Update pteridophytes to PPG I

[mutolisp]

A community-derived classification for extant lycophytes and ferns. PPG I

Abstract

"Phylogeny has long informed pteridophyte classification. As our ability to infer evolutionary trees has improved, classifications aimed at recognizing natural groups have become increasingly predictive and stable. Here, we provide a modern, comprehensive classification for lycophytes and ferns, down to the genus level, utilizing a community-based approach. We use monophyly as the primary criterion for the recognition of taxa, but also aim to preserve existing taxa and circumscriptions that are both widely accepted and consistent with our understanding of pteridophyte phylogeny. In total, this classification treats an estimated 11 916 species in 337 genera, 51 families, 14 orders, and two classes. This classification is not intended as the final word on lycophyte and fern taxonomy, but rather a summary statement of current hypotheses, derived from the best available data and shaped by those most familiar with the plants in question. We hope that it will serve as a resource for those wanting references to the recent literature on pteridophyte phylogeny and classification, a framework for guiding future investigations, and a stimulus to further discourse."

References

http://onlinelibrary.wiley.com/doi/10.1111/jse.12229/full

[mutolisp]

PPG I 分類階層表(csv format) 初步篩選臺灣有的屬，對照 Christenhusz et al. (2011)及 Tropicos )有變動的屬，

genus	family	family_ppgi
Cornopteris	Athyriaceae	Athyrium
Humata	Davalliaceae	Davallia
Araiostegia	Davalliaceae	Davallia
Dryopsis	Dryopteridaceae	Dryopteris
Acrorumohra	Dryopteridaceae	Dryopteris
Peranema	Dryopteridaceae	Dryopteris
Leptorumohra	Dryopteridaceae	Arachniodes
Cyrtogonellum	Dryopteridaceae	Polystichum
Egenolfia	Dryopteridaceae	Bolbitis
Diacalpe	Dryopteridaceae	Dryopteris
Acrophorus	Dryopteridaceae	Dryopteris
Gonocormus	Hymenophyllaceae
Microtrichomanes	Hymenophyllaceae
Mecodium	Hymenophyllaceae
Nesopteris	Hymenophyllaceae	Crepidomanes
Pleuromanes	Hymenophyllaceae
Reediella	Hymenophyllaceae
Selenodesmium	Hymenophyllaceae
Microgonium	Hymenophyllaceae
Meringium	Hymenophyllaceae
Isoetes	Isoetaceae	Isoëtes
Archangiopteris	Marattiaceae	Angiopteris
Phymatosorus	Polypodiaceae	Microsorum
Saxiglossum	Polypodiaceae
Pseudodrynaria	Polypodiaceae	Aglaomorpha
Drymotaenium	Polypodiaceae	Lepisorus
Colysis	Polypodiaceae	Leptochilus
Belvisia	Polypodiaceae	Lepisorus
Xiphopteris	Polypodiaceae	Cochlidium
Drynaria	Polypodiaceae	Aglaomorpha
Crypsinus	Polypodiaceae	Selliguea
Ctenopteris	Polypodiaceae	Prosaptia
Schellolepis	Polypodiaceae
Gymnopteris	Pteridaceae	Hemionitis
Ctenitopsis	Tectariaceae	Tectaria
Hemigramma	Tectariaceae	Tectaria
Quercifilix	Tectariaceae	Tectaria
Leptogramma	Thelypteridaceae	Stegnogramma
Dictyocline	Thelypteridaceae	Stegnogramma

pgsql 撈資料

-- genus_apg3: phylogenetic group genus
-- family_apg4: phylogenetic group family
-- plant_type: 1 is lycophytes and ferns
SELECT 
    f.*, ppgi.family 
FROM 
    (SELECT distinct genus_apg3,family_apg4 from namelist where plant_type = 1 ) as f 
LEFT OUTER JOIN 
    nomenclature.ppgi
ON 
    f.genus_apg3 = ppgi.genus 
WHERE 
    ppgi.family is null 
ORDER BY ppgi.family,f.family_apg4;

附件

臺灣蕨類名錄(政道整理)

[mutolisp]

產生總名錄來比對

COPY 
(SELECT 
    f.id,
    ppgi.fam_id,
    f.family_apg4,
    ppgi.family family_ppgi,
    f.family family_fot,
    f.genus_apg3,
    f.fullname,
    f.name,
    f.zh_name  
FROM 
    (SELECT 
        distinct id,
        family_apg4,
        family,genus_apg3,
        fullname,
        name,
        zh_name[1] 
    FROM namelist WHERE plant_type = 1 ) as f 
    LEFT OUTER JOIN 
        nomenclature.ppgi 
    ON
        f.genus_apg3 = ppgi.genus 
    ORDER BY 
        ppgi.fam_id,ppgi.family,f.family_apg4)
    TO '/tmp/twferns_for_checking.csv' CSV HEADER;