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Integrating and visualizing
taxonomic concept changes in
Heteroptera
Guanyang Zhang, Nico Franz, Arizona State University
...
How do we achieve this?
Can taxonomic names
alone do the job?
Why names are not good enough
• Same name may acquire different meanings through time
• Different names may refer to same ...
“Concept taxonomy”
• Proposed by Berendsohn, 1995.
• Referencing and reasoning with taxonomy concept and not just name
• “...
“Concept taxonomy”
Franz & Peet, 2009
Senior synonym ≠ each
synonymized concept
• Synonymy means that different taxonomic concepts
are congruent according to an...
Study objective
• Use concept taxonomy approach with an logic
process implemented in a computer program
proposed or create...
Mirid subfamilial and tribal classification
Cassis & Schuh, 2012
Two input taxonomies
• sec. Schuh, 1995  sec. Cassis & Schuh,
2012
• 8 subfamilies in both classifications
• Tribal class...
Workflow
Schuh (1995) Cassis & Schuh (2012)
1 MIRIDAE 40 MIRIDAE
2 Isometopinae 41 Isometopinae
3 Isometopini 42 Diphlebin...
Workflow
• Number each taxonomic concept/name
• State parent-child relationship within each
taxonomy. Schuh, 1995:
1 Mirid...
Workflow
• Number each taxonomic concept/name
• State parent-child relationship within each
taxonomy.
• State articulation...
Workflow
• Number each taxonomic concept/name
• State parent-child relationship within each
taxonomy.
• State articulation...
Workflow
• Use EULER/X to compare and visualize
concept relationships between the two
taxonomies
https://bitbucket.org/eul...
Schuh, 1995  Cassis & Schuh, 2012
Visualization output
2 – Cassis & Schuh (2012)
1 – Schuh (1995)
Schuh, 1995  Cassis & Schuh, 2012
Visualization output
- Merged square and octagon denotes congruent concepts
- Green box...
Schuh, 1995  Cassis & Schuh, 2012
Visualization output
- Concepts of Orthotylinae are congruent
- All lower-level concept...
Schuh, 1995  Cassis & Schuh, 2012
Visualization output
- Concepts of Orthotylini are not congruent
- Orthotylini sec. Cas...
Pentatomoidea, sec. Rider  sec. Grazia et al
Rider, 2006 Grazia et al, 2008 (DNA+morphology)
ID NAME ACCORDING TO RANK ID...
Pentatomoidea, sec. Rider  sec. Grazia et al
- Most concepts according two authors
are congruent
- Two concepts overlap
2...
Pentatomoidea, sec. Rider  sec. Grazia et al
Pentatomoidea, sec. Rider  sec. Grazia et al
Concepts of Saileriolidae(-inae)
are congruent, but raised to
family rank in...
Pentatomoidea, sec. Rider  sec. Grazia et al
Phloeidae sec. Grazia and Pentatomidae sec. Rider
overlap as Serbaninae is i...
A species/genus-level example
Bekilya group Malagasy reduviids (Peiratinae)
Mutillocoris
Mutillocoris
vadoni
Mutillocoris
tricolor
2. Villiers 1949-1964
Bekilya mira Hovacoris bipunctatus
Bekilya Ho...
Bekilya mira
Mutillocoris
Mutillocoris
tricolor
Hovacoris bipunctatus
Villiers 1964
Bekilya
Mutillocoris
vadoni
Hovacoris
...
Checklist
2. Villiers 1949-1964
1. Zhang&Weirauch, 2012
 Concept of Bekilya sec. Villiers
congruent with concept of B. mira
sec. Zh...
A complex test case
• Leucophoropterini
– 23 genera and 104 species (Menard & Schuh, 2011)
– ~200 concepts
• Taxonomic cha...
Leucophoropterini
New genera added, some genera removed and some species recognized as
Insertae sedis
Abuyogocoris None
Ai...
Full representation and resolved
articulations
Conclusion
• Feasibility of concept taxonomy approach in
mapping taxonomic concepts in Heteroptera
• All taxonomic differe...
Further information
• taxonbytes.org
• https://bitbucket.org/eulerx/euler-project
• Franz & Peet (2009)
– http://taxonbyte...
Acknowledgements
• NSF CAREER #1155984
• Ludaescher Lab @ UC Davis
Parastrachiidae? (-inae?)
Thank you!
Zhang & Franz 2014 - Integrating and Visualizing Taxonomic Concept Changes in the Heteroptera
Zhang & Franz 2014 - Integrating and Visualizing Taxonomic Concept Changes in the Heteroptera
Zhang & Franz 2014 - Integrating and Visualizing Taxonomic Concept Changes in the Heteroptera
Zhang & Franz 2014 - Integrating and Visualizing Taxonomic Concept Changes in the Heteroptera
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Zhang & Franz 2014 - Integrating and Visualizing Taxonomic Concept Changes in the Heteroptera

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Zhang & Franz 2014 - Integrating and Visualizing Taxonomic Concept Changes in the Heteroptera

  1. 1. Integrating and visualizing taxonomic concept changes in Heteroptera Guanyang Zhang, Nico Franz, Arizona State University 5th International Heteropterists’ Society Meeting, Washington DC, July 21, 2014
  2. 2. How do we achieve this? Can taxonomic names alone do the job?
  3. 3. Why names are not good enough • Same name may acquire different meanings through time • Different names may refer to same underlying taxon • Linnaean names and taxonomic perspectives tend to accumulate many-to-many relationships that are difficult to trace • Meaning-name divergence occurs constantly Franz & Peet (2009)
  4. 4. “Concept taxonomy” • Proposed by Berendsohn, 1995. • Referencing and reasoning with taxonomy concept and not just name • “A taxonomic concept is the underlying meaning, or referential extension, of a scientific name as stated by a particular author in a particular publication. It represents the author’s full-blown view of how the name reaches out to observed or unobserved objects in nature (beyond statements about type specimens). It is a direct reflection of what has been written, illustrated, and deposited by a taxonomist, regardless of his or her theoretical orientation” (Franz & Peet, 2009) • Taxonomic concepts are labelled using the abbreviation ‘sec.’ for the Latin secundum, or ‘according to’ (Berendsohn, 1995).
  5. 5. “Concept taxonomy” Franz & Peet, 2009
  6. 6. Senior synonym ≠ each synonymized concept • Synonymy means that different taxonomic concepts are congruent according to an author/publication • Synonymy does not mean ‘the same’/one concept – (Subjective) synonyms are anchored to different types and represent a matter of opinion (although often based on data and analyses) – Resurrection of synonymized names/concepts happens
  7. 7. Study objective • Use concept taxonomy approach with an logic process implemented in a computer program proposed or created by Franz & Ludaescher to align, compare and visualize alternative taxonomies and trace taxonomic history in Heteroptera • Can all taxonomic concepts be represented and related? • How resolved is the representation?
  8. 8. Mirid subfamilial and tribal classification Cassis & Schuh, 2012
  9. 9. Two input taxonomies • sec. Schuh, 1995  sec. Cassis & Schuh, 2012 • 8 subfamilies in both classifications • Tribal classification more refined in Cassis & Schuh, 2012 • Original taxonomic acts made elsewhere (e.g. Tatarnic & Cassis, 2011; Wyniger, 2010)
  10. 10. Workflow Schuh (1995) Cassis & Schuh (2012) 1 MIRIDAE 40 MIRIDAE 2 Isometopinae 41 Isometopinae 3 Isometopini 42 Diphlebini 4 Cylapinae 43 Gigantometopini 5 Cylapini 44 Isometopini 6 Psallopinae 45 Myiommini 7 Orthotylinae 46 Cylapinae 8 Halticini 47 Bothriomirini 9 Nichomachini 48 Cylapini Schuh (1995) Cassis & Schuh (20 1 MIRIDAE 40 MIRIDAE 2 Isometopinae 41 Isometopinae 3 Isometopini 42 Diphlebini 4 Cylapinae 43 Gigantometopini 5 Cylapini 44 Isometopini 6 Psallopinae 45 Myiommini 7 Orthotylinae 46 Cylapinae 8 Halticini 47 Bothriomirini 9 Nichomachini 48 Cylapini 10 Orthotylini 49 Fulviini 11 Phylinae 50 Rhinomirini 12 Auricillocorini 51 Vaniini 13 Hallodapini 52 Psallopinae 14 Leucophoropterini 53 Orthotylinae 15 Phylini 54 Austromirini 16 Pilophorini 55 Ceratocapsini 17 Bryocorinae 56 Coridromiini 18 Bryocorini 57 Halticini 19 Dicyphini 58 Nichomachini 20 Dicyphina 59 Orthotylini 21 Monaloniina 60 Phylinae 22 Odoniellina 61 Auricillocorini 23 Eccritotarsini 62 Hallodapini 24 Eccritotarsina 63 Leucophoropterini 25 Palaucorina 64 Phylini 26 Deraeocorinae 65 Pilophorini 27 Clivinemini 66 Pronotocrepini 28 Deraeocorini 67 Bryocorinae 29 Hyaliodini 68 Bryocorini 30 Saturniomirini 69 Dicyphini 31 Surinamellini 70 Dicyphina 32 Termatophylini 71 Monaloniina 33 Mirinae 72 Odoniellina 34 Herdoniini 73 Eccritotarsini 35 Hyalopeplini 74 Eccritotarsina 36 Mecistoscelini 75 Palaucorina 37 Mirini 76 Deraeocorinae 38 Resthenini 77 Clivinemini 39 Stenodemini 78 Deraeocorini 79 Hyaliodini 80 Saturniomirini 81 Surinamellini 82 Termatophylini 83 Mirinae 84 Herdoniini 85 Hyalopeplini 86 Mecistoscelini 87 Mirini 88 Resthenini 89 Stenodemini • Number each taxonomic concept/name
  11. 11. Workflow • Number each taxonomic concept/name • State parent-child relationship within each taxonomy. Schuh, 1995: 1 Miridae is parent of 2 Isometopinae 1 Miridae is parent of 17 Bryocorinae 17 Bryocorinae is parent of 19 Dicyphini 19 Dicyphini is parent of 21 Monaloniina
  12. 12. Workflow • Number each taxonomic concept/name • State parent-child relationship within each taxonomy. • State articulations between concepts in two different taxonomies Five types of articulations that express relationships – equals – overlaps – includes – is_included_in – disjoint
  13. 13. Workflow • Number each taxonomic concept/name • State parent-child relationship within each taxonomy. • State articulations between concepts in two different taxonomies – 1.xx - Schuh, 1995; 2.xx - Cassis & Schuh, 2012 – 2.66 (Pronotocrepini) is_included_in 1.13 (Hallodapini) – 2.62 (Hallodapini) is_included_in 1.13 (Hallodapini) – 2.67 (Dicyphina) equals 1.25 (Dicyphina)
  14. 14. Workflow • Use EULER/X to compare and visualize concept relationships between the two taxonomies https://bitbucket.org/eulerx/euler-project Chen et al. (2014) http://arxiv.org/pdf/1402.1992v1.pdf Bertram Ludaescher UC Davis Nico Franz, ASU
  15. 15. Schuh, 1995  Cassis & Schuh, 2012 Visualization output 2 – Cassis & Schuh (2012) 1 – Schuh (1995)
  16. 16. Schuh, 1995  Cassis & Schuh, 2012 Visualization output - Merged square and octagon denotes congruent concepts - Green box denotes unique/non-congruent concept in taxonomy 1 - Yellow octagon denotes unique/non-congruent concept in taxonomy 2 Numbers can be replaced with actual names in input 1. Schuh, 1995 2. Cassis & Schuh, 2012
  17. 17. Schuh, 1995  Cassis & Schuh, 2012 Visualization output - Concepts of Orthotylinae are congruent - All lower-level concepts are properly included in higher-level concepts 1. Schuh, 1995 2. Cassis & Schuh, 2012 Proper inclusion
  18. 18. Schuh, 1995  Cassis & Schuh, 2012 Visualization output - Concepts of Orthotylini are not congruent - Orthotylini sec. Cassis & Schuh more restrictive (2.Orthotylini) 1. Schuh, 1995 2. Cassis & Schuh, 2012
  19. 19. Pentatomoidea, sec. Rider  sec. Grazia et al Rider, 2006 Grazia et al, 2008 (DNA+morphology) ID NAME ACCORDING TO RANK ID NAME ACCORDING TO RANK 1 Pentatomoidea Rider (2006) Superfamily 21 Pentatomoidea Grazia etal (2008) Superfamily 2 Acanthosomatidae Rider (2006) Family 22 Urostylididae Grazia etal (2008) Family 3 Canopidae Rider (2006) Family 23 Saileriolidae Grazia etal (2008) Family 4 Cydnidae Rider (2006) Family 24 Plataspididae Grazia etal (2008) Family 5 Dinidoridae Rider (2006) Family 25 Phloeidae Grazia etal (2008) Family 6 Lestoniidae Rider (2006) Family 26 Serbaninae Grazia etal (2008) Subfamily 7 Megarididae Rider (2006) Family 43 Phloeinae Grazia etal (2008) Subfamily 8 Parastrachiidae Rider (2006) Family 28 Corimelaenidae Grazia etal (2008) Family 9 Pentatomidae Rider (2006) Family 29 Corimelaeninae Grazia etal (2008) Subfamily 27 Serbaninae Rider (2006) Subfamily 30 Thyreocorinae Grazia etal (2008) Subfamily 42 PentatominaeETAL Rider (2006) Subfamily 31 Parastrachiinae Grazia etal (2008) Subfamily 10 Phloeidae Rider (2006) Family 32 Cydnidae Grazia etal (2008) Family 44 Phloeinae Rider (2006) Subfamily 33 Thaumastellidae Grazia etal (2008) Family 11 Plataspididae Rider (2006) Family 34 Dinidoridae Grazia etal (2008) Family 12 Scutelleridae Rider (2006) Family 35 Tessaratomidae Grazia etal (2008) Family 13 Tessaratomidae Rider (2006) Family 36 Canopidae Grazia etal (2008) Family 14 Thaumastellidae Rider (2006) Family 37 Megarididae Grazia etal (2008) Family 15 Thyreocoridae Rider (2006) Family 38 Scutelleridae Grazia etal (2008) Family 16 Corimelaeninae Rider (2006) Subfamily 39 Lestoniidae Grazia etal (2008) Family 17 Thyreocorinae Rider (2006) Subfamily 40 Acanthosomatidae Grazia etal (2008) Family 18 Urostylididae Rider (2006) Family 41 Pentatomidae Grazia etal (2008) Family 19 Saileriolinae Rider (2006) Subfamily 20 Urostylinae Rider (2006) Subfamily
  20. 20. Pentatomoidea, sec. Rider  sec. Grazia et al - Most concepts according two authors are congruent - Two concepts overlap 2. Grazia etal 1. Rider, 2006
  21. 21. Pentatomoidea, sec. Rider  sec. Grazia et al
  22. 22. Pentatomoidea, sec. Rider  sec. Grazia et al Concepts of Saileriolidae(-inae) are congruent, but raised to family rank in 2. Grazia etal
  23. 23. Pentatomoidea, sec. Rider  sec. Grazia et al Phloeidae sec. Grazia and Pentatomidae sec. Rider overlap as Serbaninae is included in both and each contains other unique concepts Overlap
  24. 24. A species/genus-level example Bekilya group Malagasy reduviids (Peiratinae)
  25. 25. Mutillocoris Mutillocoris vadoni Mutillocoris tricolor 2. Villiers 1949-1964 Bekilya mira Hovacoris bipunctatus Bekilya Hovacoris ♂ ♀ ♂
  26. 26. Bekilya mira Mutillocoris Mutillocoris tricolor Hovacoris bipunctatus Villiers 1964 Bekilya Mutillocoris vadoni Hovacoris 1. Zhang&Weirauch, 2012
  27. 27. Checklist
  28. 28. 2. Villiers 1949-1964 1. Zhang&Weirauch, 2012  Concept of Bekilya sec. Villiers congruent with concept of B. mira sec. Zhang & Weirauch, and sec. Villiers  Generic concepts of Bekilya and Hovacoris sec. Villiers expanded  Concept of Mutillocoris sec. Villiers overlaps with with concept of Bekilya or Hovacoris sec. Zhang & Weirauch
  29. 29. A complex test case • Leucophoropterini – 23 genera and 104 species (Menard & Schuh, 2011) – ~200 concepts • Taxonomic changes/acts – Species synonymy – Subspecies synonymy – Generic synonymy – Generic reassignment/new combination – New species – New genera based on new species – New genera based on described species – Genera removed from tribe – Incertae sedis – Combination of the changes in above • Species synonymy and generic reassignment
  30. 30. Leucophoropterini New genera added, some genera removed and some species recognized as Insertae sedis Abuyogocoris None Aitkenia New species added Arafuramiris New species added Biromiris New species added Blesingia New species added; two species removed Blesingia elegans Junior synonym; transferred to different genus Blesingia latezonata Junior synonym; transferred to different genus Collessicoris None Ctypomiris New species added Gulacapsus New species added Leucophoroptera New species added; two congeners synonymized; two species transferred to this genus and synonymized with the senior synonym of the two synonymized congeners; one species transferred to another genus Leucophoroptera nitidior Junior synonym, congeneric Leucophoroptera quadrimaculata Senior synonym of one congener and two species from another genus Leucophoroptera macrozonata Transferred to different genus Papuamimus None Pseudohallodapocoris None Sejanus Three species removed to form a new genus; two species synonymized; 10 species removed and became insertae sedis (considered to be removed from the tribe in current analysis) Sejanus brunneus Junior synonym, congeneric; transferred to different genus Sejanus tasmaniae Transferred to different genus Sejanus albisignatus Transferred to different genus Sejanus intermedius Junior synonym, congeneric; transferred to different genus Sejanus melaleucae Junior synonym, congeneric; transferred to different genus Sejanus rosei Junior synonym, congeneric Sejanus rosei obscurior Junior synonym, intraspecific; transferred to different genus Sejanus additional species transferred to Ausejanus Transferred to different genus Solomonomimus None Trichocephalocapsus None Waterhouseana New species added Dilatops Removed from tribe Karoocapsus Removed from tribe Lasiolabops Removed from tribe Myrmicopsella Removed from tribe Porophoroptera Removed from tribe Schuhistes Removed from tribe Tytthus Removed from tribe Sejanus biniguni Insertae sedis (aka removed from tribe) Sejanus fasciatus Insertae sedis (aka removed from tribe) Sejanus fijiensis Insertae sedis (aka removed from tribe) Sejanus hongkong Insertae sedis (aka removed from tribe) Sejanus leai Insertae sedis (aka removed from tribe) Sejanus novecaledonicus Insertae sedis (aka removed from tribe) Sejanus occidentalis Insertae sedis (aka removed from tribe) Sejanus ruber Insertae sedis (aka removed from tribe) Sejanus rubricatus Insertae sedis (aka removed from tribe) Sejanus trivinosus Insertae sedis (aka removed from tribe) Pseudoleucophoroptera Junior synonym; genus-level Pseudoleucophoroptera mamai Transferred to different genus Pseudoleucophoroptera promeceops Transferred to different genus Missanos New genus Neaitkenia New genus Neoleucophoroptera New genus Johnstonsonius New genus Papuamiroides New genus Transleucophoroptera New genus Ausejanus New genus Austrodapus New genus Summary of taxonomic acts ~100 taxonomic acts
  31. 31. Full representation and resolved articulations
  32. 32. Conclusion • Feasibility of concept taxonomy approach in mapping taxonomic concepts in Heteroptera • All taxonomic differences can be represented • High resolution in differentiating and relating taxonomic changes • Input and knowledge from taxonomists is critical
  33. 33. Further information • taxonbytes.org • https://bitbucket.org/eulerx/euler-project • Franz & Peet (2009) – http://taxonbytes.org/pdf/FranzPeet2009- LanguageMappingTaxonomicConcepts.pdf • Franz et al. (2014) – http://www.semantic-web- journal.net/system/files/swj623.pdf • Past research and publicatios by N. Franz – http://taxonbytes.org/prior-work-on-concept- taxonomy-2013/
  34. 34. Acknowledgements • NSF CAREER #1155984 • Ludaescher Lab @ UC Davis Parastrachiidae? (-inae?)
  35. 35. Thank you!

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