Partitioning and Combining Data in Phylogenetic Analysis

Bull, James J.; Huelsenbeck, John P.; Cunningham, Colleen; Swofford, David L.; Waddell, Peter J.

doi:10.1093/sysbio/42.3.384

Cited by 828 publications

(507 citation statements)

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“…The 50% majority-rule consensus tree of the remaining trees was inferred and posterior probabilities were recorded for each branch. A partition homogeneity test in PAUP (Swofford, 2000) (100 replicates, with maxtrees set to 1000) was run with the datasets to establish whether or not the character partitions were heterogeneous (significance threshold value p = 0.05) (Bull et al, 1993).…”

Section: Phylogenetic Analysesmentioning

confidence: 99%

Amblyomma parvum Aragão, 1908 (Acari: Ixodidae): Phylogeography and systematic considerations

Lado

Nava

Labruna

et al. 2016

Ticks and Tick-borne Diseases

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Section: Phylogenetic Analysesmentioning

confidence: 99%

Amblyomma parvum Aragão, 1908 (Acari: Ixodidae): Phylogeography and systematic considerations

Lado

Nava

Labruna

et al. 2016

Ticks and Tick-borne Diseases

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“…Tree topology and clade support were used as gross measures of congruence in phylogenetic signal (Bull et al, 1993;de Queiroz et al, 1995;Wiens, 1998);…”

Section: Sequence Aligning and Phylogenetic Analysesmentioning

confidence: 99%

Molecular systematics and evolution of the Cyanocorax jays

Bonaccorso

Peterson

Navarro‐Sigüenza

et al. 2010

Molecular Phylogenetics and Evolution

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Abstract. Phylogenetic relationships were studied in the genus Cyanocorax (Aves: Corvidae) and related genera, Psilorhinus and Calocitta, a diverse group of New World jays distributed from the southern United States south to Argentina. Although the ecology and behavior of some species in the group have been studied extensively, lack of a molecular phylogeny has precluded rigorous interpretations in an evolutionary framework. Given the diverse combinations of plumage coloration, size, and morphology, the taxonomy of the group has been inconsistent and understanding of biogeographic patterns problematic. Moreover, plumage similarity between two geographically disjuct species, the Tufted Jay (Cyanocorax dickeyi) from western Mexico and the White-tailed Jay (C. mystacalis) from western Ecuador and Peru, has puzzled ornithologists for decades. Here, a phylogeny of all species in the three genera is presented, based on study of two mitochondrial and three nuclear genes. Phylogenetic trees revealed the non-monophyly of Cyanocorax, and the division of the whole assemblage in two groups: "Clade A" containing Resumen. Se estudiaron las relaciones filogenéticas en los géneros Cyanocorax, Psilorhinus y Calocitta (Aves: Corvidae), un grupo diverso de urracas del Nuevo Mundo cuyas especies se distribuyen desde el sur de los Estados Unidos hasta Argentina. Aunque la ecología y el comportamiento de algunas especies en el grupo han sido estudiadas extensamente, la falta de una filogenia molecular ha impedido la interpretación rigurosa de estos estudios en un marco evolutivo. Dadas las diversas combinaciones de coloración de plumaje, tamaño y morfología presentes en las especies del grupo, su taxonomía ha sido inconsistente y la interpretación de sus patrones biogeográficos ha sido problemática. Mas aún, la similitud de plumaje en especies que están geográficamente distantes, como Cyanocorax dickeyi del oeste de Mexico y C. mystacalis del oeste de Ecuador y Perú, ha sido difícil de interpretar. Se presenta una filogenia para todas las especies en los tres géneros, basada en el estudio de dos genes nucleares y dos genes mitocondriales. Los árboles filogenéticos mostraron la parafilia de Cyanocorax y la división de todas las especies en dos grupos: "Clado A" en el cual se encuentran Psilorhinus morio, ambas especies Calocitta, Cyanocorax violaceus, C. caeruleus, C. cristatellus, y C. cyanomelas, y "Clado B" en el cual se encuentran el resto de las especies de Cyanocorax. Las relaciones entre especies del Clado A fueron ambiguas y, en general, poco resueltas. En el Clado B, los análisis mostraron la monofilia de las especies en "Cissilopha", pero no indicaron la monofilia de C. mystacalis + C. dickeyi. La complejidad filogenética de los linajes en el grupo sugiere varias complicaciones en el entendimiento de su biogeografía y taxonomía. Con base en los resultados filogenéticos se reconoce un solo género, Cyanocorax, con Psilorhinus y Calocitta como sinónimos.

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“…However, it is still a contentious issue as to whether data can be or should be combined. Bull et al (1993) were against combining data partitions if heterogeneity is known to exist between them, while Wiens (1998) demonstrates that localized areas of conXict between data sets may not disrupt overall analyses, and in areas of data congruence, combining data strengthens the overall accuracy of the analysis. In our study, the partition homogeneity test between the cyt b and CR revealed no signiWcant diVerences (P D 0.07 > 0.01), when using an adjusted of 0.01 as suggested by Cunningham (1997).…”

Section: 00mentioning

confidence: 99%