophyletic, paraphyletic or polyphyletic Hydrotaea, yet always closely related to a certain group of species. We conclude that Ophyra, as currently defined, should not be considered a valid name, yet a detailed reconstruction of the genus Hydrotaea awaits future studies with greater increases in both taxon sampling and the number of molecular markers.     

Phylogenetic Position of Parasitic Chytrids on Diatoms: Characterization of a Novel Clade in Chytridiomycota

Chytrids are true fungi that reproduce with posteriorly uniflagellate zoospores. In the last decade, environmental DNA surveys revealed a large number of uncultured chytrids as well as undescribed order‐level novel clades in Chytridiomycota. Although many species have been morphologically described, only some DNA sequence data of parasitic chytrids are available from the database. We herein discuss five cultures of parasitic chytrids on diatoms Aulacoseira spp. and Asterionella formosa. In order to identify the chytrids examined, thallus morphologies were observed using light microscopy. We also conducted a phylogenetic analysis using 18S, 5.8S, and 28S rDNA sequences to obtain their phylogenetic positions. Based on their morphological characteristics, two cultures parasitic on As. formosa were identified as Rhizophydium planktonicum and Zygorhizidium planktonicum. The other three cultures infecting Aulacoseira spp. (two on Aulacoseira ambigua and the other on Aulacoseira granulata) were regarded as Zygorhizidium aff. melosirae. The results of the molecular phylogenetic analysis revealed that R. planktonicum belonged to the known order Chytridiales, while the two species of Zygorhizidium were placed in a novel clade that was previously reported as an undescribed clade composed of only the environmental sequences of uncultured chytrids.     

Molecular phylogeny,biogeography and chromosome evolution of Malagasy dwarf geckos of the genus Lygodactylus (Squamata,Gekkonidae)

We performed a phylogenetic analysis using nuclear (RAG‐1, RAG‐2) and mitochondrial (16S) markers, a statistical Bayesian reconstruction of ancestral distribution areas and a karyological analysis on most Malagasy species of the gekkonid genus Lygodactylus. The phylogenetic analysis largely confirms major basal branching pattern of previous molecular studies, but highlights significant differences concerning both the relationships between different species groups as well as those within groups. The biogeographic analysis supports a Malagasy origin of Lygodactylus, an oversea dispersal to continental Africa and a return to Madagascar. The L. madagascariensis group (also including a new candidate species identified herein) is the most basal clade in Lygodactylus, and the sister group of a clade with all the remaining species. The second most basal clade is the L. verticillatus group, placed as the sister group of a clade comprising African and Malagasy species. The sister lineage of the L. verticillatus group originated the African radiation through an oversea dispersal out of Madagascar. Eventually, the sister lineage of the L. capensis group originated secondary dispersals from Africa to Madagascar. In Madagascar, lineage diversification in different species groups mainly occurred from southern to northern and eastern regions. Dispersal, vicariance and paleoclimatic refugia probably played a relevant role in the evolutionary history of closely related taxa and in speciation mechanisms. The cytogenetic analysis evidenced a high karyotypic variability in Lygodactylus (from 2n = 34 to 2n = 40), which is at least partly consistent with the phylogenetic relationships and the composition of the various species group. Chromosome evolution occurred independently in different lineages, mainly through a reduction in the chromosome number and starting from a putative primitive karyotype of 2n = 40 with all telocentric elements.     

Structure and function of the hyolingual system in Hynobius and its bearing on the evolution of prey capture in terrestrial salamanders

The Hynobiidae is generally regarded as the most phylogenetically basal and least derived extant family of terrestrial salamanders. As in the other families of terrestrial salamanders, prey capture in the Hynobiidae is accomplished by lingual prehension. In Hynobius, the prey capture system appears to be a mosaic of derived and primitive features. This, in conjunction with previous studies, suggests that the hyolingual systems of all families of terrestrial salamanders have evolved various degrees of specialization since the appearance of the common ancestral condition. We propose that the generalized feeding system for the extant terrestrial salamanders includes a hyolingual skeleton comprised of one basibranchial, one pair of radial or radial-like structures, two pairs of ceratobranchials, two pairs of epibranchials, one pair of ceratohyals, and one urohyal arranged in a configuration similar to that of Hynobius; a simple, sac-like secondary tongue pad; a lift and thrust system of tongue projection; a four-part gape cycle; and a forward head and body surge. Modifications to this general plan, previously described for the disparate families, include various changes in the size, shape, and definition of the tongue pad, changes in the specific types of structures and configurations in the anterior hyolingual skeleton, secondary ossification in the posterior hyolingual skeleton, the appearance of various protrusion, projection, and flipping systems for tongue protraction, simplification of the kinematic gape profile, and loss of the forward head and body surge. The evolutionary trends in these modifications have provided a rich data set from which much phylogenetic information has been inferred. © 1996 Wiley-Liss, Inc.     

Cladistic and phylogenetic biogeography: the art and the science of discovery

All methods used in historical biogeographical analysis aim to obtain resolved area cladograms that represent historical relationships among areas in which monophyletic groups of taxa are distributed. When neither widespread nor sympatric taxa are present in the distribution of a monophyletic group, all methods obtain the same resolved area cladogram that conforms to a simple vicariance scenario. In most cases, however, the distribution of monophyletic groups of taxa is not that simple. A priori and a posteriori methods of historical biogeography differ in the way in which they deal with widespread and sympatric taxa. A posteriori methods are empirically superior to a priori methods, as they provide a more parsimonious accounting of the input data, do not eliminate or modify input data, and do not suffer from internal inconsistencies in implementation. When factual errors are corrected, the exemplar presented by M.C. Ebach & C.J. Humphries (Journal of Biogeography, 2002, 29 , 427) purporting to show inconsistencies in implementation by a posteriori methods actually corroborates the opposite. The rationale for preferring a priori methods thus corresponds to ontological rather than to epistemological considerations. We herein identify two different research programmes, cladistic biogeography (associated with a priori methods) and phylogenetic biogeography (associated with a posteriori methods). The aim of cladistic biogeography is to fit all elements of all taxon–area cladograms to a single set of area relationships, maintaining historical singularity of areas. The aim of phylogenetic biogeography is to document, most parsimoniously, the geographical context of speciation events. The recent contribution by M.C. Ebach & C.J. Humphries (Journal of Biogeography, 2002, 29 , 427) makes it clear that cladistic biogeography using a priori methods is an inductivist/verificationist research programme, whereas phylogenetic biogeography is hypothetico‐deductivist/falsificationist. Cladistic biogeography can become hypothetic‐deductive by using a posteriori methods of analysis.     

Systematics of the genus Mayazomus (Arachnida: Schizomida): the relevance of using continuous characters and pedipalp setae patterns to schizomid phylogenetics

The schizomid genus Mayazomus Reddell & Cockendolpher, 1995, endemic to south‐eastern Mexico, currently comprises seven species. It was originally proposed to accommodate two species, from Chiapas and Tabasco. Recently, five additional species from Chiapas were described. The monophyly of the genus has never been tested using cladistic analysis. We undertook a phylogenetic analysis using the seven described species of Mayazomus as the ingroup, ten exemplar species representing the most similar New World hubbardiids as the outgroup, and one protoschizomid species to root the tree. The analysis was based on 130 morphological characters (continuous and discrete characters). The resulting topologies recovered Mayazomus as paraphyletic, with Heteronochrus estor Armas & Viquez, 2010, from Guatemala nested within the genus; therefore, we formally propose its synonymy herein. Mayazomus appears to be most closely related to Rowlandius Reddell & Cokendolpher, 1995, a South American genus. This contribution also provides new characters derived from the pedipalp setae with important phylogenetic information; as well as the implementation of morphometric ratios, as continuous characters, to partially codify the shape of the male flagellum. The relationships recovered amongst the outgroups used in this contribution are a reliable baseline for future analyses of the phylogeny of the New World schizomids.     

Integrative taxonomy of the stunt nematodes of the genera Bitylenchus and Tylenchorhynchus (Nematoda,Telotylenchidae) with description of two new species and a molecular phylogeny

Stunt nematodes are characterized by phenotypic plasticity, with overlapping morphology and morphometry leading to potential misidentification. Consequently, the application of integrative taxonomic approaches is useful to species delimitation based on a combination of different perspectives, e.g. morphology and DNA sequences. We conducted nematode surveys in cultivated and natural environments in Spain and the USA, from which we identified 18 known species of the family Telotylenchidae and two new taxa within the studied samples. These species were morphologically, morphometrically, and molecularly characterized. The results of light and scanning electron microscopic observations, and molecular and phylogenetic analysis also allowed two new species to be distinguished, described herein as B itylenchus hispaniensis sp. nov. and T ylenchorhynchus mediterraneus sp. nov. The phylogenetic analysis was carried out using molecular data from nuclear ribosomal DNA genes [D2–D3 expansion segments of the large ribosomal subunit (28S), internal transcribed spacer (ITS), and partial small ribosomal subunit (18S)]. We also provide here a test of alternative hypotheses that confirms the monophyly of both Tylenchorhynchus and Bitylenchus sensu Siddiqi's classification but does not support Fortuner & Luc's conceptual view of Tylenchorhynchus as a large genus. Ancestral state reconstructions of several diagnostic morphological characters using a maximum parsimony approach showed congruence in morphological and molecular evolution for stylet knob inclination and tail tip annulation. Our analysis emphasizes some of the problems related to the taxonomy and phylogeny of nematodes of Telotylenchinae. © 2014 The Linnean Society of London     

High evolutionary rates and the origin of the Rosso Ammonitico Veronese Formation (Middle-Upper Jurassic of Italy) reptiles

The fossil record of metriorhynchids and plesiosaurians from the Rosso Ammonitico Veronese Formation (RAVFm, Middle–Upper Jurassic, Italy) is represented by elements collected between the eighteenth and twentieth centuries. All the metriorhynchid material is referred to the genus Neptunidraco. The first RAVFm plesiosaurian material was collected in the nineteenth century and referred to Plesiosaurus: elements are here described and interpreted as a chimerical association of crocodylomorph and plesiosaurian bones, providing the first co-occurrence of these clades in the RAVFm. The second plesiosaurian is the associated skeleton that we refer to Anguanax zignoi gen. et sp. nov. Bayesian phylogenetic analysis confirms the basal geosaurine affinities of Neptunidraco resulted by parsimony analysis. Using both methods, Anguanax was recovered as a basal pliosaurid, sister group of the clade including Marmornectes and Thalassophonea. Bayesian inference methods indicate that both Italian lineages diverged from other known lineages between 176 and 171 Mya, also showing divergence rates significantly higher than any other representative of their respective clades. We suggest a phase of rapid evolutionary adaptation to deeper marine environments in the ancestors of the Rosso Ammonitico Veronese reptiles as a response to the latest Liassic regressive regime in Northern Tethys.     

Molecular taxonomy of Osedax (Annelida: Siboglinidae) in the Southern Ocean

We report the discovery of three new species of Osedax in the deep Southern Ocean, expanding the diversity and geographical range of this genus of bone‐eating worms. Osedax rogersi sp. n. and Osedax crouchi sp. n. were found on a whale skeleton at 1444 m in the Kemp Caldera in the East Scotia Sea during the Chemosynthetic Ecosystems of the Southern Ocean (ChEsSo) project. The recently described species, Osedax antarcticus, found on whale bones implanted at a depth of 550–650 m off Smith Island in the Bransfield Strait, was also found inhabiting the whale skeleton in the Kemp Caldera. Osedax crouchi as well as another new species Osedax nordenskjoeldi sp. n. have also been found on the implanted whale bones off Smith Island. These two localities are approximately 1800 km apart demonstrating a wide distribution of species within the genus. We describe the three new species, O. rogersi, O. crouchi and O. nordenskjoeldi and report the second record of O. antarcticus. We also present a new phylogenetic analysis for Osedax, including data examining genetic connectivity between the Scotia Arc and the Bransfield Strait.     

Derivation of a simple microsatellite locus from a compound ancestor in the genus Mus

Many microsatellite loci contain more than a single repeat motif. These compound microsatellites are perhaps most easily explained as arising from simple ancestors. We have uncovered a contrary example in mice of the genus Mus. Sequence analysis of the locus D1MIT29 in most of the members of the genus Mus reveals that this locus is compound in all species except M. musculus, in which it is simple. Moreover, phylogenetic analyses of base substitutions in the non-repetitive flanking region gives trees which are consistent with the previously accepted phylogenetic hypothesis that M. musculus is nested within the subgenus Mus. This confirms that the history of this locus is similar to that of molecular markers previously used in phylogenetic studies of this group and, therefore, demonstrates that the simple state in this lineage is derived from a compound ancestor. We also demonstrate the utility of this type of nuclear sequence variation for phylogeographic studies in the genus Mus. Finally, our sequences reveal homoplasy for size, reemphasizing the danger of using microsatellite size variation alone when the individuals under study are not closely related. Received: 26 April 2000 / Accepted: 28 July 2000     

New insight into the identification and molecular phylogeny of dagger nematodes of the genus Xiphinema (Nematoda: Longidoridae) with description of two new species

The genus Xiphinema constitutes a large group of about 260 species of plant‐ectoparasitic nematodes. The group is polyphagous and distributed almost worldwide. Some of the species of this genus damage agricultural crops by direct feeding on root cells as well as by transmitting nepoviruses. Species discrimination in Xiphinema is complicated by phenotypic plasticity leading to potential misidentification. We conducted nematode surveys in cultivated and natural environments in Spain from 2009 to 2012, from which we identified 20 populations of Xiphinema species morphologically close to the virus‐vector nematode species Xiphinema diversicaudatum, three apomictic populations tentatively identified as species from the complex Xiphinema aceri‐pyrenaicum group, and one population morphologically different from all others that is characterized by a female tail elongate to conical and absence of uterine differentiation. We developed comparative multivariate analyses for these related species by using morphological and morphometrical features together with molecular data from nuclear ribosomal DNA genes [D2‐D3 expansion segments of large ribosomal subunit 28S, internal transcribed spacer 1 (ITS1), and partial small ribosomal subunit (18S)]. The results of multivariate, molecular, and phylogenetic analysis confirmed the morphological hypotheses and allowed the delimitation and discrimination of two new species in the genus described herein as Xiphinema baetica sp. nov. and Xiphinema turdetanensis sp. nov. , and ten known species: Xiphinema adenohystherum, Xiphinema belmontense, Xiphinema cohni, Xiphinema coxi europaeum, Xiphinema gersoni, Xiphinema hispidum, Xiphinema italiae, Xiphinema lupini, Xiphinema nuragicum, and Xiphinema turcicum. Multivariate analyses based on quantitative and qualitative characters and phylogenetic relationships of Xiphinema spp. based on the three molecular ribosomal markers resulted in a partial consensus of these species grouping as nematode populations were maintained for the majority of morphospecies groups (e.g. morphospecies groups 5 and 6), but not in some others (e.g. position of Xiphinema granatum), demonstrating the usefulness of these analyses for helping in the diagnosis and identification of Xiphinema spp. The clade topology of phylogenetic trees of D2‐D3 and partial 18S regions in this study were congruent in supporting the polyphyletic status of some characters, such as the female tail shape and the degree of development of the genital system in species with both genital branches equally developed. This is the most complete phylogenetic study for Xiphinema non‐americanum‐group species. Agreement between phylogenetic trees and some morphological characters (uterine spines, pseudo‐Z organ, and tail shape) was tested by reconstruction of their histories on rDNA‐based trees using parsimony and Bayesian approaches. Thus, integrative taxonomy, based on the combination of multivariate, molecular analyses with morphology, constitutes a new insight into the identification of Xiphinema species. © 2013 The Linnean Society of London     

Major Lineages of the Genus <Emphasis Type="Italic">Lilium</Emphasis> (Liliaceae) Based on nrDNA ITS Sequences,with Special Emphasis on the Korean Species

We present most comprehensive phylogenetic analysis of 196 accessions of Lilium representing 83 species and 14 varieties of Lilium and three outgroup genera (Cardiocrinum, Notholirion, and Fritillaria) to investigate infrageneric relationships within Lilium as well as to determine the origin and evolution of Korean species of Lilium. We used the internal transcribed spacer sequences of nuclear ribosomal DNA and phylogenetic analysis using maximum parsimony and Bayesian inference identified several major lineages within Lilium. Only one section, Martagon, turned out to be monophyletic in the study. Three sections, Archelirion, Liriotypus, and Pseudolirium, are not monophyletic because two, one, and two species in each section were placed in other lineage, respectively. Two major lineages of section Leucolirion were confirmed in this study, and as several previous studies suggested, section Sinomartagon is highly polyphyletic. The origin of Lilium hansonii, a Korean endemic to Ullung Island, is perplexing given the fact that it has ribotype of Martagon, while its cpDNA haplotype is similar to Sinomartagon. The origin of another endemic, Lilium amabile, is equally elusive and additional phylogenetic and phylogeographic studies will shed light on their evolutions in Korea. We determined that Lilium callosum var. flavum originated from L. callosum in Southern Korea.