کد مقاله کد نشریه سال انتشار مقاله انگلیسی نسخه تمام متن
6369854 1623836 2015 13 صفحه PDF دانلود رایگان
عنوان انگلیسی مقاله ISI
Identifiability of the unrooted species tree topology under the coalescent model with time-reversible substitution processes, site-specific rate variation, and invariable sites
ترجمه فارسی عنوان
قابلیت شناسایی توپولوژی درخت گونه ای بدون مدل در مدل کولسیتاس با فرآیندهای جایگزینی برگشت پذیر، تغییرات سرعت خاص سایت و سایت های غیر قابل تغییر
کلمات کلیدی
موضوعات مرتبط
علوم زیستی و بیوفناوری علوم کشاورزی و بیولوژیک علوم کشاورزی و بیولوژیک (عمومی)
چکیده انگلیسی


- Phylogenetic species tree estimation is considered for analyzing next-gen data.
- The coalescent model is used as a model for single-gene phylogenies.
- The general time-reversible (GTR) substitution model is used for sequence evolution.
- Models allowing site-specific rate variation and invariable sites are considered.
- Identifiability of the n-taxon unrooted species tree topology is proven.

The inference of the evolutionary history of a collection of organisms is a problem of fundamental importance in evolutionary biology. The abundance of DNA sequence data arising from genome sequencing projects has led to significant challenges in the inference of these phylogenetic relationships. Among these challenges is the inference of the evolutionary history of a collection of species based on sequence information from several distinct genes sampled throughout the genome. It is widely accepted that each individual gene has its own phylogeny, which may not agree with the species tree. Many possible causes of this gene tree incongruence are known. The best studied is the incomplete lineage sorting, which is commonly modeled by the coalescent process. Numerous methods based on the coalescent process have been proposed for the estimation of the phylogenetic species tree given DNA sequence data. However, use of these methods assumes that the phylogenetic species tree can be identified from DNA sequence data at the leaves of the tree, although this has not been formally established. We prove that the unrooted topology of the n-leaf phylogenetic species tree is generically identifiable given observed data at the leaves of the tree that are assumed to have arisen from the coalescent process under a time-reversible substitution process with the possibility of site-specific rate variation modeled by the discrete gamma distribution and a proportion of invariable sites.

ناشر
Database: Elsevier - ScienceDirect (ساینس دایرکت)
Journal: Journal of Theoretical Biology - Volume 374, 7 June 2015, Pages 35-47
نویسندگان
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