Natural Hybrid Origin of the Controversial “Species” Clematis × pinnata (Ranunculaceae) Based on Multidisciplinary Evidence

Interspecific hybridization is common and has often been viewed as a driving force of plant diversity. However, it raises taxonomic problems and thus impacts biodiversity estimation and biological conservation. Although previous molecular phylogenetic studies suggested that interspecific hybridization may be rather common in Clematis, and artificial hybridization has been widely applied to produce new Clematis cultivars for nearly two centuries, the issue of natural hybridization of Clematis has never been addressed in detail. In this study, we tested the hybrid origin of a mesophytic and cold-adapted vine species, Clematis pinnata, which is a rare and taxonomically controversial taxon endemic to northern China. Using field investigations, flow cytometry (FCM), phylogenomic analysis, morphological statistics, and niche modeling, we tested hybrid origin and species status of C. pinnata. The FCM results showed that all the tested species were homoploid (2n = 16). Phylonet and HyDe analyses based on transcriptome data showed the hybrid origins of C. × pinnata from either C. brevicaudata × C. heracleifolia or C. brevicaudata × C. tubulosa. The plastome phylogeny depicted that C. × pinnata in different sampling sites originated by different hybridization events. Morphological analysis showed intermediacy of C. × pinnata between its putative parental species in many qualitative and quantitative characters. Niche modeling results suggested that C. × pinnata had not been adapted to a novel ecological niche independent of its putative parents. These findings demonstrated that plants of C. × pinnata did not formed a self-evolved clade and should not be treated as a species. The present study also suggests that interspecific hybridization is a common mechanism in Clematis to generate diversity and variation, and it may play an important role in the evolution and diversification of this genus. Our study implies that morphological diversity caused by natural hybridization may overstate the real species diversity in Clematis.

Download Full-text

Molecular evidence and ecological niche modeling reveal an extensive hybrid zone among three Bursera species (section Bullockia)

PLoS ONE ◽

10.1371/journal.pone.0260382 ◽

2021 ◽

Vol 16 (11) ◽

pp. e0260382

Author(s):

Eduardo Quintero Melecio ◽

Yessica Rico ◽

Andrés Lira Noriega ◽

Antonio González Rodríguez

Keyword(s):

Interspecific Hybridization ◽

Hybrid Zone ◽

Dna Sequences ◽

Ecological Niche ◽

Ecological Niche Modeling ◽

Molecular Data ◽

Niche Modeling ◽

Hybrid Origin ◽

Putative Hybrid ◽

Molecular Evidence

The genus Bursera, includes ~100 shrub and trees species in tropical dry forests with its center of diversification and endemism in Mexico. Morphologically intermediate individuals have commonly been observed in Mexican Bursera in areas where closely related species coexist. These individuals are assumed to result from interspecific hybridization, but no molecular evidence has supported their hybrid origins. This study aimed to investigate the existence of interspecific hybridization among three Mexican Bursera species (Bullockia section: B. cuneata, B. palmeri and B. bipinnata) from nine populations based on DNA sequences (three nuclear and four chloroplast regions) and ecological niche modeling for three past and two future scenario projections. Results from the only two polymorphic nuclear regions (PEPC, ETS) supported the hybrid origin of morphologically intermediate individuals and revealed that B. cuneata and B. bipinnata are the parental species that are genetically closer to the putative hybrids. Ecological niche modeling accurately predicted the occurrence of putative hybrid populations and showed a potential hybrid zone extending in a larger area (74,000 km2) than previously thought. Paleo-reconstructions showed a potential hybrid zone existing from the Last Glacial Maximum (~ 21 kya) that has increased since the late Holocene to the present. Future ecological niche projections show an increment of suitability of the potential hybrid zone for 2050 and 2070 relative to the present. Hybrid zone changes responded mostly to an increase in elevational ranges. Our study provides the first insight of an extensive hybrid zone among three Mexican Bursera species based on molecular data and ecological niche modeling.

Download Full-text

Black spicules from a new interstitial opheliid polychaete Thoracophelia minuta sp. nov. (Annelida: Opheliidae)

Scientific Reports ◽

10.1038/s41598-020-80702-6 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Naoto Jimi ◽

Shinta Fujimoto ◽

Mami Takehara ◽

Satoshi Imura

Keyword(s):

Developmental Biology ◽

Phylogenetic Analysis ◽

New Species ◽

Morphological Diversity ◽

The Body ◽

Evolutionary Significance ◽

Research Subject ◽

Ecological Diversity ◽

Coelomic Cavity ◽

Molecular Phylogenetic

AbstractThe phylum Annelida exhibits high morphological diversity coupled with its extensive ecological diversity, and the process of its evolution has been an attractive research subject for many researchers. Its representatives are also extensively studied in fields of ecology and developmental biology and important in many other biology related disciplines. The study of biomineralisation is one of them. Some annelid groups are well known to form calcified tubes but other forms of biomineralisation are also known. Herein, we report a new interstitial annelid species with black spicules, Thoracophelia minuta sp. nov., from Yoichi, Hokkaido, Japan. Spicules are minute calcium carbonate inclusions found across the body and in this new species, numerous black rod-like inclusions of calcium-rich composition are distributed in the coelomic cavity. The new species can be distinguished from other known species of the genus by these conspicuous spicules, shape of branchiae and body formula. Further, the new species’ body size is apparently smaller than its congeners. Based on our molecular phylogenetic analysis using 18S and 28S sequences, we discuss the evolutionary significance of the new species’ spicules and also the species' progenetic origin.

Download Full-text

Molecular evidence for the hybrid origin of Rosa lichiangensis (Rosaceae)

Phytotaxa ◽

10.11646/phytotaxa.222.3.5 ◽

2015 ◽

Vol 222 (3) ◽

pp. 221 ◽

Cited By ~ 1

Author(s):

Zhangming Zhu ◽

Xinfen Gao

Keyword(s):

Significant Role ◽

Single Copy ◽

Morphological Characters ◽

Molecular Data ◽

Natural Hybridization ◽

Hybrid Origin ◽

Molecular Evidence ◽

Nuclear Marker

Natural hybridization was assumed to play a significant role in the diversification of Rosa. Rosa lichiangensis was suspected to be of hybrid origin based on its intermediate morphological characters between R. soulieana and R. multiflora var. cathayensis. In this study, four chloroplast regions (ndhC-trnV, ndhF-rpl32, ndhJ-trnF, and psbJ-petA) and a single copy nuclear marker (GAPDH) were used to test the hybrid origin of R. lichiangensis. The results from molecular data supported the hybrid origin of R. lichiangensis and further identified R. soulieana as its maternal progenitor and R. multiflora var. cathayensis as the paternal progenitor.

Download Full-text

Genome-wide sequence-based genotyping supports a nonhybrid origin of Castanea alabamensis

10.1101/680371 ◽

2019 ◽

Author(s):

M. Taylor Perkins ◽

Tetyana Zhebentyayeva ◽

Paul H. Sisco ◽

J. Hill Craddock

Keyword(s):

North American ◽

Distinct Group ◽

Morphological Diversity ◽

Hybrid Origin ◽

Putative Hybrid ◽

Eastern United States ◽

The North ◽

Snp Data ◽

Genome Wide ◽

Conservation Concern

AbstractThe genus Castanea in North America contains multiple tree and shrub taxa of conservation concern. The two species within the group, American chestnut (Castanea dentata) and chinquapin (C. pumila sensu lato), display remarkable morphological diversity across their distributions in the eastern United States and southern Ontario. Previous investigators have hypothesized that hybridization between C. dentata and C. pumila has played an important role in generating morphological variation in wild populations. A putative hybrid taxon, Castanea alabamensis, was identified in northern Alabama in the early 20th century; however, the question of its hybridity has been unresolved. We tested the hypothesized hybrid origin of C. alabamensis using genome-wide sequence-based genotyping of C. alabamensis, all currently recognized North American Castanea taxa, and two Asian Castanea species at >100,000 single-nucleotide polymorphism (SNP) loci. With these data, we generated a high-resolution phylogeny, tested for admixture among taxa, and analyzed population genetic structure of the study taxa. Bayesian clustering and principal components analysis provided no evidence of admixture between C. dentata and C. pumila in C. alabamensis genomes. Phylogenetic analysis of genome-wide SNP data indicated that C. alabamensis forms a distinct group within C. pumila sensu lato. Our results are consistent with the model of a nonhybrid origin for C. alabamensis. Our finding of C. alabamensis as a genetically and morphologically distinct group within the North American chinquapin complex provides further impetus for the study and conservation of the North American Castanea species.

Download Full-text

Phylogenetics of the mycoheterotrophic genus Thismia (Thismiaceae: Dioscoreales) with a focus on the Old World taxa: delineation of novel natural groups and insights into the evolution of morphological traits

Botanical Journal of the Linnean Society ◽

10.1093/botlinnean/boaa017 ◽

2020 ◽

Vol 193 (3) ◽

pp. 287-315 ◽

Cited By ~ 2

Author(s):

Ekaterina A Shepeleva ◽

Mikhail I Schelkunov ◽

Michal Hroneš ◽

Michal Sochor ◽

Martin Dančák ◽

...

Keyword(s):

Significant Proportion ◽

Morphological Diversity ◽

Taxonomic Revision ◽

Morphological Characters ◽

Morphological Description ◽

Molecular Evidence ◽

Ancestral State ◽

Old World ◽

Molecular Phylogenetic ◽

Floral Characters

Abstract Thismia is a genus of > 80 mycoheterotrophic species characterized by a peculiar appearance and complex floral morphology. A significant proportion of the species and morphological diversity of Thismia has only been uncovered in the past two decades, and new discoveries continue to be made. Given that many new data have recently become available, and the most comprehensive taxonomic revision of the genus from 1938 addresses less than half of the currently known species, previous hypotheses for species relationships and infrageneric taxonomic classification in Thismia was in need of review. Extensive molecular phylogenetic studies of Thismia at the genus level have never been presented. We investigate the phylogenetic relationships of 41 species (and one variety) of Thismia from the Old World. Our study comprises 68 specimens (for 28 of which the data were newly generated), including outgroup taxa broadly representing Thismiaceae (= Burmanniaceae p.p. sensuAPG IV, 2016), and is based on two nuclear and one mitochondrial marker. We use maximum likelihood and Bayesian inference to infer relationships among the taxa. We also constructed a morphological dataset of 12 mostly floral characters, comparing these characters to hypotheses based on molecular evidence to identify putative synapomorphies for major clades and to discuss hypotheses regarding the evolution of structural traits in the genus. Our analyses indicate that the majority of currently accepted infrageneric taxa of Thismia are polyphyletic. We find support for the monophyly of the Old World group, in which we recognize five well-supported lineages (clades); the only New World species studied appears to be related to the Neotropical genus Tiputinia. Ancestral state reconstructions demonstrate that the evolution of most morphological characters was homoplastic, but we identify characters that provide each of the five clades of Old World Thismia with a unique morphological description. The geographical distribution of the species under study is also shown to be consistent with the major clades. Our investigation provides a phylogenetic basis for the development of a novel sectional classification of Thismia reflecting morphological and geographical traits.

Download Full-text

Phylogenomic analysis of echinoderm class relationships supports Asterozoa

Proceedings of The Royal Society B Biological Sciences ◽

10.1098/rspb.2014.0479 ◽

2014 ◽

Vol 281 (1786) ◽

pp. 20140479 ◽

Cited By ~ 75

Author(s):

Maximilian J. Telford ◽

Christopher J. Lowe ◽

Christopher B. Cameron ◽

Olga Ortega-Martinez ◽

Jochanan Aronowicz ◽

...

Keyword(s):

Convergent Evolution ◽

Sea Urchins ◽

Phylogenetic Signal ◽

Strong Support ◽

Phylogenomic Analysis ◽

Phylogenetic Studies ◽

Phylogenetic Methods ◽

Complete Dataset ◽

Type Larva ◽

Molecular Phylogenetic

While some aspects of the phylogeny of the five living echinoderm classes are clear, the position of the ophiuroids (brittlestars) relative to asteroids (starfish), echinoids (sea urchins) and holothurians (sea cucumbers) is controversial. Ophiuroids have a pluteus-type larva in common with echinoids giving some support to an ophiuroid/echinoid/holothurian clade named Cryptosyringida. Most molecular phylogenetic studies, however, support an ophiuroid/asteroid clade (Asterozoa) implying either convergent evolution of the pluteus or reversals to an auricularia-type larva in asteroids and holothurians. A recent study of 10 genes from four of the five echinoderm classes used ‘phylogenetic signal dissection’ to separate alignment positions into subsets of (i) suboptimal, heterogeneously evolving sites (invariant plus rapidly changing) and (ii) the remaining optimal, homogeneously evolving sites. Along with most previous molecular phylogenetic studies, their set of heterogeneous sites, expected to be more prone to systematic error, support Asterozoa. The homogeneous sites, in contrast, support an ophiuroid/echinoid grouping, consistent with the cryptosyringid clade, leading them to posit homology of the ophiopluteus and echinopluteus. Our new dataset comprises 219 genes from all echinoderm classes; analyses using probabilistic Bayesian phylogenetic methods strongly support Asterozoa. The most reliable, slowly evolving quartile of genes also gives highest support for Asterozoa; this support diminishes in second and third quartiles and the fastest changing quartile places the ophiuroids close to the root. Using phylogenetic signal dissection, we find heterogenous sites support an unlikely grouping of Ophiuroidea + Holothuria while homogeneous sites again strongly support Asterozoa. Our large and taxonomically complete dataset finds no support for the cryptosyringid hypothesis; in showing strong support for the Asterozoa, our preferred topology leaves the question of homology of pluteus larvae open.

Download Full-text

A molecular phylogenetic analysis of strombid gastropod morphological diversity

Molecular Phylogenetics and Evolution ◽

10.1016/j.ympev.2006.05.027 ◽

2006 ◽

Vol 41 (2) ◽

pp. 436-444 ◽

Cited By ~ 27

Author(s):

Jared M. Latiolais ◽

Michael S. Taylor ◽

Kaustuv Roy ◽

Michael E. Hellberg

Keyword(s):

Phylogenetic Analysis ◽

Morphological Diversity ◽

Molecular Phylogenetic Analysis ◽

Molecular Phylogenetic

Download Full-text

Morphological and molecular analyses reveal two new species of Guepinia from China

Phytotaxa ◽

10.11646/phytotaxa.475.2.3 ◽

2020 ◽

Vol 475 (2) ◽

pp. 91-101

Author(s):

YANG SHEN ◽

LI FAN

Keyword(s):

New Species ◽

Phylogenetic Analyses ◽

Northern China ◽

Molecular Analyses ◽

Two New Species ◽

Molecular Phylogenetic ◽

Reddish Orange

Guepinia alba sp. nov. and G. shanxiense sp. nov. are described and illustrated from Northern China in this paper. Morphologically, G. alba is distinguished from other Guepinia species by whitish basidiomata and 4-spored basidia while G. shanxiense is diagnosed by reddish orange basidiomata and ellipsoid to oblong ellipsoid basidiospores. Molecular phylogenetic analyses based on ITS and nrLSU sequences support the establishment of the two new species.

Download Full-text

Hybrid Origin and Genomic Mosaicism of Dubautia scabra (Hawaiian Silversword Alliance; Asteraceae, Madiinae)

Systematic Botany ◽

10.1600/036364408785679815 ◽

2008 ◽

Vol 33 (3) ◽

pp. 589-597 ◽

Cited By ~ 16

Author(s):

Elizabeth A. Friar ◽

Linda M. Prince ◽

Jennifer M. Cruse-Sanders ◽

Mitchell E. McGlaughlin ◽

Charles A. Butterworth ◽

...

Keyword(s):

Single Copy ◽

Nuclear Genes ◽

Hybrid Origin ◽

Internal Transcribed Spacer Region ◽

Hybrid Species ◽

Cytogenetic Data ◽

Molecular Phylogenetic ◽

Distinct Lineage ◽

Phylogenetic Hypotheses ◽

Genomic Regions

Incongruence among different estimates of species relationships in plants, from different molecules, cytogenetic data, biogeographic data, morphological/anatomical data or other sources, has been used frequently as an indication of introgression, hybrid species origin, or chloroplast (cp) capture. In plants, these incongruences are most often seen between data derived from the nuclear vs. the cp genomes and the nuclear markers used for comparison usually have been from the nuclear ribosomal (nr) internal transcribed spacer region (ITS). The amount of genomic material shared between introgressing species can be highly variable. In some of these cases, other nuclear genomic regions have moved between species without leaving a signature on the nrITS. An example of well-supported phylogenetic incongruence is the placement of Dubautia scabra (DC.) D. D. Keck in the Hawaiian silversword alliance (HSA); evolutionary hypotheses for D. scabra based on molecular as opposed to cytogenetic data are strongly discordant. In this paper, we test these two conflicting phylogenetic hypotheses regarding the evolutionary relationships of Dubautia scabra using evidence from six low-copy nuclear genes, as well as multiple chloroplast noncoding regions and nrITS. The nrITS region is also examined for the presence of multiple copy types. Incongruence between inferred relationships based on nuclear chromosomal arrangements and molecular phylogenetic data from chloroplast DNA and nrITS is resolved in favor of a hypothesis of ancient hybridization rather than cytogenetic homoplasy involving dysploidy. Most single-copy nuclear genes track histories of D. scabra compatible with cytogenetic data whereas chloroplast and nrITS data track a common, different history that appears to reflect hybridization with a chromosomally distinct lineage that also occurs on Maui Nui and Hawai'i (the Big Island).

Download Full-text

The Phylogenetic Position of Vincetoxicum pannonicum (Borhidi) Holub Supports the Species' Allopolyploid Hybrid Origin

Acta Societatis Botanicorum Poloniae ◽

10.5586/asbp.8931 ◽

2020 ◽

Vol 89 (3) ◽

Cited By ~ 1

Author(s):

Orsolya Horváth ◽

Levente Laczkó ◽

Zsuzsa Lisztes-Szabó ◽

Attila Molnár V. ◽

Agnieszka Popiela ◽

...

Keyword(s):

Genome Size ◽

Hybrid Origin ◽

Phylogenetic Position ◽

Gene Trees ◽

Separate Species ◽

Diploid Parent ◽

Hybridization Event ◽

Pollen Donor ◽

Molecular Phylogenetic ◽

Allotetraploid Hybrid

The Pannonian endemic species Vincetoxicum pannonicum was described from specimens collected in Hungary and occurs at only few locations. It is considered “vulnerable” according to the International Red List. The chromosome set was reported to be tetraploid, and the species was hypothesized to be an allotetraploid hybrid of the Balkan species V. fuscatum and the Adriatic species hirundinaria subsp. adriaticum. We investigated the origin of V. pannonicum using molecular phylogenetic methods by separately analyzing the multicopy nuclear ribosomal internal transcribed spacer (nrITS) and the plastid-encoded trnH-psbA DNA regions and by evaluating discrepancies between the produced gene trees. Paralogs in the nrITS region clustered in two main groups, one of which was closest to V. fuscatum, and the other included V. hirundinaria subsp. adriaticum. According to trnH-psbA sequences, V. pannonicum and V. hirundinaria subsp. adriaticum formed a single group. Our results show that V. pannonicum diversified because of hybrid speciation, in which V. fuscatum was the pollen donor. We discovered a similar placement of V. maeoticum, which suggests a further hybridization event between V. fuscatum and a species of the V. hirundinaria group. Our genome-size estimate indicates almost sixfold larger genome size in V. pannonicum compared to the maternal diploid parent, suggesting hexaploidy; however, V. pannonicum is tetraploid. This may suggest cytological diploidization in the allopolyploid V. pannonicum. We observed substantial genetic distance between V. hirundinaria subsp. adriaticum and all other subspecies of V. hirundinaria, and we therefore propose that V. adriaticum should be regarded as a separate species.

Download Full-text