Abstract:
BACKGROUND:The detection and avoidance of "long-branch effects" in phylogenetic inference represents a longstanding challenge for molecular phylogenetic investigations. A consequence of parallelism and convergence, long-branch effects arise in phylogenetic inference when there is unequal molecular divergence among lineages, and they can positively mislead inference based on parsimony especially, but also inference based on maximum likelihood and Bayesian approaches. Long-branch effects have been exhaustively examined by simulation studies that have compared the performance of different inference methods in specific model trees and branch length spaces. RESULTS:In this paper, by generalizing the phylogenetic signal and noise analysis to quartets with uneven subtending branches, we quantify the utility of molecular characters for resolution of quartet phylogenies via parsimony. Our quantification incorporates contributions toward the correct tree from either signal or homoplasy (i.e. "the right result for either the right reason or the wrong reason"). We also characterize a highly conservative lower bound of utility that incorporates contributions to the correct tree only when they correspond to true, unobscured parsimony-informative sites (i.e. "the right result for the right reason"). We apply the generalized signal and noise analysis to classic quartet phylogenies in which long-branch effects can arise due to unequal rates of evolution or an asymmetrical topology. Application of the analysis leads to identification of branch length conditions in which inference will be inconsistent and reveals insights regarding how to improve sampling of molecular loci and taxa in order to correctly resolve phylogenies in which long-branch effects are hypothesized to exist. CONCLUSIONS:The generalized signal and noise analysis provides analytical prediction of utility of characters evolving at diverse rates of evolution to resolve quartet phylogenies with unequal branch lengths. The analysis can be applied to identifying characters evolving at appropriate rates to resolve phylogenies in which long-branch effects are hypothesized to occur.
journal_name
BMC Evol Bioljournal_title
BMC evolutionary biologyauthors
Su Z,Townsend JPdoi
10.1186/s12862-015-0364-7subject
Has Abstractpub_date
2015-05-14 00:00:00pages
86issn
1471-2148pii
10.1186/s12862-015-0364-7journal_volume
15pub_type
杂志文章abstract:BACKGROUND:The coral skeleton consists of CaCO3 deposited upon an organic matrix primarily as aragonite. Currently galaxin, from Galaxea fascicularis, is the only soluble protein component of the organic matrix that has been characterized from a coral. Three genes related to galaxin were identified in the coral Acropor...
journal_title:BMC evolutionary biology
pub_type: 杂志文章
doi:10.1186/1471-2148-9-178
更新日期:2009-07-29 00:00:00
abstract:BACKGROUND:The LysM receptor-like kinases (LysM-RLKs) are important to both plant defense and symbiosis. Previous studies described three clades of LysM-RLKs: LysM-I/LYKs (10+ exons per gene and containing conserved kinase residues), LysM-II/LYRs (1-5 exons per gene, lacking conserved kinase residues), and LysM-III (tw...
journal_title:BMC evolutionary biology
pub_type: 杂志文章
doi:10.1186/s12862-019-1467-3
更新日期:2019-07-11 00:00:00
abstract:BACKGROUND:A complex of incipient species with different degrees of morphological or ecological differentiation provides an ideal model for studying species divergence. We examined the phylogeography and the evolutionary history of the Rhododendron pseudochrysanthum s. l. RESULTS:Systematic inconsistency was detected ...
journal_title:BMC evolutionary biology
pub_type: 杂志文章
doi:10.1186/1471-2148-11-108
更新日期:2011-04-19 00:00:00
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journal_title:BMC evolutionary biology
pub_type: 杂志文章
doi:10.1186/s12862-015-0506-y
更新日期:2015-10-12 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:2014-11-25 00:00:00
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journal_title:BMC evolutionary biology
pub_type: 杂志文章
doi:10.1186/s12862-016-0649-5
更新日期:2016-04-14 00:00:00
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pub_type: 杂志文章
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更新日期:2019-12-19 00:00:00
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journal_title:BMC evolutionary biology
pub_type: 杂志文章
doi:10.1186/1471-2148-13-135
更新日期:2013-07-03 00:00:00
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journal_title:BMC evolutionary biology
pub_type: 杂志文章
doi:10.1186/1471-2148-7-S2-S2
更新日期:2007-08-16 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:2015-11-10 00:00:00
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journal_title:BMC evolutionary biology
pub_type: 杂志文章
doi:10.1186/s12862-015-0457-3
更新日期:2015-09-02 00:00:00
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journal_title:BMC evolutionary biology
pub_type: 杂志文章
doi:10.1186/s12862-015-0307-3
更新日期:2015-03-09 00:00:00
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journal_title:BMC evolutionary biology
pub_type: 杂志文章
doi:10.1186/s12862-018-1343-6
更新日期:2019-01-16 00:00:00
abstract:BACKGROUND:Long-term monitoring of the biological impacts of the radioactive pollution caused by the Fukushima nuclear accident in March 2011 is required to understand what has occurred in organisms living in the polluted areas. Here, we investigated spatial and temporal changes of the abnormality rate (AR) in both fie...
journal_title:BMC evolutionary biology
pub_type: 杂志文章
doi:10.1186/s12862-015-0297-1
更新日期:2015-02-10 00:00:00
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pub_type: 杂志文章
doi:10.1186/1471-2148-14-39
更新日期:2014-03-04 00:00:00
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journal_title:BMC evolutionary biology
pub_type: 杂志文章
doi:10.1186/1471-2148-8-257
更新日期:2008-09-22 00:00:00
abstract:BACKGROUND:Lymnaeidae snails play a prominent role in the transmission of helminths, mainly trematodes of medical and veterinary importance (e.g., Fasciola liver flukes). As this family exhibits a great diversity in shell morphology but extremely homogeneous anatomical traits, the systematics of Lymnaeidae has long bee...
journal_title:BMC evolutionary biology
pub_type: 杂志文章
doi:10.1186/1471-2148-10-381
更新日期:2010-12-09 00:00:00
abstract:BACKGROUND:A prerequisite for a duplication to spread through and persist in a given population is retaining expression of both gene copies. Yet changing a gene's dosage is frequently detrimental to fitness. Consequently, dosage-sensitive genes are less likely to duplicate. However, in cases where the level of gene pro...
journal_title:BMC evolutionary biology
pub_type: 杂志文章
doi:10.1186/1471-2148-9-193
更新日期:2009-08-07 00:00:00
abstract:BACKGROUND:Retrotransposons have been suggested to provide a substrate for non-allelic homologous recombination (NAHR) and thereby promote gene family expansion. Their precise role, however, is controversial. Here we ask whether retrotransposons contributed to the recent expansions of the Androgen-binding protein (Abp)...
journal_title:BMC evolutionary biology
pub_type: 杂志文章
doi:10.1186/1471-2148-13-107
更新日期:2013-05-29 00:00:00
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journal_title:BMC evolutionary biology
pub_type: 杂志文章
doi:10.1186/1471-2148-13-105
更新日期:2013-05-28 00:00:00
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journal_title:BMC evolutionary biology
pub_type: 杂志文章
doi:10.1186/1471-2148-10-76
更新日期:2010-03-12 00:00:00
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journal_title:BMC evolutionary biology
pub_type: 杂志文章
doi:10.1186/s12862-016-0701-5
更新日期:2016-06-16 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:2019-02-26 00:00:00
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journal_title:BMC evolutionary biology
pub_type: 杂志文章
doi:10.1186/1471-2148-10-135
更新日期:2010-05-06 00:00:00
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journal_title:BMC evolutionary biology
pub_type: 杂志文章
doi:10.1186/1471-2148-12-216
更新日期:2012-11-12 00:00:00
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journal_title:BMC evolutionary biology
pub_type: 杂志文章
doi:10.1186/1471-2148-10-110
更新日期:2010-04-27 00:00:00
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journal_title:BMC evolutionary biology
pub_type: 杂志文章
doi:10.1186/1471-2148-9-41
更新日期:2009-02-18 00:00:00
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journal_title:BMC evolutionary biology
pub_type: 杂志文章
doi:10.1186/s12862-014-0250-8
更新日期:2014-12-12 00:00:00
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journal_title:BMC evolutionary biology
pub_type: 杂志文章
doi:10.1186/1471-2148-10-386
更新日期:2010-12-15 00:00:00
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journal_title:BMC evolutionary biology
pub_type: 杂志文章
doi:10.1186/1471-2148-13-103
更新日期:2013-05-24 00:00:00