Assessing the impact of phylogenetic incongruence on taxonomy, floral evolution, biogeographical history, and phylogenetic diversity

Zhang, Qiang; Feild, Taylor S.; Antonelli, Alexandre

doi:10.3732/ajb.1400527

Cited by 29 publications

(31 citation statements)

References 94 publications

(128 reference statements)

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“…A combined analysis of nuclear ITS sequences and two plastid loci by Antonelli and Sanmartín (2011) gave similar relationships, differing most notably in the position of H. orientale (nested among Antillean species with morphology, sister to Tafalla with the molecular data). However, an analysis of three plastid loci by Zhang et al (2011) placed H. orientale at the base of the genus and nested three species previously assigned to Tafalla (H. arborescens from the Antilles, H. gentryi and H. neblinae from South America) in the Antillean-Central American clade that included all other species of subgenus Hedyosmum. Zhang et al (2015) showed that the conflict is due to incongruence between ITS and plastid genes and argued that the ITS tree is closer to the species phylogeny because of its congruence with morphological data, with the conflicting plastid results most likely due to ancient hybridization and chloroplast capture.…”

Section: Asteropollis Plantmentioning

confidence: 83%

“…However, an analysis of three plastid loci by Zhang et al (2011) placed H. orientale at the base of the genus and nested three species previously assigned to Tafalla (H. arborescens from the Antilles, H. gentryi and H. neblinae from South America) in the Antillean-Central American clade that included all other species of subgenus Hedyosmum. Zhang et al (2015) showed that the conflict is due to incongruence between ITS and plastid genes and argued that the ITS tree is closer to the species phylogeny because of its congruence with morphological data, with the conflicting plastid results most likely due to ancient hybridization and chloroplast capture. These uncertainties should not affect the inferred relationship between the Asteropollis plant and Hedyosmum as a whole.…”

Section: Asteropollis Plantmentioning

confidence: 83%

“…Phylogenetic studies of relationships within Hedyosmum present a striking example of incongruence between molecular data sets from the nucleus and the plastid (Zhang et al, 2015). In the morphological analysis of Eklund et al (2004), the basal split was into subgenus Hedyosmum, represented by two Antillean species and the Asian species H. orientale, and a larger clade including three Antillean-Central American species and all South American species, corresponding to subgenus Tafalla of Todzia (1988).…”

Section: Asteropollis Plantmentioning

confidence: 99%

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Phylogenetic Analyses of Cretaceous Fossils Related to Chloranthaceae and their Evolutionary Implications

Doyle

Endress

2018

Bot. Rev.

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Chloranthaceae were one of the first common lines during the early radiation of angiosperms, possibly reflecting adaptation to more open habitats. Phylogenetic analyses clarify the position of Cretaceous mesofossils in molecular trees of Recent taxa. Plants that produced Asteropollis pollen, with tepals adnate to a single carpel, are nested in crown group Chloranthaceae with Hedyosmum; Canrightiopsis, with three stamens and no perianth, is sister to Sarcandra and Chloranthus; and Canrightia is a stem relative that illustrates a still bisexual stage in floral reduction. Plants that produced Pennipollis pollen are related to Chloranthaceae and/or Ceratophyllum rather than monocots. Appomattoxia, which produced Tucanopollis pollen, has equivocal affinities, but Pseudoasterophyllites, with similar pollen and stems with reduced leaves, may be a link between Chloranthaceae and Ceratophyllum. These results imply that flowers became unisexual before losing the perianth, while bisexual flowers in Canrightiopsis, Sarcandra, and Chloranthus are secondarily derived from unisexual flowers.

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Section: Asteropollis Plantmentioning

confidence: 83%

Section: Asteropollis Plantmentioning

confidence: 83%

Section: Asteropollis Plantmentioning

confidence: 99%

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Phylogenetic Analyses of Cretaceous Fossils Related to Chloranthaceae and their Evolutionary Implications

Doyle

Endress

2018

Bot. Rev.

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“…In addition to hybridization, phylogenetic incongruence can be a result of incomplete lineage sorting (Gurushidze & al., 2010;Blair & al., 2012;Zhang & al., 2015) or a failure to distinguish paralogous from orthologous sequences when using multi-copy markers such as ITS and ETS (Álvarez & Wendel, 2003). However, we consider these alternative explanations less plausible than hybridization because they are unable to account for the higher chromosome numbers of most taxa that were found to have incongruent phylogenetic positions in the nuclear and plastid phylogenetic trees.…”

Section: Discussionmentioning

confidence: 99%

The delimitation and evolutionary history of the Australasian Lautusoid group of Senecio (Asteraceae: Senecioneae)

Liew

Memory

Ortiz‐Barrientos

et al. 2018

TAXON

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Senecio (Asteraceae: Senecioneae) is one of the largest genera of flowering plants and its infrageneric delimitation has been impeded by its large size (> 1000 species), large morphological variation and widespread incongruence between phylogenies derived from different datasets. As part of efforts to improve our understanding of the evolutionary relationships among infrageneric Senecio groups, nuclear (nrITS, ETS) and plastid (psbA–trnH, trnL and trnL–F) DNA sequence data were used to study the delimitation of the Australasian Lautusoid group of Senecio. These data were also used to understand the evolutionary origins of polyploid species that have been placed in this informally recognized group. The results of our phylogenetic analyses indicate that Australasian Senecio compose four separate and distantly related lineages, which are here informally named the Disciform s.str., Lautusoid, Odoratus s.l., and Quadridentatus groups. A new delimitation of the Lautusoid group is presented that includes species previously placed in this group based on morphological similarities, as well as some that were previously assigned to other informally recognized Senecio groups. This brings the total number of confirmed members of the Lautusoid group to 15 species. Six allopolyploid species were identified that resulted from hybridization between members of the Lautusoid group and species of the three other Australasian Senecio lineages. Our findings indicate that hybridization has played an important role in the evolutionary diversification of Australasian Senecio and provide a framework for further studies into their evolutionary history.

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“…5). Moreover, analyses based on different genomes (nuclear vs. plastid) not only lead to disagreements in the evolutionary relationships of taxa, but also greatly affected other phylogeny-based inferences and interpretations relating to taxonomy, morphological evolution, historical biogeography, and phylogenetic diversity (Zhang et al 2015). Therefore, the most reliable infrageneric classification of Bomarea will be achieved through combined analyses of morphological, palynological, and molecular data from more extentive sampling-of all the species in the genus.…”

Section: Discussionmentioning

confidence: 99%

Pollen morphology and its taxonomic significance in the genus Bomarea Mirb. (Alstroemeriaceae) - II. Subgenus Bomarea

2015

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Pollen morphology of 52 species (out of c. 79) of the Bomarea subgenus Bomarea was examined using light microscopy and scanning electron microscopy (SEM), or using SEM alone. The studied species of Bomarea were stenopalynous, characterized by large, oblate, monosulcate monads with reticulate exine sculpture in most species. Wide variation was observed in quantitative palynological features. The studied taxa were divided into four major groups based on exine ornamentation observed under SEM: microreticulate, reticulate, coarsely rugulate, and psilate-perforate. The reticulate exine sculpture may be a plesiomorphic character state for the genus Bomarea, and the coarsely rugulate and finely rugulate-perforate or psilate-perforate exine sculptures may have evolved independently more than once. In agglomerative hierarchical clustering (AHC) analyses of the genus Bomarea using quantitative pollen data, the studied species were distributed in either two (similarity-based) or four (dissimilarity-based) major clusters. Neither the recent molecular phylogenetic analyses nor the AHC analyses of Bomarea have recovered clades/clusters that represent traditionally recognized subgeneric taxa for the genus. Therefore, the most reliable infrageneric classification of Bomarea can be achieved by combining morphological, palynological, and molecular data from more extentive sampling of all the species.

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Assessing the impact of phylogenetic incongruence on taxonomy, floral evolution, biogeographical history, and phylogenetic diversity

Abstract: Our study demonstrated that phylogenetic conflict not only affects the inference of organismal relationships but also impacts our understanding of biogeographical history, morphological evolution, and phylogenetic diversity.

Cited by 29 publications

References 94 publications

Phylogenetic Analyses of Cretaceous Fossils Related to Chloranthaceae and their Evolutionary Implications

Phylogenetic Analyses of Cretaceous Fossils Related to Chloranthaceae and their Evolutionary Implications

The delimitation and evolutionary history of the Australasian Lautusoid group of Senecio (Asteraceae: Senecioneae)

Pollen morphology and its taxonomic significance in the genus Bomarea Mirb. (Alstroemeriaceae) - II. Subgenus Bomarea

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