TreeBASE Search-Matrix 4535 of study 1105

@ARTICLE{TreeBASE2Ref17708, author = {Feng-Jie Sun and Stephen R. Downie and Ronald L. Hartman}, title = {An ITS-Based Phylogenetic Analysis of the Perennial, Endemic Apiaceae Subfamily Apioideae of Western North America.}, year = {2004}, keywords = {}, doi = {}, url = {}, pmid = {}, journal = {Systematic Botany}, volume = {}, number = {}, pages = {}, abstract = {Phylogenetic analyses of 159 DNA sequences from the nuclear rDNA internal transcribed spacer region were conducted to evaluate the monophyly of the herbaceous, perennial genera of Apiaceae subfamily Apioideae endemic to North America (north of Mexico) and to determine the relationships of those elements that currently comprise Cymopterus within the group. The results of a previous phylogenetic study were equivocal in suggesting monophyly for these perennial, endemic taxa and revealed Cymopterus to be polyphyletic, with its species closely linked with those of Aletes, Lomatium, Musineon, Oreoxis, Orogenia, Podistera, Pseudocymopterus, Pteryxia, and Tauschia. Herein, we expand sampling to include comprehensive representation of Aletes, Cymopterus, Musineon, Oreoxis, Orogenia, Podistera, Pseudocymopterus, and Pteryxia and greater representation of Lomatium and Tauschia. We also include all members of two genera not examined previously, Glehnia and Oreonana, as well as additional outgroup genera from the Angelica clade of the apioid superclade. Our results indicate that the perennial, endemic apioid umbellifers of North America constitute a (weakly supported) monophyletic group, with Angelica and the meso-American Arracacia clade comprising two of several possible sister groups. The two subspecies of Glehnia littoralis ally with Angelica and Peucedanum japonicum; Oreonana shows affinity with several species of Cymopterus and Lomatium. The lack of resolution in the ITS trees precludes unambiguous hypotheses of relationship among these perennial, endemic umbellifers but does show that many of these genera, where resolved, are not monophyletic. Indeed, Cymopterus and Lomatium are highly polyphyletic and permeate all major clades resolved in the molecule-derived trees. Evidence from branch lengths and low sequence divergence suggests that that this group of North American umbellifers underwent rapid radiation, likely during the geoclimatic events of the Late Tertiary and Quaternary.} }

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Matrix 4535 of Study 1105

Citation title: "An ITS-Based Phylogenetic Analysis of the Perennial, Endemic Apiaceae Subfamily Apioideae of Western North America.".

This study was previously identified under the legacy study ID S1010 (Status: Published).

Matrices

Title: POY Implied Alignment, all genes, molecular only

Description: Legacy TreeBASE Matrix ID = M4352

Rows

Taxon Label	Row Segments	Characters 1?–30
Nemomydas brachyrhynchus	(none)	T-TA-T--AT----G----C----------
Neolophonotus bimaculatus	(none)	T-TA-T--AT----G----C----------
Neoitamus cyanurus	(none)	T-TA-T--AT----G----C----------
Nicocles politus	(none)	T-TA-T--AT----G----C--------T-
Nusa infumata	(none)	T-TA-T--AT----G----C----------
Ommatius tibialis	(none)	T-TA-T--AT----G----C----------
Opomydas townsendi	(none)	T-TA-T--AT----G----C----------
Ospriocerus aeacus	(none)	T-TA-T--AT----G----C--------T-
Pegesimallus laticornis	(none)	T-TA-T--AT----G----C----------
Perasis transvaalensis	(none)	T-TA-T--AT----G----C----------
Philonicus albiceps	(none)	T-TA-T--AT----G----C----------
Philodicus tenuipes	(none)	??????????????????????????????
Phycus frommeri	(none)	T-TA-T--AT----G----C----------
Pilica formidolosa	(none)	T-TATT--AT----G-C--C-T--------
Plesiomma sp Guanacaste	(none)	T-AA-T---G----G----C----------
Pogonioefferia pogonias	(none)	T-TA-T--AT----G----C----------
Promachus amastrus	(none)	T-TA-T--AT----G----C----------
Proctacanthus philadelphicus	(none)	T-TA-T--AT----G----C----------
Prorates sp Escalante	(none)	T-TA-T--AT----G----C----------
Prolepsis tristis	(none)	T-TA-T--AT----G----C--------T-
Rhabdogaster pedion	(none)	T-TA-T--TG----G----C----T-----
Rhipidocephala sp HaroldJohnson	(none)	T-TA-T--AT----G----C----------
Saropogon luteus	(none)	T-TA-T--AT----G----C-----T----
Scylaticus costalis	(none)	T-TA-T--AT----G----C--------T-
Stenopogon rufibarbis	(none)	T-TA-T--AT----G----C----------
Stiphrolamyra angularis	(none)	T-TA-T--AT----G----C----------
Stichopogon elegantulus	(none)	T-TA-T--AT----G----C----------
Stichopogon punctum	(none)	T-TA-T--AT----G----C----------
Stichopogon trifasciatus	(none)	T-TA-T--AT----GC---C----------
Tillobroma punctipennis	(none)	T-TA-T--AT----G----C--------T-
Tipulogaster glabrata	(none)	T-TA-T--AT----G----C----------
Tolmerus atricapillus	(none)	T-TA-T--AT----G----C----------
Trichoura sp Tierberg	(none)	T-TA-T--GG----G----C----------
Trichardis effrena	(none)	T-TA-T--AT----G----C----------
Willistonina bilineata	(none)	T-TA-T--AT----G----C--------T-
Ablautus coquilletti	(none)	T-TA-T--AT----G----C----------
Acnephalum cylindricum	(none)	T-TA-T--AT----G----C----T-----
Afroestricus chiastoneurus	(none)	T-TA-T--AT----G----C----------
Afroleptomydas sp Clanwilliam	(none)	T-TA-T--AT----G----C---------T
Apiocera painteri	(none)	??????????????????????????????
Apsilocephala longistyla	(none)	T-TA-T--AT----G----C----------
Asilus crabroniformis	(none)	T-TA-T--AT----G----C----------
Asilus sericeus	(none)	T-TA-T--AT----G----C----------
Atomosia puella	(none)	T-TA-T--AT----G----C----------
Beameromyia bifida	(none)	T-TA-T--AT----G----C----------
Bombylius major	(none)	T-TA-T--AT----G----C----------
Cerotainia albipilosa	(none)	T-TA-T--AT----G----C-T--------
Ceraturgus fasciatus	(none)	T-TA-T--AT---GG----C--------T-
Choerades bella	(none)	T-TA-T--AT----G----C----------
Clephydroneura sp Kepong	(none)	TATA-T-AAT----G---CC----------
Connomyia varipennis	(none)	T-TA-T--AT----G----C--------T-
Cyrtopogon rattus	(none)	T-TA-T--AT----G----C----------
Damalis annulata	(none)	T-TA-T--AT----G----C----------
Damalis monochaetes	(none)	T-TA-T--AT----G----C----------
Dasophrys crenulatus	(none)	T-TA-T--AT----G----C----------
Dasypogon diadema	(none)	T-TA-T--AT----G----C----------
Dioctria atricapillus	(none)	T-TA-TA-AT--G-G----C-------T--
Diogmites grossus	(none)	T-TA-T--AT----G----C------T---
Dioctria hyalipennis	(none)	T-TA-T--AT----G----C----------
Dioctria rufipes	(none)	T-TA-T--AT----G----C-------T--
Dysmachus trigonus	(none)	T-TA-T--ATG---G----C----------
Emphysomera conopsoides	(none)	T-TT-T--AT-G--G----C----------
Emphysomera pallidapex	(none)	T-TA-T--AT----G----C----------
Eudioctria albius	(none)	T-TA-T--AT----G----C----------
Euscelidia pulchra	(none)	T-TA-T--AT----G----C----------
Gonioscelis ventralis	(none)	T-TA-T--AT----G----C----------
Hemigephyra atra	(none)	T-TA-T--AT----G----C----------
Holcocephala abdominalis	(none)	T-TA-T--AT----G----C----------
Holcocephala calva	(none)	T-TA-T--AT----G----C----------
Hoplistomerus nobilis	(none)	T-TA-T--AT----G----C----------
Lamyra gulo	(none)	T-TA-T--TG----G--C-CT---------
Laphria aktis	(none)	T-TA-T--AT----G----C----------
Laphystia tolandi	(none)	T-TA-T--AT----G----C--T-------
Lasiopogon aldrichii	(none)	T-TA-T--AT----G----C----------
Lasiopogon cinctus	(none)	T-TA-T--AT----G----C----------
Lasiocnemus lugens	(none)	T-TA-T--AT----G----C----------
Laxenecera albicincta	(none)	T-TA-T--AT----G----C----------
Leptogaster arida	(none)	T-TA-T--AT----G----C----------
Leptarthrus brevirostris	(none)	T-TA-T--AT----G----C--------T-
Leptogaster cylindrica	(none)	T-TA-T--AT----G----C----------
Lestomyia fraudiger	(none)	T-TA-T--AT----G----C----------
Lycostommyia albifacies	(none)	T-TA-T--AT----G----C----------
Machimus occidentalis	(none)	T-TA-T--AT----G----C----------
Megaphorus pulchrus	(none)	T-TA-T--AT----G----C----------
Microstylum sp Karkloof	(none)	T-TA-T--AT----G----C--------T-
Mitrodetus dentitarsis	(none)	T-TA-T--AT----G----C----------
Molobratia teutonus	(none)	T-TA-T--AT----G----C---T------
Mydas clavatus	(none)	T-TA-T--AT----G----C----------

Columns

None of the columns has a description.