کد مقاله کد نشریه سال انتشار مقاله انگلیسی نسخه تمام متن
6368987 1623803 2016 9 صفحه PDF دانلود رایگان
عنوان انگلیسی مقاله ISI
Reversible polymorphism-aware phylogenetic models and their application to tree inference
ترجمه فارسی عنوان
مدل های فیلوژنتیک آشکار چندشکل برگشت پذیر و کاربرد آنها در نتیجه گیری درخت
کلمات کلیدی
درخت گونه، فیلوژنتیک، مرتب سازی نسل ناقص مدل جایگزینی، مدل فیلوژنتیک آگاه به چندامفری معکوس،
موضوعات مرتبط
علوم زیستی و بیوفناوری علوم کشاورزی و بیولوژیک علوم کشاورزی و بیولوژیک (عمومی)
چکیده انگلیسی


- Species tree inference from genome-wide population data.
- Takes incomplete lineage sorting into account.
- Analytical solution of stationary distribution and formal proof of reversibility.
- Reversibility ensures swiftness and stability.
- Increase of sample size per species improves estimations without raising runtime.
- Comparison to the Wright-Fisher diffusion.

We present a reversible Polymorphism-Aware Phylogenetic Model (revPoMo) for species tree estimation from genome-wide data. revPoMo enables the reconstruction of large scale species trees for many within-species samples. It expands the alphabet of DNA substitution models to include polymorphic states, thereby, naturally accounting for incomplete lineage sorting. We implemented revPoMo in the maximum likelihood software IQ-TREE. A simulation study and an application to great apes data show that the runtimes of our approach and standard substitution models are comparable but that revPoMo has much better accuracy in estimating trees, divergence times and mutation rates. The advantage of revPoMo is that an increase of sample size per species improves estimations but does not increase runtime. Therefore, revPoMo is a valuable tool with several applications, from speciation dating to species tree reconstruction.

ناشر
Database: Elsevier - ScienceDirect (ساینس دایرکت)
Journal: Journal of Theoretical Biology - Volume 407, 21 October 2016, Pages 362-370
نویسندگان
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