Abstract:
BACKGROUND:Amongst the most commonly used molecular markers for plant phylogenetic studies are the nuclear ribosomal internal transcribed spacers (ITS). Intra-individual variability of these multicopy regions is a very common phenomenon in plants, the causes of which are debated in literature. Phylogenetic reconstruction under these conditions is inherently difficult. Our approach is to consider this problem as a special case of the general biological question of how to infer the characteristics of hosts (represented here by plant individuals) from features of their associates (represented by cloned sequences here). RESULTS:Six general transformation functions are introduced, covering the transformation of associate characters to discrete and continuous host characters, and the transformation of associate distances to host distances. A pure distance-based framework is established in which these transformation functions are applied to ITS sequences collected from the angiosperm genera Acer, Fagus and Zelkova. The formulae are also applied to allelic data of three different loci obtained from Rosa spp. The functions are validated by (1) phylogeny-independent measures of treelikeness; (2) correlation with independent host characters; (3) visualization using splits graphs and comparison with published data on the test organisms. The results agree well with these three measures and the datasets examined as well as with the theoretical predictions and previous results in the literature. High-quality distance matrices are obtained with four of the six transformation formulae. We demonstrate that one of them represents a generalization of the Sørensen coefficient, which is widely applied in ecology. CONCLUSION:Because of their generality, the transformation functions may be applied to a wide range of biological problems that are interpretable in terms of hosts and associates. Regarding cloned sequences, the formulae have a high potential to accurately reflect evolutionary relationships within angiosperm genera, and to identify hybrids and ancestral taxa. These results corroborate earlier ones which showed that treelikeness measures are a valuable tool in comparative studies of biological distance functions.
journal_name
BMC Evol Bioljournal_title
BMC evolutionary biologyauthors
Göker M,Grimm GWdoi
10.1186/1471-2148-8-86subject
Has Abstractpub_date
2008-03-18 00:00:00pages
86issn
1471-2148pii
1471-2148-8-86journal_volume
8pub_type
杂志文章abstract:BACKGROUND:One hypothesis for the function of sleep is that it serves as a mechanism to conserve energy. Recent studies have suggested that increased sleep can be an adaptive mechanism to improve survival under food deprivation in Drosophila melanogaster. To test the generality of this hypothesis, we compared sleep and...
journal_title:BMC evolutionary biology
pub_type: 杂志文章
doi:10.1186/s12862-020-01691-8
更新日期:2020-09-22 00:00:00
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journal_title:BMC evolutionary biology
pub_type: 杂志文章
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更新日期:2009-12-02 00:00:00
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journal_title:BMC evolutionary biology
pub_type: 杂志文章
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journal_title:BMC evolutionary biology
pub_type: 杂志文章
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更新日期:2013-06-10 00:00:00
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更新日期:2017-04-14 00:00:00
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更新日期:2017-04-26 00:00:00
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journal_title:BMC evolutionary biology
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pub_type: 杂志文章
doi:10.1186/s12862-017-1018-8
更新日期:2017-08-04 00:00:00
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更新日期:2017-01-31 00:00:00
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更新日期:2016-08-27 00:00:00
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pub_type: 杂志文章
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pub_type: 杂志文章
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journal_title:BMC evolutionary biology
pub_type: 杂志文章
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journal_title:BMC evolutionary biology
pub_type: 杂志文章
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更新日期:2009-05-05 00:00:00
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pub_type: 杂志文章
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pub_type: 杂志文章
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更新日期:2015-06-11 00:00:00
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journal_title:BMC evolutionary biology
pub_type: 杂志文章
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更新日期:2016-01-27 00:00:00