加载中…系统发育基因组学
(2016-10-26 17:47:09)
标签：
系统发育基因组学进化 |
分类： 文献阅读 |
Title: Phylogenomic Analyses of Large-scale Nuclear
Genes Provide
Abstract:
The Rosids
is one of the largest groups of flowering plants, with 140 families
and ~70,000 species. Previous phylogenetic studies of
the rosids have primarily utilized organelle genes
that likely differ in evolutionary histories
from nuclear genes. To better understand the
evolutionary history of rosids, it is necessary to
investigate their phylogenetic relationships using nuclear
genes. Here, we employed large-scale phylogenomic
datasets composed of nuclear genes, including
891 clusters of putative orthologous genes.
Combined with comprehensive taxon sampling covering
63 species representing 14 out of the 17
orders, we reconstructed the rosids phylogeny
with coalescence and concatenation methods,
yielding similar tree topologies from all
datasets. However, these topologies did not agree on
the placement of Zygophyllales. Through
comprehensive analyses, we found that
missing data and gene tree heterogeneity were
potential factors that may mislead concatenation
methods, in particular, large amounts of missing
data under high gene tree heterogeneity. Our
results provided new insights into the deep
phylogenetic relationships of the rosids, and
demonstrated that coalescence methods may effectively resolve
the phylogenetic relationships of the rosids with
missing data under high gene tree
heterogeneity.
Author:
Lei Zhao, Xia
Li, ... De-Zhu Li
Plant Germplasm and
Genomics Center, Germplasm Bank of Wild Species, Kunming Institute
of
E-mail:
dzl@mail.kib.ac.cn; guozhenhua@mail.kib.ac.cn
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研究背景：蔷薇类是形态学和生态学很重要的一大类植物，前人一般使用叶绿体和线粒体基因来揭示其部分的演化关系，但是其中还存在很多不确定关系，有很多争议。高通量测序技术已经广泛运用于推测演化关系，但是随之而来的除了数据量增大，还有基因-物种树冲突。传统的串联
(concatenated) 形成超级矩阵的方法，假设所有的基因具有相同的进化历史，这就忽视了一些重要的进化过程：谱系分选
(ILS)，水平基因转移(HGT)和基因的复制与丢失(GDL)。
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