Editing Clinopodium douglasii (section)

=== Molecular phylogenetic work and current status ===

Beginning in the 1990s, the growth of [[molecular phylogenetics]] led to the findings that existing concepts of ''Satureja'' and ''Micromeria'' were [[polyphyletic]] and led to more circumscribed [[monophyletic]] definitions of these genera.<ref name="brauchler-etal-2005"/> In 1995, Philip D. Cantino and Steven J. Wagstaff, carried out the first molecular phylogenetic tree that included this species, based on a [[restriction site]] analysis. They concluded that ''Calamintha'' and a number of [[New World]] [[Mentheae]] genera and species, including then-''Satureja douglasii'', formed a distinct [[clade]] separate from ''Satureja'' [[sensu stricto]] (represented by ''[[Satureja montana]]'') and from ''Micromeria''.<ref name="wagstaff-etal-1995">{{Cite journal| doi = 10.1002/j.1537-2197.1995.tb15705.x| jstor = 2445975| volume = 82| issue = 7| pages = 886–892| last1 = Wagstaff| first1 = Steven J| last2 = Olmstead| first2 = Richard G| last3 = Cantino| first3 = Philip D| title = Parsimony analysis of cpDNA restriction site variation in subfamily Nepetoideae (Labiatae)| journal = American Journal of Botany| access-date = 2024-12-03| date = 1995| url = https://www.researchgate.net/publication/322842912}}</ref> In 1998, they recommended use of ''Clinopodium'' as a synonym for ''Calamintha'' and that the former was the older name that took priority, and that species of sect. ''Hesperothymus'' also be transferred to a new, broadly-defined genus ''Clinopodium'', specifically listing ''Clinopodium douglasii'' (Benth.) Kuntze as the preferred name for this species.<ref name="cantino-wagstaff-1998">{{Cite journal| doi = 10.2307/2807719| jstor = 2807719| volume = 50| issue = 1| pages = 63–70| last1 = Cantino| first1 = Philip D| last2 = Wagstaff| first2 = Steven J| title = A reexamination of North American ''Satureja'' s.l. (Lamiaceae) in light of molecular evidence| journal = Brittonia| date = 1998| bibcode = 1998Britt..50...63C| url = https://www.researchgate.net/publication/225329158}}</ref> This concept of ''Clinopodium'' was endorsed in later synoptical works on the family Lamiaceae and the genus ''Micromeria'' published in the 2000s.<ref name="bauchler-2008"/><ref name="harley-etal-2004">{{Cite book| publisher = Springer| doi = 10.1007/978-3-642-18617-2_11| isbn = 9783642186172| pages = 167–275| editor = Joachim W. Kadereit| last1 = Harley| first1 = RM| last2 = Atkins| first2 = S| last3 = Budantsev| first3 = AL| last4 = Cantino| first4 = PD| last5 = etc| title = Flowering Plants: Dicotyledons: Lamiales (except Acanthaceae including Avicenniaceae)| chapter = Labiatae| location = Berlin| series = The Families and Genera of Vascular Plants| volume = 7| date = 2004| chapter-url = https://www.researchgate.net/publication/251405438}}</ref>

In 2010, Christian Bräuchler and coauthors published a large scale molecular phylogenetic analysis of the subtribe Menthinae based on [[DNA sequencing]] of both [[nuclear DNA|nuclear]] [[Internal transcribed spacer|ITS]] and several regions of [[chloroplast DNA]]. The resulting phylogeny showed strong support for three distinct clades within the Menthinae: ''Satureja'', ''Micromeria'', and a "''Clinopodium'' group" that included a "New World" subgroup that in turn included ''Clinopodium douglasii'' along with a number of other New World species, variously under the name ''Clinopodium'' and the names of 22 other genera. The relationship of ''C. douglasii'' to other members of the New World group was not well-resolved in this analysis. The polyphyletic nature of ''Clinopodium'' was acknowledged, but no further name changes were recommended until systematic nomenclatural work was carried out on this complex group.<ref name="Brauchler-2010">{{Cite journal| doi = 10.1016/j.ympev.2010.01.016| volume = 55| issue = 2| pages = 501–523| last1 = Bräuchler| first1 = Christian| last2 = Meimberg| first2 = Harald| last3 = Heubl| first3 = Günther| title = Molecular phylogeny of Menthinae (Lamiaceae, Nepetoideae, Mentheae): Taxonomy, biogeography and conflicts| url =| journal = Molecular Phylogenetics and Evolution| date = 2010| pmid = 20152913| bibcode = 2010MolPE..55..501B}}</ref> In the 2010s, further molecular phylogenetic work on the subtribe Menthinae by  Bryan T. Drew and Kenneth J. Sytsma using various chloroplast and nuclear DNA sequences more clearly resolved the cladistic structure of this group and the relationships of ''Clinopodium douglasii''.<ref name="drew-sytsma-2012">{{Cite journal| doi = 10.3732/ajb.1100549| volume = 99| issue = 5| pages = 933–953| last1 = Drew| first1 = Bryan T.| last2 = Sytsma| first2 = Kenneth J.| title = Phylogenetics, biogeography, and staminal evolution in the tribe Mentheae (Lamiaceae)| journal = American Journal of Botany| date = 2012| pmid = 22539517| url = https://bsapubs.onlinelibrary.wiley.com/doi/10.3732/ajb.1100549}}</ref><ref name="drew-etal-2017">{{Cite journal| doi = 10.3732/ajb.1700225| volume = 104| issue = 11| pages = 1695–1707| last1 = Drew| first1 = Bryan T.| last2 = Liu| first2 = Sitong| last3 = Bonifacino| first3 = Jose M.| last4 = Sytsma| first4 = Kenneth J.| title = Amphitropical disjunctions in New World Menthinae: Three Pliocene dispersals to South America following late Miocene dispersal to North America from the Old World| journal = American Journal of Botany| date = 2017| pmid = 29158343| url = https://bsapubs.onlinelibrary.wiley.com/doi/10.3732/ajb.1700225}}</ref>

The phylogeny depicted below is based on those outlined in Bräuchler (2010),<ref name="Brauchler-2010"/> Drew & Sytsma (2012),<ref name="drew-sytsma-2012"/> and Drew, et al. (2017),<ref name="drew-etal-2017"/> and follows the cladistic terminology given in Bräuchler (2010):

{{clade
|label1=[[Menthinae]]
|1= {{clade
  |1= {{clade
  |1= ''Satureja'' group (including ''Thymus'')
  |2= ''Micromeria'' group
  }}
  |2= {{clade
    |1= ''[[Mentha]]''/''[[Cyclotrichium]]'' group
    |2={{clade
      |1= {{clade
          |1=  ''Clinopodium'' sensu strictu 
          |2= {{clade
              |1= ''[[Bystropogon]]''
              |2= "''[[Acinos]]''"/''[[Ziziphora]]'' group
    }}
  }}
      |2= {{clade
          |1=  ''Clinopodium dalmaticum''/[[Mentha arvensis|"''Mentha''" ''arvensis'']] group
          |2= "'''New World group'''"
         }}
       }}
     }}
  }}        
}}

The New World group includes ''Clinopodium douglasii'' and a large number of other species of ''Clinopodium'' [[sensu lato]], as well as 22 named genera. Within the New World group, the phylogenetic trees in the papers by Drew, et al. suggest a relationship between ''C. douglasii'' and several South American species currently classified as ''Clinopodium'', such as ''[[Clinopodium sericifolium|C. sericifolium]]'' and ''[[Clinopodium taxifolium|C. taxifolium]]'', as well as the South American genus ''[[Minthostachys]]''.<ref name="drew-sytsma-2012"/><ref name="drew-etal-2017"/>

{{As of|2024|November}}, [[Plants of the World Online]] continued to place the species in the genus ''Micromeria'',<ref name=POWO_160336-2/> though databases such as the [[Jepson Herbarium]] eFlora,<ref name="jeps-2012"/> [[iNaturalist]],<ref>iNaturalist: [https://www.inaturalist.org/taxa/53203-Clinopodium-douglasii Yerba Buena (''Clinopodium douglasii'')]</ref> Calflora,<ref>Calflora: [https://www.calflora.org/app/taxon?crn=11541 ''Clinopodium douglasii''  (Benth.) Kuntze]</ref> and the [[USDA]] PLANTS Database<ref name="USDA-PLANTS">United States Department of Agriculture PLANTS Database, Plant Profile: [https://plants.sc.egov.usda.gov/plant-profile/CLDO2 ''Clinopodium douglasii'' (Benth.) Kuntze]</ref> place the species in ''Clinopodium''.