Reconsidering the generation time hypothesis based on nuclear ribosomal <it>ITS </it>sequence comparisons in annual and perennial angiosperms
<p>Abstract</p> <p>Background</p> <p>Differences in plant annual/perennial habit are hypothesized to cause a generation time effect on divergence rates. Previous studies that compared rates of divergence for internal transcribed spacer (<it>ITS</it>1 and <...
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| Format: | Article |
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BMC
2008-12-01
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| Series: | BMC Evolutionary Biology |
| Online Access: | http://www.biomedcentral.com/1471-2148/8/344 |
| _version_ | 1818787488504741888 |
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| author | Fiz-Palacios Omar Soria-Hernanz David F Braverman John M Hamilton Matthew B |
| author_facet | Fiz-Palacios Omar Soria-Hernanz David F Braverman John M Hamilton Matthew B |
| author_sort | Fiz-Palacios Omar |
| collection | DOAJ |
| description | <p>Abstract</p> <p>Background</p> <p>Differences in plant annual/perennial habit are hypothesized to cause a generation time effect on divergence rates. Previous studies that compared rates of divergence for internal transcribed spacer (<it>ITS</it>1 and <it>ITS</it>2) sequences of nuclear ribosomal DNA (nrDNA) in angiosperms have reached contradictory conclusions about whether differences in generation times (or other life history features) are associated with divergence rate heterogeneity. We compared annual/perennial <it>ITS </it>divergence rates using published sequence data, employing sampling criteria to control for possible artifacts that might obscure any actual rate variation caused by annual/perennial differences.</p> <p>Results</p> <p>Relative rate tests employing <it>ITS </it>sequences from 16 phylogenetically-independent annual/perennial species pairs rejected rate homogeneity in only a few comparisons, with annuals more frequently exhibiting faster substitution rates. Treating branch length differences categorically (annual faster or perennial faster regardless of magnitude) with a sign test often indicated an excess of annuals with faster substitution rates. Annuals showed an approximately 1.6-fold rate acceleration in nucleotide substitution models for <it>ITS</it>. Relative rates of three nuclear loci and two chloroplast regions for the annual <it>Arabidopsis thaliana </it>compared with two closely related <it>Arabidopsis </it>perennials indicated that divergence was faster for the annual. In contrast, <it>A. thaliana ITS </it>divergence rates were sometimes faster and sometimes slower than the perennial. In simulations, divergence rate differences of at least 3.5-fold were required to reject rate constancy in > 80 % of replicates using a nucleotide substitution model observed for the combination of <it>ITS</it>1 and <it>ITS</it>2. Simulations also showed that categorical treatment of branch length differences detected rate heterogeneity > 80% of the time with a 1.5-fold or greater rate difference.</p> <p>Conclusion</p> <p>Although rate homogeneity was not rejected in many comparisons, in cases of significant rate heterogeneity annuals frequently exhibited faster substitution rates. Our results suggest that annual taxa may exhibit a less than 2-fold rate acceleration at <it>ITS</it>. Since the rate difference is small and <it>ITS </it>lacks statistical power to reject rate homogeneity, further studies with greater power will be required to adequately test the hypothesis that annual and perennial plants have heterogeneous substitution rates. <it>Arabidopsis </it>sequence data suggest that relative rate tests based on multiple loci may be able to distinguish a weak acceleration in annual plants. The failure to detect rate heterogeneity with <it>ITS </it>in past studies may be largely a product of low statistical power.</p> |
| first_indexed | 2024-12-18T14:08:34Z |
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| institution | Directory Open Access Journal |
| issn | 1471-2148 |
| language | English |
| last_indexed | 2024-12-18T14:08:34Z |
| publishDate | 2008-12-01 |
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| spelling | doaj.art-fcb15e2087354a8582bacc3ac7d30f4b2022-12-21T21:05:11ZengBMCBMC Evolutionary Biology1471-21482008-12-018134410.1186/1471-2148-8-344Reconsidering the generation time hypothesis based on nuclear ribosomal <it>ITS </it>sequence comparisons in annual and perennial angiospermsFiz-Palacios OmarSoria-Hernanz David FBraverman John MHamilton Matthew B<p>Abstract</p> <p>Background</p> <p>Differences in plant annual/perennial habit are hypothesized to cause a generation time effect on divergence rates. Previous studies that compared rates of divergence for internal transcribed spacer (<it>ITS</it>1 and <it>ITS</it>2) sequences of nuclear ribosomal DNA (nrDNA) in angiosperms have reached contradictory conclusions about whether differences in generation times (or other life history features) are associated with divergence rate heterogeneity. We compared annual/perennial <it>ITS </it>divergence rates using published sequence data, employing sampling criteria to control for possible artifacts that might obscure any actual rate variation caused by annual/perennial differences.</p> <p>Results</p> <p>Relative rate tests employing <it>ITS </it>sequences from 16 phylogenetically-independent annual/perennial species pairs rejected rate homogeneity in only a few comparisons, with annuals more frequently exhibiting faster substitution rates. Treating branch length differences categorically (annual faster or perennial faster regardless of magnitude) with a sign test often indicated an excess of annuals with faster substitution rates. Annuals showed an approximately 1.6-fold rate acceleration in nucleotide substitution models for <it>ITS</it>. Relative rates of three nuclear loci and two chloroplast regions for the annual <it>Arabidopsis thaliana </it>compared with two closely related <it>Arabidopsis </it>perennials indicated that divergence was faster for the annual. In contrast, <it>A. thaliana ITS </it>divergence rates were sometimes faster and sometimes slower than the perennial. In simulations, divergence rate differences of at least 3.5-fold were required to reject rate constancy in > 80 % of replicates using a nucleotide substitution model observed for the combination of <it>ITS</it>1 and <it>ITS</it>2. Simulations also showed that categorical treatment of branch length differences detected rate heterogeneity > 80% of the time with a 1.5-fold or greater rate difference.</p> <p>Conclusion</p> <p>Although rate homogeneity was not rejected in many comparisons, in cases of significant rate heterogeneity annuals frequently exhibited faster substitution rates. Our results suggest that annual taxa may exhibit a less than 2-fold rate acceleration at <it>ITS</it>. Since the rate difference is small and <it>ITS </it>lacks statistical power to reject rate homogeneity, further studies with greater power will be required to adequately test the hypothesis that annual and perennial plants have heterogeneous substitution rates. <it>Arabidopsis </it>sequence data suggest that relative rate tests based on multiple loci may be able to distinguish a weak acceleration in annual plants. The failure to detect rate heterogeneity with <it>ITS </it>in past studies may be largely a product of low statistical power.</p>http://www.biomedcentral.com/1471-2148/8/344 |
| spellingShingle | Fiz-Palacios Omar Soria-Hernanz David F Braverman John M Hamilton Matthew B Reconsidering the generation time hypothesis based on nuclear ribosomal <it>ITS </it>sequence comparisons in annual and perennial angiosperms BMC Evolutionary Biology |
| title | Reconsidering the generation time hypothesis based on nuclear ribosomal <it>ITS </it>sequence comparisons in annual and perennial angiosperms |
| title_full | Reconsidering the generation time hypothesis based on nuclear ribosomal <it>ITS </it>sequence comparisons in annual and perennial angiosperms |
| title_fullStr | Reconsidering the generation time hypothesis based on nuclear ribosomal <it>ITS </it>sequence comparisons in annual and perennial angiosperms |
| title_full_unstemmed | Reconsidering the generation time hypothesis based on nuclear ribosomal <it>ITS </it>sequence comparisons in annual and perennial angiosperms |
| title_short | Reconsidering the generation time hypothesis based on nuclear ribosomal <it>ITS </it>sequence comparisons in annual and perennial angiosperms |
| title_sort | reconsidering the generation time hypothesis based on nuclear ribosomal it its it sequence comparisons in annual and perennial angiosperms |
| url | http://www.biomedcentral.com/1471-2148/8/344 |
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