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Mark W Chase - One of the best experts on this subject based on the ideXlab platform.

  • plant dna barcodes and assessment of phylogenetic community structure of a tropical mixed dipterocarp forest in brunei darussalam borneo
    PLOS ONE, 2017
    Co-Authors: Jacqueline Heckenhauer, Mark W Chase, Kamariah Abu Salim, Kyle G Dexter, Toby R Pennington, Sylvester Tan, Maria Kaye
    Abstract:

    DNA barcoding is a fast and reliable tool to assess and monitor biodiversity and, via community phylogenetics, to investigate ecological and evolutionary processes that may be responsible for the community structure of forests. In this study, DNA barcodes for the two widely used plastid coding regions rbcL and matK are used to contribute to identification of morphologically undetermined individuals, as well as to investigate phylogenetic structure of tree communities in 70 subplots (10 × 10m) of a 25-ha forest-dynamics plot in Brunei (Borneo, Southeast Asia). The combined matrix (rbcL + matK) comprised 555 haplotypes (from ≥154 genera, 68 families and 25 orders sensu APG, Angiosperm Phylogeny Group, 2016), making a substantial contribution to tree barcode sequences from Southeast Asia. Barcode sequences were used to reconstruct phylogenetic relationships using maximum likelihood, both with and without constraining the topology of taxonomic orders to match that proposed by the Angiosperm Phylogeny Group. A third phylogenetic tree was reconstructed using the program Phylomatic to investigate the influence of phylogenetic resolution on results. Detection of non-random patterns of community assembly was determined by net relatedness index (NRI) and nearest taxon index (NTI). In most cases, community assembly was either random or phylogenetically clustered, which likely indicates the importance to community structure of habitat filtering based on phylogenetically correlated traits in determining community structure. Different phylogenetic trees gave similar overall results, but the Phylomatic tree produced greater variation across plots for NRI and NTI values, presumably due to noise introduced by using an unresolved phylogenetic tree. Our results suggest that using a DNA barcode tree has benefits over the traditionally used Phylomatic approach by increasing precision and accuracy and allowing the incorporation of taxonomically unidentified individuals into analyses.

  • An update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants: APG IV
    Botanical Journal of the Linnean Society, 2016
    Co-Authors: Kare Bremer, James L Reveal, Pamela S. Soltis, Douglas E. Soltis, Mark W Chase, Peter F. Stevens
    Abstract:

    A revised and updated classification for the families of the flowering plants is provided. Newly adopted orders include Austrobaileyales, Canellales, Gunnerales, Crossosomatales and Celastrales. Pertinent literature published since the first APG classification is included, such that many additional families are now placed in the phylogenetic scheme. Among these are Hydnoraceae (Piperales), Nartheciaceae (Dioscoreales), Corsiaceae (Liliales), Triuridaceae (Pandanales), Hanguanaceae (Commelinales), Bromeliacae, Mayacaceae and Rapateaceae (all Poales), Barbeuiaceae and Gisekiaceae (both Caryophyllales), Geissolomataceae, Strasburgeriaceae and Vitaceae (unplaced to order, but included in the rosids), Zygophyllaceae (unplaced to order, but included in eurosids I), Bonnetiaceae, Ctenolophonaceae, Elatinaceae, Ixonanthaceae, Lophopyxidaceae, Podostemaceae (Malpighiales), Paracryphiaceae (unplaced in euasterid II), Sladeniaceae, Pentaphylacaceae (Ericales) and Cardiopteridaceae (Aquifoliales). Several major families are recircumscribed. Salicaceae are expanded to include a large part of Flacourtiaceae, including the type genus of that family; another portion of former Flacourtiaceae is assigned to an expanded circumscription of Achariaceae. Euphorbiaceae are restricted to the uniovulate subfamilies; Phyllanthoideae are recognized as Phyllanthaceae and Oldfieldioideae as Picrodendraceae. Scrophulariaceae are recircumscribed to include Buddlejaceae and Myoporaceae and exclude several former members; these are assigned to Calceolariaceae, Orobanchaceae and Plantaginaceae. We expand the use of bracketing families that could be included optionally in broader circumscriptions with other related families; these include Agapanthaceae and Amaryllidaceae in Alliaceae s.l. , Agavaceae, Hyacinthaceae and Ruscaceae (among many other Asparagales) in Asparagaceae s.l. , Dichapetalaceae in Chrysobalanaceae, Turneraceae in Passifloraceae, Erythroxylaceae in Rhizophoraceae, and Diervillaceae, Dipsacaceae, Linnaeaceae, Morinaceae and Valerianaceae in Caprifoliaceae s.l. © 2003 The Linnean Society of London, Botanical Journal of the Linnean Society , 2003, 141 , 399‐436.

  • Results from an online survey of family delimitation in Angiosperms and ferns: recommendations to the Angiosperm Phylogeny Group for thorny problems in plant classification
    Botanical Journal of the Linnean Society, 2015
    Co-Authors: Maarten J. M. Christenhusz, Michael F. Fay, Maria S. Vorontsova, Mark W Chase
    Abstract:

    The Angiosperm Phylogeny Group (APG) started with ordinal relationships for Angiosperm families and later came to concentrate more on issues surrounding family delimitation, generally taking a conservative approach (favouring lumping over splitting when choices were otherwise fairly evenly balanced). The history of the APG approach to classification is elaborated here, and long-term trends in taxon size are also discussed. Twenty-three questions relating to family delimitation of Angiosperms (21) and ferns (two) were identified, and an open, web-based survey was conducted to determine which solutions were preferred by the botanical community. There were a total of 441 responses from 42 countries. The full survey results are presented and discussed. In general, among respondents, there was a good balance between lumping and splitting, although a much smaller percentage self-identified as splitters. Recommendations to APG for a set of specific family delimitation issues in Angiosperms and ferns are made. We followed the majority vote in all but four cases and recommended ten splitting and 13 lumping options. We found that decisions were made by respondents on a case-by-case basis. Many respondents favoured lumping as a means of gaining stability by leaving circumscription issues at the lower taxonomic levels, which are of more concern to specialists (i.e. at subfamilial and tribal levels). We estimate that APG IV will not differ substantially from APG III. © 2015 The Linnean Society of London, Botanical Journal of the Linnean Society, 2015, 178, 501–528.

  • Familial relationships of the monocot order Liliales based on a molecular phylogenetic analysis using four plastid loci: matK, rbcL, atpB and atpF‐H
    Botanical Journal of the Linnean Society, 2013
    Co-Authors: Jung Sung Kim, Mark W Chase, Michael F. Fay, Jeong-ki Hong, Joo-hwan Kim
    Abstract:

    Many molecular studies have shown the monocot order Liliales to be well supported; morphologically, it is defined by synapomorphies of tepalar nectaries and extrorse anthers, in contrast with septal nectaries and introrse anthers commonly found in other monocots, especially Asparagales, with which it was often confused in the past. It comprises c. 1500 species, 67 genera and 9–11 families. Although monophyly is clear, the phylogenetic relationships among some of the families are still unclear. In this study, we examine the inter- and infrafamilial relationships among Liliales in phylogenetic analyses based on four plastid loci (matK, rbcL, atpB and atpF-H). We performed phylogenetic analyses and constructed maximum parsimony and Bayesian trees for 49 genera and 148 taxa in ten families of Liliales sensu Angiosperm Phylogeny Group (APG) III using the combined DNA data. The monophyly of Liliales, except for Corsiaceae (Arachnitis), was strongly supported by both analyses. Campynemataceae were sister to the rest of the order, excluding Corsiaceae. The other families formed two well-defined clades, (Colchicaceae + Alstroemeriaceae) and (Liliaceae, Smilacaceae, (Rhipogonaceae + Philesiaceae)), and one weakly supported clade with Melanthiaceae and Petermanniaceae. Subfamilial and tribal circumscriptions for the three larger families, Colchicaceae, Melanthiaceae and Liliaceae, agreed well with the results of this study, except for the subfamily Calochortoideae of Liliaceae, which was split into two separate clades of Calochortus and Tricyrtis. In addition, we found several taxa with a 10-bp inversion in matK, which could contribute additional homoplasy to these analyses if included without re-coding. Phylogenetic relationships among families of Liliales were better defined here than in a previous molecular analysis, although the placement of Corsiaceae with plastid data remains problematic. Based on these results, reconsideration of the circumscriptions of Rhipogonaceae + Philesiaceae and the subfamilial circumscription for Calochortoideae of Liliaceae is suggested. © 2013 The Linnean Society of London

  • APG III: Bibliographical Information and Synonymy of Magnoliidae
    Phytotaxa, 2011
    Co-Authors: James L Reveal, Mark W Chase
    Abstract:

    An updated classification of the orders and families of flowering plants was published in 2009 by the Angiosperm Phylogeny Group along with two companion papers, one a linear arrangement of the taxa, and a second treating the land plants above the rank of order. These papers are combined with full synonymy and bibliographic information along with an index to the names.

Zhihui Zhao - One of the best experts on this subject based on the ideXlab platform.

  • RESEARCH ARTICLE Genome-Wide Characterization of Simple Sequence Repeat (SSR) Loci in Chinese Jujube and Jujube SSR Primer Transferability
    2016
    Co-Authors: Jing Xiao, Mengjun Liu, Jin Zhao, Ping Liu, Li Dai, Zhihui Zhao
    Abstract:

    Chinese jujube (Ziziphus jujuba), an economically important species in the Rhamnaceae family, is a popular fruit tree in Asia. Here, we surveyed and characterized simple sequence repeats (SSRs) in the jujube genome. A total of 436,676 SSR loci were identified, with an average distance of 0.93 Kb between the loci. A large proportion of the SSRs included mononucleotide, dinucleotide and trinucleotide repeat motifs, which accounted for 64.87%, 24.40%, and 8.74 % of all repeats, respectively. Among the mononucleotide repeats, A/T was the most common, whereas AT/TA was the most common dinucleotide repeat. A total of 30,565 primer pairs were successfully designed and screened using a series of criteria. Moreover, 725 of 1,000 randomly selected primer pairs were effective among 6 cultivars, and 511 of these primer pairs were polymorphic. Sequencing the amplicons of two SSRs across three jujube cultivars revealed variations in the repeats. The transferability of jujube SSR primers proved that 35/64 SSRs could be transferred across family boundary. Using jujube SSR primers, clustering analysis results from 15 species were highly consistent with the Angiosperm Phylogeny Group (APGIII) System. The genome-wide characterization of SSRs in Chinese jujube is very valuable for whole-genome characterization and marker-as-sisted selection in jujube breeding. In addition, the transferability of jujube SSR primers could provide a solid foundation for their further utilization

  • genome wide characterization of simple sequence repeat ssr loci in chinese jujube and jujube ssr primer transferability
    PLOS ONE, 2015
    Co-Authors: Jing Xiao, Mengjun Liu, Jin Zhao, Ping Liu, Li Dai, Zhihui Zhao
    Abstract:

    Chinese jujube (Ziziphus jujuba), an economically important species in the Rhamnaceae family, is a popular fruit tree in Asia. Here, we surveyed and characterized simple sequence repeats (SSRs) in the jujube genome. A total of 436,676 SSR loci were identified, with an average distance of 0.93 Kb between the loci. A large proportion of the SSRs included mononucleotide, dinucleotide and trinucleotide repeat motifs, which accounted for 64.87%, 24.40%, and 8.74% of all repeats, respectively. Among the mononucleotide repeats, A/T was the most common, whereas AT/TA was the most common dinucleotide repeat. A total of 30,565 primer pairs were successfully designed and screened using a series of criteria. Moreover, 725 of 1,000 randomly selected primer pairs were effective among 6 cultivars, and 511 of these primer pairs were polymorphic. Sequencing the amplicons of two SSRs across three jujube cultivars revealed variations in the repeats. The transferability of jujube SSR primers proved that 35/64 SSRs could be transferred across family boundary. Using jujube SSR primers, clustering analysis results from 15 species were highly consistent with the Angiosperm Phylogeny Group (APGIII) System. The genome-wide characterization of SSRs in Chinese jujube is very valuable for whole-genome characterization and marker-assisted selection in jujube breeding. In addition, the transferability of jujube SSR primers could provide a solid foundation for their further utilization.

Jing Xiao - One of the best experts on this subject based on the ideXlab platform.

  • RESEARCH ARTICLE Genome-Wide Characterization of Simple Sequence Repeat (SSR) Loci in Chinese Jujube and Jujube SSR Primer Transferability
    2016
    Co-Authors: Jing Xiao, Mengjun Liu, Jin Zhao, Ping Liu, Li Dai, Zhihui Zhao
    Abstract:

    Chinese jujube (Ziziphus jujuba), an economically important species in the Rhamnaceae family, is a popular fruit tree in Asia. Here, we surveyed and characterized simple sequence repeats (SSRs) in the jujube genome. A total of 436,676 SSR loci were identified, with an average distance of 0.93 Kb between the loci. A large proportion of the SSRs included mononucleotide, dinucleotide and trinucleotide repeat motifs, which accounted for 64.87%, 24.40%, and 8.74 % of all repeats, respectively. Among the mononucleotide repeats, A/T was the most common, whereas AT/TA was the most common dinucleotide repeat. A total of 30,565 primer pairs were successfully designed and screened using a series of criteria. Moreover, 725 of 1,000 randomly selected primer pairs were effective among 6 cultivars, and 511 of these primer pairs were polymorphic. Sequencing the amplicons of two SSRs across three jujube cultivars revealed variations in the repeats. The transferability of jujube SSR primers proved that 35/64 SSRs could be transferred across family boundary. Using jujube SSR primers, clustering analysis results from 15 species were highly consistent with the Angiosperm Phylogeny Group (APGIII) System. The genome-wide characterization of SSRs in Chinese jujube is very valuable for whole-genome characterization and marker-as-sisted selection in jujube breeding. In addition, the transferability of jujube SSR primers could provide a solid foundation for their further utilization

  • genome wide characterization of simple sequence repeat ssr loci in chinese jujube and jujube ssr primer transferability
    PLOS ONE, 2015
    Co-Authors: Jing Xiao, Mengjun Liu, Jin Zhao, Ping Liu, Li Dai, Zhihui Zhao
    Abstract:

    Chinese jujube (Ziziphus jujuba), an economically important species in the Rhamnaceae family, is a popular fruit tree in Asia. Here, we surveyed and characterized simple sequence repeats (SSRs) in the jujube genome. A total of 436,676 SSR loci were identified, with an average distance of 0.93 Kb between the loci. A large proportion of the SSRs included mononucleotide, dinucleotide and trinucleotide repeat motifs, which accounted for 64.87%, 24.40%, and 8.74% of all repeats, respectively. Among the mononucleotide repeats, A/T was the most common, whereas AT/TA was the most common dinucleotide repeat. A total of 30,565 primer pairs were successfully designed and screened using a series of criteria. Moreover, 725 of 1,000 randomly selected primer pairs were effective among 6 cultivars, and 511 of these primer pairs were polymorphic. Sequencing the amplicons of two SSRs across three jujube cultivars revealed variations in the repeats. The transferability of jujube SSR primers proved that 35/64 SSRs could be transferred across family boundary. Using jujube SSR primers, clustering analysis results from 15 species were highly consistent with the Angiosperm Phylogeny Group (APGIII) System. The genome-wide characterization of SSRs in Chinese jujube is very valuable for whole-genome characterization and marker-assisted selection in jujube breeding. In addition, the transferability of jujube SSR primers could provide a solid foundation for their further utilization.

Peter F. Stevens - One of the best experts on this subject based on the ideXlab platform.

  • An update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants: APG IV
    Botanical Journal of the Linnean Society, 2016
    Co-Authors: Kare Bremer, James L Reveal, Pamela S. Soltis, Douglas E. Soltis, Mark W Chase, Peter F. Stevens
    Abstract:

    A revised and updated classification for the families of the flowering plants is provided. Newly adopted orders include Austrobaileyales, Canellales, Gunnerales, Crossosomatales and Celastrales. Pertinent literature published since the first APG classification is included, such that many additional families are now placed in the phylogenetic scheme. Among these are Hydnoraceae (Piperales), Nartheciaceae (Dioscoreales), Corsiaceae (Liliales), Triuridaceae (Pandanales), Hanguanaceae (Commelinales), Bromeliacae, Mayacaceae and Rapateaceae (all Poales), Barbeuiaceae and Gisekiaceae (both Caryophyllales), Geissolomataceae, Strasburgeriaceae and Vitaceae (unplaced to order, but included in the rosids), Zygophyllaceae (unplaced to order, but included in eurosids I), Bonnetiaceae, Ctenolophonaceae, Elatinaceae, Ixonanthaceae, Lophopyxidaceae, Podostemaceae (Malpighiales), Paracryphiaceae (unplaced in euasterid II), Sladeniaceae, Pentaphylacaceae (Ericales) and Cardiopteridaceae (Aquifoliales). Several major families are recircumscribed. Salicaceae are expanded to include a large part of Flacourtiaceae, including the type genus of that family; another portion of former Flacourtiaceae is assigned to an expanded circumscription of Achariaceae. Euphorbiaceae are restricted to the uniovulate subfamilies; Phyllanthoideae are recognized as Phyllanthaceae and Oldfieldioideae as Picrodendraceae. Scrophulariaceae are recircumscribed to include Buddlejaceae and Myoporaceae and exclude several former members; these are assigned to Calceolariaceae, Orobanchaceae and Plantaginaceae. We expand the use of bracketing families that could be included optionally in broader circumscriptions with other related families; these include Agapanthaceae and Amaryllidaceae in Alliaceae s.l. , Agavaceae, Hyacinthaceae and Ruscaceae (among many other Asparagales) in Asparagaceae s.l. , Dichapetalaceae in Chrysobalanaceae, Turneraceae in Passifloraceae, Erythroxylaceae in Rhizophoraceae, and Diervillaceae, Dipsacaceae, Linnaeaceae, Morinaceae and Valerianaceae in Caprifoliaceae s.l. © 2003 The Linnean Society of London, Botanical Journal of the Linnean Society , 2003, 141 , 399‐436.

  • The Linear Angiosperm Phylogeny Group (LAPG) III: A linear sequence of the families in APG III
    Botanical Journal of the Linnean Society, 2009
    Co-Authors: Elspeth Haston, Peter F. Stevens, Mark W Chase, James E. Richardson, David Harris
    Abstract:

    The publication of the third Angiosperm Phylogeny Group (APG) classification (APG III. 2009. An update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants: APG III. Botanical Journal of the Linnean Society161: 128–131) has resulted in the need for a revised systematic listing of the accepted families. This linear APG III (LAPG III) sequence of families is presented here. © 2009 The Linnean Society of London, Botanical Journal of the Linnean Society, 2009, 161, 128–131.

  • a linear sequence of Angiosperm Phylogeny Group ii families
    Taxon, 2007
    Co-Authors: Elspeth Haston, Peter F. Stevens, Mark W Chase, James E. Richardson, David Harris
    Abstract:

    This paper discusses the need for an up-to-date linear sequence of Angiosperm families based on the APG system. The methods used to generate the sequence are clearly laid out, and the sequence is provided in a simple numbered list of 479 families. The need for a consensus classification of families is also discussed.

  • A linear sequence of Angiosperm Phylogeny Group II families
    1
    Co-Authors: Elspeth Haston, Peter F. Stevens, Mark W Chase, James E. Richardson, David Harris
    Abstract:

    Este articulo analiza la necesidad de una secuencia lineal actualizada de familias de Angiospermas basada en el sistema APG. Los metodos utilizados para generar la secuencia estan claramente establecidos y la secuencia se proporciona en una lista numerada simple de 479 familias. Tambien se discute la necesidad de una clasificacion consensuada de familias

David Harris - One of the best experts on this subject based on the ideXlab platform.

  • The Linear Angiosperm Phylogeny Group (LAPG) III: A linear sequence of the families in APG III
    Botanical Journal of the Linnean Society, 2009
    Co-Authors: Elspeth Haston, Peter F. Stevens, Mark W Chase, James E. Richardson, David Harris
    Abstract:

    The publication of the third Angiosperm Phylogeny Group (APG) classification (APG III. 2009. An update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants: APG III. Botanical Journal of the Linnean Society161: 128–131) has resulted in the need for a revised systematic listing of the accepted families. This linear APG III (LAPG III) sequence of families is presented here. © 2009 The Linnean Society of London, Botanical Journal of the Linnean Society, 2009, 161, 128–131.

  • a linear sequence of Angiosperm Phylogeny Group ii families
    Taxon, 2007
    Co-Authors: Elspeth Haston, Peter F. Stevens, Mark W Chase, James E. Richardson, David Harris
    Abstract:

    This paper discusses the need for an up-to-date linear sequence of Angiosperm families based on the APG system. The methods used to generate the sequence are clearly laid out, and the sequence is provided in a simple numbered list of 479 families. The need for a consensus classification of families is also discussed.

  • A linear sequence of Angiosperm Phylogeny Group II families
    1
    Co-Authors: Elspeth Haston, Peter F. Stevens, Mark W Chase, James E. Richardson, David Harris
    Abstract:

    Este articulo analiza la necesidad de una secuencia lineal actualizada de familias de Angiospermas basada en el sistema APG. Los metodos utilizados para generar la secuencia estan claramente establecidos y la secuencia se proporciona en una lista numerada simple de 479 familias. Tambien se discute la necesidad de una clasificacion consensuada de familias