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  • 1
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    Online Resource
    Biogeography and Divergence in Guaiacum sanctum (Zygophyllaceae) Revealed in Chloroplast DNA: Implications for Conservation in the Florida Keys
    Wiley ; 2009
    In:  Biotropica Vol. 41, No. 1 ( 2009-01), p. 120-127
    Details
    In: Biotropica, Wiley, Vol. 41, No. 1 ( 2009-01), p. 120-127
    Abstract: Guaiacum sanctum (lignumvitae, guayacán) consta de árboles de importancia económica y en peligro de extinción y endémicos a neotrópicos secos. Estos árboles históricamente se cosecharon en abundancia y ahora G. sanctum se encuentra entre las especies nombradas por UICN y CITES. Guaiacum sanctum se encontraba por todo Florida Keys, pero fragmentación del hábitat antropogénico y explotación han dejado solamente una populación significante, en Lignumvitae Key. La ecología de esta populación adicionalmente es sujeta a efectos mediados por huracanes y por un parasito endémico. Perfiles genéticos se determinaron para la populación Lignumvitae y populaciones de origen putativas de G. sanctum para asesar variabilidad y para poner a prueba hipótesis biogeográficas. Estos datos se analizaron con analices filogenéticos y analices estadísticos de mezquindad. Los resultados se interpretaron más fácilmente indicando una fragmentación histórica seguida por aislamiento a la larga. Sin embargo, dispersión recién o flujo de genes no pudieron ser excluidos por completo. Ambos tipos de análisis firmemente apoyan una significante divergencia genética entre populaciones caribeñas y mexicanas de G. sanctum y asimismo sugieren dispersión bidireccional de G. sanctum a Lignumvitae Key de ambos el Caribe y de México. Estos resultados informan el preceso de restablecer G. sanctum en las Keys.
    Type of Medium: Online Resource
    ISSN: 0006-3606 , 1744-7429
    URL: Issue
    URL: Article
    DOI: 10.1111/btp.2008.41.issue-1
    DOI: 10.1111/j.1744-7429.2008.00453.x
    RVK:
    WA 15000
    Language: English
    Publisher: Wiley
    Publication Date: 2009
    detail.hit.zdb_id: 2052061-X
    SSG: 12
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  • 2
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    Grass plastomes reveal unexpected paraphyly with endemic species of Micrairoideae from India and new haplotype markers in Arundinoideae
    Wiley ; 2017
    In:  American Journal of Botany Vol. 104, No. 2 ( 2017-02), p. 286-295
    Details
    In: American Journal of Botany, Wiley, Vol. 104, No. 2 ( 2017-02), p. 286-295
    Abstract: We investigated the little‐studied Arundinoideae/Micrairoideae clade of grasses with an innovative plastome phylogenomic approach. This method gives robust results for taxa of uncertain phylogenetic placement. Arundinoideae comprise ∼45 species, although historically was much larger. Arundinoideae is notable for the widely invasive Phragmites australis . Micrairoideae comprise nine genera and ∼200 species. Some are threatened with extinction, including Hubbardia , some Isachne spp., and Limnopoa . Two micrairoid genera, Eriachne and Pheidochloa , exhibit C 4 photosynthesis in this otherwise C 3 subfamily and represent an independent origin of the C 4 pathway among grasses. METHODS: Five new plastomes were sequenced with next‐generation sequencing‐by‐synthesis methods. Plastomes were assembled by de novo methods and phylogenetically analyzed with eight other recently published arundinoid or micrairoid plastomes and 11 outgroup species. Stable carbon isotope ratios were determined for micrairoid and arundinoid species to investigate ambiguities in the proxy evidence for C 4 photosynthesis. KEY RESULTS: Phylogenomic analyses showed strong support for ingroup nodes in the Arundinoideae/Micrairoideae subtree, including a paraphyletic clade of Hubbardieae with Isachneae. Anatomical, biochemical, and positively selected sites data are ambiguous with regard to the photosynthetic pathways in Micrairoideae. Species of Hubbardia , Isachne , and Limnopoa were definitively shown by δ 13 C measurements to be C 3 and Eriachne to be C 4 . CONCLUSIONS: Our plastome phylogenomic analyses for Micrairoideae are the first phylogenetic results to indicate paraphyly between Isachneae and Hubbardieae. The definitive δ 13 C data for four genera of Micrairoideae indicates the breadth of variation possible in the proxy evidence for photosynthetic pathways of both C 3 and C 4 taxa.
    Type of Medium: Online Resource
    ISSN: 0002-9122 , 1537-2197
    URL: Article
    DOI: 10.3732/ajb.1600285
    RVK:
    WA 15000
    Language: English
    Publisher: Wiley
    Publication Date: 2017
    detail.hit.zdb_id: 2053581-8
    SSG: 12
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  • 3
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    A multi–step comparison of short–read full plastome sequence assembly methods in grasses
    Wiley ; 2014
    In:  TAXON Vol. 63, No. 4 ( 2014-08), p. 899-910
    Details
    In: TAXON, Wiley, Vol. 63, No. 4 ( 2014-08), p. 899-910
    Abstract: Technological advances have allowed phylogenomic studies of plants, such as full chloroplast genome (plastome) analysis, to become increasingly popular and economically feasible. Although next–generation short–read sequencing allows for full plastomes to be sequenced relatively rapidly, it requires additional attention using software to assemble these reads into comprehensive sequences. Here we compare the use of three de novo assemblers combined with three contig assembly methods. Seven plastome sequences were analyzed. Three of these were Sanger–sequenced. The other four were assembled from short, single–end read files generated from next–generation libraries. These plastomes represented a total of six grass species (Poaceae), one of which was sequenced in duplicate by the two methods to allow direct comparisons for accuracy. Enumeration of missing sequence and ambiguities allowed for assessments of completeness and efficiency. All methods that used de Bruijn–based de novo assemblers were shown to produce assemblies comparable to the Sanger–sequenced plastomes but were not equally efficient. Contig assembly methods that utilized automatable and repeatable processes were generally more efficient and advantageous when applied to larger scale projects with many full plastomes. However, contig assembly methods that were less automatable and required more manual attention did show utility in determining plastomes with lower read depth that were not able to be assembled when automatable procedures were implemented. Although the methods here were used exclusively to generate grass plastomes, these could be applied to other taxonomic groups if previously sequenced plastomes were available. In addition to comparing sequencing methods, a supplemental guide for short–read plastome assembly and applicable scripts were generated for this study.
    Type of Medium: Online Resource
    ISSN: 0040-0262 , 1996-8175
    URL: Article
    DOI: 10.12705/634.5
    Language: English
    Publisher: Wiley
    Publication Date: 2014
    detail.hit.zdb_id: 2081189-5
    detail.hit.zdb_id: 204216-2
    SSG: 12
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  • 4
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    Phylogenetic diversity is maintained despite richness losses over time in restored tallgrass prairie plant communities
    Wiley ; 2017
    In:  Journal of Applied Ecology Vol. 54, No. 1 ( 2017-02), p. 137-144
    Details
    In: Journal of Applied Ecology, Wiley, Vol. 54, No. 1 ( 2017-02), p. 137-144
    Abstract: These results suggest that species losses over time are not biased towards species with or without close relatives in the community. If phylogenetic diversity (PD) reflects functional trait diversity in communities, then local declines in species richness may not necessarily mean the loss of ecosystem function in restoration projects. However, PD of restored communities may be limited by low establishment rates for most species. Conservation practitioners should consider PD with careful planning to maintain overall community diversity and potentially maximize ecosystem function and services in restorations. This perspective will require a deeper understanding of the relationships between phylogenetic relatedness and traits associated with competition and fitness.
    Type of Medium: Online Resource
    ISSN: 0021-8901 , 1365-2664
    URL: Issue
    URL: Article
    DOI: 10.1111/jpe.2017.54.issue-1
    DOI: 10.1111/1365-2664.12639
    Language: English
    Publisher: Wiley
    Publication Date: 2017
    detail.hit.zdb_id: 2020408-5
    detail.hit.zdb_id: 410405-5
    SSG: 12
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  • 5
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    Plastome phylogenomics and phylogenetic diversity of endangered and threatened grassland species (Poaceae) in a North American tallgrass prairie
    Wiley ; 2020
    In:  Ecology and Evolution Vol. 10, No. 14 ( 2020-07), p. 7602-7615
    Details
    In: Ecology and Evolution, Wiley, Vol. 10, No. 14 ( 2020-07), p. 7602-7615
    Abstract: Native grasslands are one of the most endangered ecosystems in North America. In this study, we examined the ecological and evolutionary roles of endangered and threatened (e/t) grasses by establishing robust evolutionary relationships with other nonthreatened native and introduced grass species of the community. We hypothesized that the phylogenomic distribution of e/t species of grasses in Illinois would be phylogenetically clustered because closely related species would be vulnerable to the same threats and have similar requirements for survival. This study presents the first time a phylogeny based on complete plastome DNA of Poaceae was analyzed by phylogenetic diversity analysis. To avoid the disturbance of e/t populations, DNA was extracted from herbarium specimens. Next‐generation sequencing (NGS) techniques were used to sequence DNA of plastid genomes (plastomes). The resulting phylogenomic tree was analyzed by phylogenetic diversity metrics. The extracted DNA successfully produced complete plastomes demonstrating that herbarium material is a practical source of DNA for genomic studies. The phylogenomic tree was strongly supported and defined Dichanthelium as a separate clade from Panicum . The phylogenetic metrics revealed phylogenetic clustering of e/t species, confirming our hypothesis.
    Type of Medium: Online Resource
    ISSN: 2045-7758 , 2045-7758
    URL: Issue
    URL: Article
    DOI: 10.1002/ece3.v10.14
    DOI: 10.1002/ece3.6484
    Language: English
    Publisher: Wiley
    Publication Date: 2020
    detail.hit.zdb_id: 2635675-2
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  • 6
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    Biogeography and phylogenomics of New World Bambusoideae (Poaceae), revisited
    Wiley ; 2014
    In:  American Journal of Botany Vol. 101, No. 5 ( 2014-05), p. 886-891
    Details
    In: American Journal of Botany, Wiley, Vol. 101, No. 5 ( 2014-05), p. 886-891
    Abstract: • Premise of the study: New World Bambusoideae have only recently been studied in a phylogenomic context. Plastome sequences were determined and analyzed from Arundinaria appalachiana , A. tecta , and Olyra latifolia , to refine our knowledge of their evolution and historical biogeography. A correction is noted regarding an error in an earlier report on the biogeography of Cryptochloa . • Methods: Single‐end DNA libraries were prepared and sequenced on the Illumina platform. Complete plastomes were assembled and analyzed with 13 other Poaceae. • Key results: Complete sampling in Arundinaria and an additional species of Olyreae gave a more detailed picture of their evolution/historical biogeography. Phylogenomic analyses indicated that the first major divergence in Arundinaria occurred around 2.3 to 3.2 mya and that Arundinaria tecta and A . appalachiana diverged from their common ancestor around 0.57 to 0.82 mya. Estimates of the divergence of Olyra latifolia from Cryptochloa strictiflora ranged from 14.6 to 20.7 mya. The age of the stem node of Olyreae ranged from an estimated 26.9 to 38.2 mya. • Conclusions: Estimates of divergences in Arundinaria can be correlated with paleoclimatic events including an early Pliocene warming, subsequent cooling, and North American glaciations. Discriminating between alternate evolutionary/biogeographic scenarios in Olyreae is challenging.
    Type of Medium: Online Resource
    ISSN: 0002-9122 , 1537-2197
    URL: Article
    DOI: 10.3732/ajb.1400063
    RVK:
    WA 15000
    Language: English
    Publisher: Wiley
    Publication Date: 2014
    detail.hit.zdb_id: 2053581-8
    SSG: 12
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  • 7
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    Online Resource
    Phylogenetics of Paniceae (Poaceae)
    Wiley ; 2001
    In:  American Journal of Botany Vol. 88, No. 11 ( 2001-11), p. 1988-1992
    Details
    In: American Journal of Botany, Wiley, Vol. 88, No. 11 ( 2001-11), p. 1988-1992
    Abstract: Paniceae demonstrate unique variability of photosynthetic physiology and anatomy, including both non‐Kranz and Kranz species and all subtypes of the latter. This variability suggests hypotheses of independent origin or reversals (e.g., from C 4 to C 3 ). These hypotheses can be tested by phylogenetic analysis of independent molecular characters. The molecular phylogeny of 57 species of Paniceae was explored using sequences from the grass‐specific insert found in the plastid locus rpoC2. Phylogenetic analyses confirmed some long‐recognized alliances in Paniceae, some recent molecular phylogenetic results, and suggested new relationships. Broadly, Paniceae were found to be paraphyletic with Andropogoneae, Panicum was found to be polyphyletic, and Oplismenus hirtellus was resolved as the sister group to the remaining ingroup species. A particularly well‐supported clade in the rpoC2 tree included four genera with non‐Kranz species and three with distinctively keeled paleas. As previously suggested, the PCK (phosphoenol pyruvate carboxykinase) C 4 subtype arose once within Paniceae. All clades with non‐Kranz species had Kranz ancestors or sister taxa suggesting repeated loss of the Kranz syndrome.
    Type of Medium: Online Resource
    ISSN: 0002-9122 , 1537-2197
    URL: Article
    DOI: 10.2307/3558426
    RVK:
    WA 15000
    Language: English
    Publisher: Wiley
    Publication Date: 2001
    detail.hit.zdb_id: 2053581-8
    SSG: 12
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  • 8
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    Online Resource
    PHYLOGENY OF NORTH AMERICAN ORYZOID GRASSES AS CONSTRUED FROM MAPS OF PLASTID DNA RESTRICTION SITES
    Wiley ; 1993
    In:  American Journal of Botany Vol. 80, No. 1 ( 1993-01), p. 83-88
    Details
    In: American Journal of Botany, Wiley, Vol. 80, No. 1 ( 1993-01), p. 83-88
    Abstract: Restriction sites for six enzymes were mapped for the plastid DNAs of eight species of oryzoid grasses from temperate North America together with Olyra latifolia using biotin‐labeled probes from Oryza sativa . Cladistic analysis of the data indicated the existence of one, most‐parsimonious cladogram of 56 steps. Two species of Leersia differed by only one restriction site mutation, and two species of Zizania differed by only two mutations, whereas Luziola fluitans and L. bahiensis differed by 15 mutations. The restriction sites data strongly support two monophyletic clades corresponding to Oryzinae and Zizaniinae, but only weakly support the traditionally hypothesized alliance of Zizaniinae with other monoecious oryzoid grasses.
    Type of Medium: Online Resource
    ISSN: 0002-9122 , 1537-2197
    URL: Issue
    URL: Article
    DOI: 10.1002/ajb2.1993.80.issue-1
    DOI: 10.1002/j.1537-2197.1993.tb13770.x
    RVK:
    WA 15000
    Language: English
    Publisher: Wiley
    Publication Date: 1993
    detail.hit.zdb_id: 2053581-8
    SSG: 12
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  • 9
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    Online Resource
    The role of hemiparasitic plants: influencing tallgrass prairie quality, diversity, and structure
    Wiley ; 2017
    In:  Restoration Ecology Vol. 25, No. 3 ( 2017-05), p. 405-413
    Details
    In: Restoration Ecology, Wiley, Vol. 25, No. 3 ( 2017-05), p. 405-413
    Abstract: Wood betony, Orobanchaceae ( Pedicularis canadensis ) and bastard toadflax, Santalaceae ( Comandra umbellata ) are two root‐hemiparasitic plant species found in tallgrass prairie communities. Natural resource managers are interested in utilizing these species as “pseudograzers” in grasslands to reduce competitively dominant grasses and thereby increase ecological diversity and quality in prairie restorations and urban plantings. We performed an observational field study at 5 tallgrass prairie sites to investigate the association of hemiparasite abundance with metrics of phylogenetic and ecological diversity, as well as floristic quality. Although no reduction in C 4 grasses was detected, there was a significant association between hemiparasite abundance and increased floristic quality at all 5 sites. Hemiparasite abundance and species richness were positively correlated at one restoration site. In a greenhouse mesocosm experiment, we investigated response to parasitism by P. canadensis in 6 species representing different plant functional groups of the tallgrass prairie. The annual legume partridge pea, Fabaceae ( Chamaecrista fasciculata ) had the greatest significant dry biomass reduction among 6 host species, but the C 4 grass big bluestem, Poaceae ( Andropogon gerardii ) had significantly greater aboveground biomass when grown with the hemiparasite. Overall, host species biomass as a total community was significantly reduced in mesocosms, consistent with other investigations that demonstrate influence on community structure by hemiparasitic plant species. Although hemiparasites were not acting as pseudograzers, they have the potential to influence community structure in grassland restorations and remnants.
    Type of Medium: Online Resource
    ISSN: 1061-2971 , 1526-100X
    URL: Issue
    URL: Article
    DOI: 10.1111/rec.2017.25.issue-3
    DOI: 10.1111/rec.12446
    Language: English
    Publisher: Wiley
    Publication Date: 2017
    detail.hit.zdb_id: 2020952-6
    detail.hit.zdb_id: 914746-9
    SSG: 12
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  • 10
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    Online Resource
    Alliances of M uhlenbergia (Poaceae) within New World Eragrostideae are identified by phylogenetic analysis of mapped restriction sites from plastid DNAs
    Wiley ; 1994
    In:  American Journal of Botany Vol. 81, No. 5 ( 1994-05), p. 622-629
    Details
    In: American Journal of Botany, Wiley, Vol. 81, No. 5 ( 1994-05), p. 622-629
    Abstract: Restriction sites for six enzymes were mapped for the plastid DNAs of 25 species of Eragrostideae, one species of Cynodonteae ( Eustachys distichophylla ), and one species of Pooideae. Of the 124 restriction sites observed, 67 were variably present and shared by two or more species. These data were analyzed by the parsimony method using equal and unequal weights and by bootstrap analysis. The cladistic analyses established that members of the Muhlenbergiinae, including the genera Muhlenbergia, Blepharoneuron, Bealia, Chaboissaea, Lycurus , and Pereilema , share seven restriction site mutations and are strongly supported by the data as a monophyletic subtribe. Surprisingly, Redfieldia flexuosa also clustered with the Muhlenbergiinae in the analysis, perhaps indicative of a past interspecific hybridization event. The restriction sites data also weakly support a relationship (six shared mutations) between Erioneuron, Munroa , and Dasyochloa.
    Type of Medium: Online Resource
    ISSN: 0002-9122 , 1537-2197
    URL: Issue
    URL: Article
    DOI: 10.1002/ajb2.1994.81.issue-5
    DOI: 10.1002/j.1537-2197.1994.tb15493.x
    RVK:
    WA 15000
    Language: English
    Publisher: Wiley
    Publication Date: 1994
    detail.hit.zdb_id: 2053581-8
    SSG: 12
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