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  • 1
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    Evolutionary relationships of the ancient fern lineage the adder's tongues (Ophioglossaceae) with description of Sahashia gen. nov
    Wiley ; 2020
    In:  Cladistics Vol. 36, No. 4 ( 2020-08), p. 380-393
    Details
    In: Cladistics, Wiley, Vol. 36, No. 4 ( 2020-08), p. 380-393
    Abstract: As an ancient lineage of ferns, Ophioglossaceae are evolutionarily among the most fascinating because they have the highest chromosome count of any known organism as well as the presence of sporophores, subterranean gametophytes, eusporangiate sporangia without annuli, and endophytic fungi. Previous studies have produced conflicting results, identifyingsome lineages with unresolved relationships, and have paid much attention to the subfamily Botrychioideae. But the other species‐rich subfamily, Ophioglossoideae, has remained largely understudied and only up to 12 accessions of Ophioglossoideae have been sampled. In this study, DNA sequences of seven plastid markers of 149 accessions (75 in Ophioglossoideae) representing approximately 82 species (approximately 74% of estimated species diversity sensu J. Syst. Evol., 2016, 54, 563) in the family, and two Marattiaceae and two Psilotaceae, are used to infer a phylogeny. Our major results include: (1) Ophioglossaceae are resolved as monophyletic with strong support, and so are all four subfamilies and genera sensu PPG I except Botrypus and Ophioglossum ; (2) a new genus Sahashia is segregated from Botrypus so that the monophyly of Botrypus can be retained; (3) the monophyly of Ophioglossum in its current circumscription is uncertain in spite of our large character sampling; (4) there is substantial cryptic speciation in Ophioderma detected by our molecular and morphological study; (5) the recognition of Holubiella is advocated based on its morphology and its sister relationship with Sceptridium ; and (6) a novel sister relationship between Botrychium and the JHS clade ( Japanobotrychium + ( Holubiella  +  Sceptridium )) is discovered.
    Type of Medium: Online Resource
    ISSN: 0748-3007 , 1096-0031
    URL: Issue
    URL: Article
    DOI: 10.1111/cla.v36.4
    DOI: 10.1111/cla.12408
    Language: English
    Publisher: Wiley
    Publication Date: 2020
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  • 2
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    A global plastid phylogeny of the cliff fern family Woodsiaceae and a two‐genus classification of Woodsiaceae with the description of × Woodsimatium nothogen. nov.
    Wiley ; 2019
    In:  TAXON Vol. 68, No. 6 ( 2019-12), p. 1149-1172
    Details
    In: TAXON, Wiley, Vol. 68, No. 6 ( 2019-12), p. 1149-1172
    Abstract: The taxonomy of the cliff fern family Woodsiaceae has been controversial with 22–59 species in 1–7 genera recognized in various classifications. This is mainly due to limited taxon sampling (up to 33 accessions representing up to 21 species) and poor resolution in molecular studies so far. In the present study, DNA sequences of five plastid markers ( atpA , matK, rbcL, rps4 + rps4‐trnS, trnL + trnL‐F ) of 152 accessions representing ca. 43 out of ca. 65 species estimated of Woodsiaceae (122 accessions), and 30 non‐Woodsiaceae accessions from the most closely related four families (Athyriaceae, Blechnaceae, Onocleaceae, Thelypteridaceae) were used to infer a phylogeny. Our major results include: (1) Woodsiaceae are strongly supported as monophyletic; (2) Two major clades representing the deepest split in Woodsiaceae are identified, corresponding to the two recently proposed subfamilies, Woodsioideae and Protowoodsioideae; (3) Within Woodsioideae and Protowoodsioideae, two and three well‐supported subclades, respectively, are determined; (4) Cheilanthopsis is resolved as paraphyletic in relation to Hymenocystis (sampled for the first time) and Protowoodsia ; (5) Physematium and Woodsiopsis are paraphyletic in relation to a clade containing Cheilanthopsis , Hymenocystis , and Protowoodsia ; (6) Evolution of 13 morphological characters is inferred in a phylogenetic context, and morphological synapomorphies of each of the five major subclades are identified; (7) We propose to recognize two genera in Woodsiaceae based on deep divergence (ca. 45 Ma), morphology, chromosome number, and geographic distribution: Physematium (syn.: Cheilanthopsis , Hymenocystis , Protowoodsia , Woodsiopsis ) and Woodsia (syn.: Eriosoriopsis ), and Physematium is further divided into three subgenera and Woodsia into two subgenera; (8) we describe ×Woodsimatium , a hybrid genus (nothogen. nov.) between the two genera recognized. A taxonomic synopsis of the family is provided, and 15 new combinations are made.
    Type of Medium: Online Resource
    ISSN: 0040-0262 , 1996-8175
    URL: Issue
    URL: Article
    DOI: 10.1002/tax.v68.6
    DOI: 10.1002/tax.12180
    Language: English
    Publisher: Wiley
    Publication Date: 2019
    detail.hit.zdb_id: 2081189-5
    detail.hit.zdb_id: 204216-2
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  • 3
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    Circumscription and phylogeny of the fern family Tectariaceae based on plastid and nuclear markers, with the description of two new genera: Draconopteris and Malaifilix (Tectariaceae)
    Wiley ; 2016
    In:  TAXON Vol. 65, No. 4 ( 2016-08), p. 723-738
    Details
    In: TAXON, Wiley, Vol. 65, No. 4 ( 2016-08), p. 723-738
    Abstract: The circumscription and the phylogeny of the fern family Tectariaceae have been controversial. Previous molecular studies have supported the monophyly of this family, with 4–5 genera. However, these studies were exclusively based on plastid markers and relatively small sampling, especially of the non‐Tectaria genera. In the present study, DNA sequences of eight plastid and one nuclear markers of 25 accessions representing 19 species of Tectaria and 58 accessions representing ca. 90% of the non‐Tectaria species in the family (including Arthropteris) were used to infer a phylogeny using maximum likelihood (ML), Bayesian inference, and maximum parsimony. Our major results include: (1) Tectaria as currently circumscribed is not monophyletic and can be divided into three genera: Tectaria s.str., Draconopteris (gen. nov.) from Central to South America, and Malaifilix (gen. nov.) from Malesia; (2) Draconopteris and Malaifilix, the two new genera, together with Pteridrys, form a strongly supported clade; (3) in our ML analyses, the clade containing Draconopteris, Malaifilix, and Pteridrys (the DMP clade) is resolved as sister to the rest of Tectariaceae and Arthropteris is sister to Tectaria + (Hypoderris + Triplophyllum), suggesting that Arthropteris should be treated as a member of Tectariaceae, and thus Tectariaceae contains seven genera: Arthropteris, Draconopteris, Hypoderris, Malaifilix, Pteridrys, Tectaria, and Triplophyllum; (4) with the well‐supported relationships among the members of Tectariaceae, anastomosing venation in the family is inferred to have evolved independently at least three times; (5) Nephrolepis is strongly supported as sister to a clade containing Cyclopeltis, Dracoglossum, and Lomariopsis, and thus we advocate that Lomariopsidaceae include these four genera (plus the unsampled Thysanosoria); and (6) intercontinental dispersal appears to have played an important role in shaping the extant distribution of Tectariaceae.
    Type of Medium: Online Resource
    ISSN: 0040-0262 , 1996-8175
    URL: Article
    DOI: 10.12705/654.3
    Language: English
    Publisher: Wiley
    Publication Date: 2016
    detail.hit.zdb_id: 2081189-5
    detail.hit.zdb_id: 204216-2
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  • 4
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    Pteridryaceae: A new fern family of Polypodiineae (Polypodiales) including taxonomic treatments
    Wiley ; 2018
    In:  Journal of Systematics and Evolution Vol. 56, No. 2 ( 2018-03), p. 148-173
    Details
    In: Journal of Systematics and Evolution, Wiley, Vol. 56, No. 2 ( 2018-03), p. 148-173
    Abstract: We undertook phylogenetic analyses to resolve the relationships of Pteridrys and related taxa based on six plastid markers ( atpA , atpB , matK & rps16‐matK , rbcL , rps4 & rps4‐trnS , and trnL & trnL‐F ) and nuclear pgiC . We included 195 accessions representing approximately 147 species in 38 genera, and seven of the nine families in Polypodiineae (eupolypods I). Tectariaceae s.l. (i.e., Arthropteris , Draconopteris , Hypoderris , Malaifilix , Pteridrys , Tectaria , and Triplophyllum in addition to Polydictyum ) is recovered as monophyletic (97% maximum likelihood bootstrap value), but with low ( 〈 50%) maximum parsimony jackknife value. The family Tectariaceae s.l. is therefore the only family in ferns without a corresponding non‐parametric‐based strong support in spite of our data totaling 9616 aligned base pairs. Tectariaceae s.l. can not be unambiguously recognized by any of the 13 morphological characters analyzed. However, if the clade composed of Draconopteris , Malaifilix , Polydictyum , and Pteridrys (DMPP) is recognized as a distinct family, at least four morphological characters enable the distinction of the DMPP clade from its sister clade. Considering the uncertainty in the monophyly, the diagnosability, and the deep divergence, we propose to establish a new family, Pteridryaceae, to accommodate the DMPP clade. Species of Pteridryaceae share mostly the following characteristics: erect to suberect rhizomes, reduced basal pinnae, anastomosing or free venation, absence of catenate hairs at the leaf surface, and perine ornamentation lacking spines or spinules. Identification keys are provided for the four genera and 31 species of the DMPP clade (or Pteridryaceae). Reflecting the presented results, the recognition of Arthropteridaceae is the preferred taxonomic status of the Arthropteris clade.
    Type of Medium: Online Resource
    ISSN: 1674-4918 , 1759-6831
    URL: Issue
    URL: Article
    DOI: 10.1111/jse.v56.2
    DOI: 10.1111/jse.12305
    Language: English
    Publisher: Wiley
    Publication Date: 2018
    detail.hit.zdb_id: 2516638-4
    SSG: 6,25
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  • 5
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    A large‐scale phylogeny of the lycophyte genus Selaginella (Selaginellaceae: Lycopodiopsida) based on plastid and nuclear loci
    Wiley ; 2016
    In:  Cladistics Vol. 32, No. 4 ( 2016-08), p. 360-389
    Details
    In: Cladistics, Wiley, Vol. 32, No. 4 ( 2016-08), p. 360-389
    Abstract: The lycophyte genus Selaginella alone constitutes the family Selaginellaceae, the largest of the lycophyte families. The genus is estimated to contain 700–800 species distributed on all continents except Antarctica, with highest species diversity in tropical and subtropical regions. The monophyly of Selaginella in this broad sense has rarely been doubted, whereas its intrageneric classification has been notoriously contentious. Previous molecular studies were based on very sparse sampling of Selaginella (up to 62 species) and often used DNA sequence data from one genome. In the present study, DNA sequences of one plastid ( rbcL ) and one nuclear ( ITS ) locus from 394 accessions representing approximately 200 species of Selaginella worldwide were used to infer a phylogeny using maximum likelihood, Bayesian inference and maximum parsimony methods. The study identifies strongly supported major clades and well resolves relationships among them. Major results include: (i) six deep‐level clades are discovered representing the deep splits of Selaginella ; and (ii) 20 major clades representing 20 major evolutionary lineages are identified, which differ from one another in molecular, macro‐morphological, ecological and spore features, and/or geographical distribution.
    Type of Medium: Online Resource
    ISSN: 0748-3007 , 1096-0031
    URL: Issue
    URL: Article
    DOI: 10.1111/cla.2016.32.issue-4
    DOI: 10.1111/cla.12136
    Language: English
    Publisher: Wiley
    Publication Date: 2016
    detail.hit.zdb_id: 1462608-1
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  • 6
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    A global plastid phylogeny of the fern genus Asplenium (Aspleniaceae)
    Wiley ; 2020
    In:  Cladistics Vol. 36, No. 1 ( 2020-02), p. 22-71
    Details
    In: Cladistics, Wiley, Vol. 36, No. 1 ( 2020-02), p. 22-71
    Abstract: The infrageneric relationships and taxonomy of the largest fern genus, Asplenium (Aspleniaceae), have remained poorly understood. Previous studies have focused mainly on specific species complexes involving a few or dozens of species only, or have achieved a large taxon sampling but only one plastid marker was used. In the present study, DNA sequences from six plastid markers ( atpB , rbcL , rps4 , rps4 ‐ trnS , trnL and trnL‐F ) of 1030 accessions (616 of them newly sequenced here) representing c . 420 species of Asplenium (60% of estimated species diversity), 16 species of Hymenasplenium , three Diplaziopsidaceae, and four Rhachidosoraceae were used to produce the largest genus‐level phylogeny yet for ferns. Our major results include: (i) Asplenium as broadly circumscribed is monophyletic based on our inclusion of representatives of 32 of 38 named segregate genera; (ii) 11 major clades in Asplenium are identified, and their relationships are mostly well‐resolved and strongly supported; (iii) numerous species, unsampled in previous studies, suggest new relationships and numerous cryptic species and species complexes in Asplenium ; and (iv) the accrued molecular evidence provides an essential foundation for further investigations of complex patterns of geographical diversification, speciation and reticulate evolution in this family.
    Type of Medium: Online Resource
    ISSN: 0748-3007 , 1096-0031
    URL: Issue
    URL: Article
    DOI: 10.1111/cla.v36.1
    DOI: 10.1111/cla.12384
    Language: English
    Publisher: Wiley
    Publication Date: 2020
    detail.hit.zdb_id: 1462608-1
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  • 7
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    Lectotypification of the name Lilium lancifolium (Liliaceae)
    Wiley ; 2017
    In:  TAXON Vol. 66, No. 1 ( 2017-02), p. 172-174
    Details
    In: TAXON, Wiley, Vol. 66, No. 1 ( 2017-02), p. 172-174
    Abstract: We discuss the typification of the name Lilium lancifolium (Liliaceae). We designate a specimen from UPS as the lectotype.
    Type of Medium: Online Resource
    ISSN: 0040-0262 , 1996-8175
    URL: Article
    DOI: 10.12705/661.12
    Language: English
    Publisher: Wiley
    Publication Date: 2017
    detail.hit.zdb_id: 2081189-5
    detail.hit.zdb_id: 204216-2
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  • 8
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    A global plastid phylogeny of the brake fern genus Pteris (Pteridaceae) and related genera in the Pteridoideae
    Wiley ; 2015
    In:  Cladistics Vol. 31, No. 4 ( 2015-08), p. 406-423
    Details
    In: Cladistics, Wiley, Vol. 31, No. 4 ( 2015-08), p. 406-423
    Abstract: The brake fern genus Pteris belongs to the Pteridaceae subfamily Pteridoideae. It contains 200–250 species distributed on all continents except Antarctica, with its highest species diversity in tropical and subtropical regions. The monophyly of Pteris has long been in question because of its great morphological diversity and because of the controversial relationships of the Australian endemic monospecific genus Platyzoma . The circumscription of the Pteridoideae has likewise been uncertain. Previous studies typically had sparse sampling of Pteris species and related genera and used limited DNA sequence data. In the present study, DNA sequences of six plastid loci of 146 accessions representing 119 species of Pteris (including the type of the genus) and 18 related genera were used to infer a phylogeny using maximum‐likelihood, Bayesian‐inference and maximum‐parsimony methods. Our major results include: (i) the previous uncertain relationships of Platyzoma were due to long‐branch attraction; (ii) Afropteris , Neurocallis , Ochropteris and Platyzoma are all embedded within a well‐supported Pteris sensu lato ; (iii) the traditionally circumscribed Jamesonia is paraphyletic in relation to a monophyletic Eriosorus ; (iv) Pteridoideae contains 15 genera: Actiniopteris , Anogramma , Austrogramme , Cerosora , Cosentinia , Eriosorus , Jamesonia , Nephopteris (no molecular data), Onychium , Pityrogramma , Pteris , Pterozonium , Syngramma , Taenitis and Tryonia ; and (v) 15 well‐supported clades within Pteris are identified, which differ from one another on molecular, morphological and geographical grounds, and represent 15 major evolutionary lineages.
    Type of Medium: Online Resource
    ISSN: 0748-3007 , 1096-0031
    URL: Issue
    URL: Article
    DOI: 10.1111/cla.2015.31.issue-4
    DOI: 10.1111/cla.12094
    Language: English
    Publisher: Wiley
    Publication Date: 2015
    detail.hit.zdb_id: 1462608-1
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  • 9
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    A global phylogeny of Lycopodiaceae (Lycopodiales; lycophytes) with the description of a new genus, Brownseya , from Oceania
    Wiley ; 2022
    In:  TAXON Vol. 71, No. 1 ( 2022-02), p. 25-51
    Details
    In: TAXON, Wiley, Vol. 71, No. 1 ( 2022-02), p. 25-51
    Abstract: Lycopodiaceae are one of the oldest lineages of any living vascular plants and contain about 400 species distributed on all continents except Antarctica, with its highest diversity in tropical regions. Previous studies on the morphology, anatomy, and molecular systematics of Lycopodiaceae have made substantial progress in understanding the diversity and evolution of the family, but major issues remain. In particular, earlier studies had relatively sparse taxon sampling, some critical relationships among the genera have not been well resolved, and the monophyly of some genera (e.g., Huperzia , Lycopodiella , Pseudolycopodiella , Spinulum ) has not been robustly tested with large sampling. In this study, we apply maximum likelihood, maximum parsimony, and Bayesian inference to a dataset of 1150 (918 newly generated) DNA sequences of seven plastid markers ( atpA , psbA‐trnH , rbcL , rps4 , rps4‐trnS , trnL , trnL‐F ) of 334 accessions representing ca. 155 (ca. 39% of all) species in the family to infer a global phylogeny. Our major results include: (1) the tree is resolved into three primary clades corresponding to the three subfamilies, Huperzioideae, Lycopodioideae, and Lycopodielloideae; (2) these three primary clades are resolved into 17 major clades, of which 16 represent genera recognized in the PPG I classification, while Lycopodiella serpentina is resolved as sister to Palhinhaea , and thus a new genus, Brownseya , is described, and a key to genera of Lycopodielloideae is given; (3) Phylloglossum is strongly or moderately supported as sister to Phlegmariurus in ML and MP analyses (but not in BI analysis), and thus our evidence supports the recognition of Phlegmariurus in order to maintain a monophyletic Huperzia ; (4) Lycopodiella is sister to Pseudolycopodiella and they together are sister to Lateristachys  + ( Brownseya +  Palhinhaea ); (5) Huperzia , Lycopodiella , Pseudolycopodiella , and Spinulum are each strongly supported as monophyletic; (6) spore morphology is well consistent with the phylogenetic relationships in the family; and (7) based on these results we recognize 17 genera in three subfamilies in the family.
    Type of Medium: Online Resource
    ISSN: 0040-0262 , 1996-8175
    URL: Issue
    URL: Article
    DOI: 10.1002/tax.v71.1
    DOI: 10.1002/tax.12597
    Language: English
    Publisher: Wiley
    Publication Date: 2022
    detail.hit.zdb_id: 2081189-5
    detail.hit.zdb_id: 204216-2
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  • 10
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    Chromosome‐level de novo genome assembly and whole‐genome resequencing of the threatened species Acanthochlamys bracteata (Velloziaceae) provide insights into alpine plant divergence in a biodiversity hotspot
    Wiley ; 2022
    In:  Molecular Ecology Resources Vol. 22, No. 4 ( 2022-05), p. 1582-1595
    Details
    In: Molecular Ecology Resources, Wiley, Vol. 22, No. 4 ( 2022-05), p. 1582-1595
    Abstract: The Hengduan Mountains region is an important hotspot of alpine plant diversity and endemism. Acanthochlamys bracteata is a species of a threatened monotypic genus endemic to the Hengduan Mountains. In this study, we present a high‐quality, chromosome‐level reference genome for A .  bracteata , constructed using long reads, short reads and Hi‐C technology. We characterized its genetic diversity, population structure, demographic history and gene flow by resequencing individuals collected across its distribution. Comparative genomics analyses based on sequence information from single‐copy orthologous genes revealed that A . bracteata and Dioscorea rotundata diverged ~104.5 million years ago. Whole‐genome resequencing based on population genetic analysis revealed that the division of the 14 populations into 10 distinct clusters reflected geographical divergence, and three separate high levels of gene flow occurred sequentially between isolated populations of the Hengduan Mountains, a finding which is consistent with the turnover between ice ages and interglacial periods. Our findings indicate that Quaternary climatic changes played an important role in shaping the genetic structure and demographic trajectories of A . bracteata , and provide critical insights into the genetic status and evolutionary history of this poorly understood species, and possibly other alpine plants with a similar distribution. This study demonstrates the usefulness of population genomics for evaluating the effects of past climatic changes and identifying conservation units for the conservation and management of threatened species. Our high‐quality genome represents a valuable resource for future studies of the underlying molecular mechanisms of adaptive evolution and provides insight for further comparative genomic analysis with other Velloziaceae species.
    Type of Medium: Online Resource
    ISSN: 1755-098X , 1755-0998
    URL: Issue
    URL: Article
    DOI: 10.1111/men.v22.4
    DOI: 10.1111/1755-0998.13562
    Language: English
    Publisher: Wiley
    Publication Date: 2022
    detail.hit.zdb_id: 2406833-0
    SSG: 12
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