Abstract:
BACKGROUND:The chloroplast genes matK and rbcL have been proposed as a "core" DNA barcode for identifying plant species. Published estimates of successful species identification using these loci (70-80%) may be inflated because they may have involved comparisons among distantly related species within target genera. To assess the ability of the proposed two-locus barcode to discriminate closely related species, we carried out a hierarchically structured set of comparisons within Viburnum, a clade of woody angiosperms containing ca. 170 species (some 70 of which are currently used in horticulture). For 112 Viburnum species, we evaluated rbcL + matK, as well as the chloroplast regions rpl32-trnL, trnH-psbA, trnK, and the nuclear ribosomal internal transcribed spacer region (nrITS). RESULTS:At most, rbcL + matK could discriminate 53% of all Viburnum species, with only 18% of the comparisons having genetic distances >1%. When comparisons were progressively restricted to species within major Viburnum subclades, there was a significant decrease in both the discriminatory power and the genetic distances. trnH-psbA and nrITS show much higher levels of variation and potential discriminatory power, and their use in plant barcoding should be reconsidered. As barcoding has often been used to discriminate species within local areas, we also compared Viburnum species within two regions, Japan and Mexico and Central America. Greater success in discriminating among the Japanese species reflects the deeper evolutionary history of Viburnum in that area, as compared to the recent radiation of a single clade into the mountains of Latin America. CONCLUSIONS:We found very low levels of discrimination among closely related species of Viburnum, and low levels of variation in the proposed barcoding loci may limit success within other clades of long-lived woody plants. Inclusion of the supplementary barcodes trnH-psbA and nrITS increased discrimination rates but were often more effective alone rather than in combination with rbcL + matK. We surmise that the efficacy of barcoding in plants has often been overestimated because of the lack of comparisons among closely related species. Phylogenetic information must be incorporated to properly evaluate relatedness in assessing the utility of barcoding loci.
journal_name
BMC Evol Bioljournal_title
BMC evolutionary biologyauthors
Clement WL,Donoghue MJdoi
10.1186/1471-2148-12-73subject
Has Abstractpub_date
2012-05-30 00:00:00pages
73issn
1471-2148pii
1471-2148-12-73journal_volume
12pub_type
杂志文章abstract:BACKGROUND:PHOSPHATE1 (PHO1) gene family members have diverse roles in plant growth and development, and they have been studied in Arabidopsis, rice, and Physcomitrella. However, it has yet to be described in other plants. Therefore, we surveyed the evolutionary patterns of genomes within the plant PHO1 gene family, fo...
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
abstract:: ...
journal_title:BMC evolutionary biology
pub_type:
doi:10.1186/s12862-019-1368-5
更新日期:2019-02-26 00:00:00
abstract:BACKGROUND:Although phylogenomic analyses are increasingly used to reveal evolutionary relationships among ciliates, relatively few nuclear protein-coding gene markers have been tested for their suitability as candidates for inferring phylogenies within this group. In this study, we investigate the utility of the heat-...
journal_title:BMC evolutionary biology
pub_type: 杂志文章
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更新日期:2020-07-16 00:00:00
abstract:BACKGROUND:Anchored hybrid enrichment is a form of next-generation sequencing that uses oligonucleotide probes to target conserved regions of the genome flanked by less conserved regions in order to acquire data useful for phylogenetic inference from a broad range of taxa. Once a probe kit is developed, anchored hybrid...
journal_title:BMC evolutionary biology
pub_type: 杂志文章
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更新日期:2016-06-29 00:00:00
abstract:BACKGROUND:A multiscale network of two galectins Galectin-1 (Gal-1) and Galectin-8 (Gal-8) patterns the avian limb skeleton. Among vertebrates with paired appendages, chondrichthyan fins typically have one or more cartilage plates and many repeating parallel endoskeletal elements, actinopterygian fins have more varied ...
journal_title:BMC evolutionary biology
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abstract:BACKGROUND:The Rhinopomatidae, traditionally considered to be one of the most ancient chiropteran clades, remains one of the least known groups of Rhinolophoidea. No relevant fossil record is available for this family. Whereas there have been extensive radiations in related families Rhinolophidae and Hipposideridae, th...
journal_title:BMC evolutionary biology
pub_type: 杂志文章
doi:10.1186/1471-2148-7-165
更新日期:2007-09-14 00:00:00
abstract:BACKGROUND:Partitioning involves estimating independent models of molecular evolution for different subsets of sites in a sequence alignment, and has been shown to improve phylogenetic inference. Current methods for estimating best-fit partitioning schemes, however, are only computationally feasible with datasets of fe...
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更新日期:2014-04-17 00:00:00
abstract:BACKGROUND:Polymorphisms of single amino acid repeats (SARPs) are a potential source of genetic variation for rapidly evolving morphological traits. Here, we characterize variation in and test for an association between SARPs and head shape, a trait under strong sexual selection, in the stalk-eyed fly, Teleopsis dalman...
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更新日期:2010-07-27 00:00:00
abstract:BACKGROUND:The Hox family of transcription factors has a fundamental role in segmentation pathways and axial patterning of embryonic development and their clustered organization is linked with the regulatory mechanisms governing their coordinated expression along embryonic axes. Among chordates, of particular interest ...
journal_title:BMC evolutionary biology
pub_type: 杂志文章
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更新日期:2011-11-15 00:00:00
abstract:BACKGROUND:How vascular systems and their respiratory pigments evolved is still debated. While many animals present a vascular system, hemoglobin exists as a blood pigment only in a few groups (vertebrates, annelids, a few arthropod and mollusk species). Hemoglobins are formed of globin sub-units, belonging to multigen...
journal_title:BMC evolutionary biology
pub_type: 杂志文章
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更新日期:2020-12-29 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:2010-04-27 00:00:00
abstract:BACKGROUND:Freshwater unionoidean bivalves, and species representing two marine bivalve orders (Mytiloida and Veneroida), exhibit a mode of mtDNA inheritance involving distinct maternal (F) and paternal (M) transmission routes concomitant with highly divergent gender-associated mtDNA genomes. Additionally, male unionoi...
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pub_type: 杂志文章
doi:10.1186/1471-2148-8-165
更新日期:2008-05-31 00:00:00
abstract:BACKGROUND:Socially cued anticipatory plasticity (SCAP) has been proposed as a widespread mechanism of adaptive life-history shifts in semelparous species with extreme male mating investment. Such mating systems evolved several times independently in spiders and male reproductive success should critically depend on tim...
journal_title:BMC evolutionary biology
pub_type: 杂志文章
doi:10.1186/s12862-016-0736-7
更新日期:2016-08-26 00:00:00
abstract:BACKGROUND:Factors promoting the emergence of sharp phylogeographic breaks include restricted dispersal, habitat discontinuity, physical barriers, disruptive selection, mating incompatibility, genetic surfing and secondary contact. Disentangling the role of each in any particular system can be difficult, especially whe...
journal_title:BMC evolutionary biology
pub_type: 杂志文章
doi:10.1186/1471-2148-12-78
更新日期:2012-06-06 00:00:00
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pub_type: 杂志文章
doi:10.1186/s12862-015-0316-2
更新日期:2015-03-13 00:00:00
abstract:BACKGROUND:The Neotropical Region is known for its biodiversity and ranks third in number of known termite species. However, biogeographic and phylogeographic information of termites of this region is limited compared to other world geographic regions. Nasutitermes corniger is widely distributed in the region and is of...
journal_title:BMC evolutionary biology
pub_type: 杂志文章
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更新日期:2017-11-23 00:00:00
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journal_title:BMC evolutionary biology
pub_type: 杂志文章
doi:10.1186/s12862-019-1472-6
更新日期:2019-07-23 00:00:00
abstract:BACKGROUND:Ants of the genus Lasius are ecologically important and an important system for evolutionary research. Progress in evolutionary research has been hindered by the lack of a well-founded phylogeny of the subgenera, with three previous attempts disagreeing. Here we employed two mitochondrial genes (cytochrome c...
journal_title:BMC evolutionary biology
pub_type: 杂志文章
doi:10.1186/1471-2148-8-237
更新日期:2008-08-19 00:00:00
abstract:BACKGROUND:Synonymous or silent mutations are usually thought to evolve neutrally. However, accumulating recent evidence has demonstrated that silent mutations may destabilize RNA structures or disrupt cis regulatory motifs superimposed on coding sequences. Such observations suggest the existence of stretches of codon ...
journal_title:BMC evolutionary biology
pub_type: 杂志文章
doi:10.1186/1471-2148-13-164
更新日期:2013-08-04 00:00:00
abstract:BACKGROUND:Publication of the first diatom genome, that of Thalassiosira pseudonana, established it as a model species for experimental and genomic studies of diatoms. Virtually every ensuing study has treated T. pseudonana as a marine diatom, with genomic and experimental data valued for their insights into the ecolog...
journal_title:BMC evolutionary biology
pub_type: 杂志文章
doi:10.1186/1471-2148-11-125
更新日期:2011-05-14 00:00:00
abstract:BACKGROUND:G protein-coupled receptors (GPCRs) constitute a large family of integral transmembrane receptor proteins that play a central role in signal transduction in eukaryotes. The genome of the protochordate Ciona intestinalis has a compact size with an ancestral complement of many diversified gene families of vert...
journal_title:BMC evolutionary biology
pub_type: 杂志文章
doi:10.1186/1471-2148-8-129
更新日期:2008-05-01 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:2016-10-13 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:2011-09-26 00:00:00
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pub_type: 杂志文章
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更新日期:2018-06-15 00:00:00
abstract:BACKGROUND:Hepatitis B virus (HBV) is an important infectious agent that causes widespread concern because billions of people are infected by at least 8 different HBV genotypes worldwide. However, reconstruction of the phylogenetic relationship between HBV genotypes is difficult. Specifically, the phylogenetic relation...
journal_title:BMC evolutionary biology
pub_type: 杂志文章
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更新日期:2013-06-11 00:00:00
abstract:BACKGROUND:Extended parental care is a complex reproductive strategy in which progenitors actively look after their offspring up to - or beyond - the first juvenile stage in order to maximize their fitness. Although the euarthropod fossil record has produced several examples of brood-care, the appearance of extended pa...
journal_title:BMC evolutionary biology
pub_type: 杂志文章
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更新日期:2018-09-29 00:00:00
abstract:BACKGROUND:Horizontal gene transfer plays an important role in evolution because it sometimes allows recipient lineages to adapt to new ecological niches. High genes transfer frequencies were inferred for prokaryotic and early eukaryotic evolution. Does horizontal gene transfer also impact phylogenetic reconstruction o...
journal_title:BMC evolutionary biology
pub_type: 杂志文章
doi:10.1186/1471-2148-7-45
更新日期:2007-03-21 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:2010-11-18 00:00:00
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pub_type: 杂志文章
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更新日期:2019-07-26 00:00:00
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pub_type: 杂志文章
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更新日期:2014-06-25 00:00:00