A comprehensive analysis of the phylogenetic signal in ramp sequences in 211 vertebrates.
A comprehensive analysis of the phylogenetic signal in ramp sequences in 211 vertebrates.
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DOI：
10.1038/s41598-020-78803-3
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发表时间：
2021-01-12
影响因子：
4.6
通讯作者：
Ridge PG
中科院分区：
文献类型：
--
作者：
McKinnon LM;Miller JB;Whiting MF;Kauwe JSK;Ridge PG
当在基因开头发现稀有且翻译缓慢的密码子时，斜坡序列会提高翻译速度和准确性。在这里，展示了系统发育构建体中斜坡序列的首次分析结果。对 247 种脊椎动物（114 种哺乳动物和 133 种非哺乳动物）的斜坡序列进行了比较，其中斜坡序列的存在和不存在在简约和最大似然框架中作为二元特征进行分析。此外，斜坡序列被映射到开放生命之树合成树，以确定发生的并行和反转的数量，并将这些结果与随机排列进行比较。对斜坡序列存在和不存在的简约性和最大似然分析恢复了与已建立的系统发育高度一致的系统发育。此外，81% 的脊椎动物斜坡和 81.2% 的其他脊椎动物斜坡的平行度和反转少于 1000 个随机排列的树的平均值。与随机机会相比，完全直系同源斜坡序列的卡方分析得出 p 值 < 0.001。斜坡序列恢复了与其他系统发育学方法相当的系统发育。尽管并非所有斜坡序列似乎都具有系统发育信号，但跟踪物种形成的斜坡序列比随机机会预期的要多。因此，如果考虑到许多直向同源物，斜坡序列可以与其他系统发育学方法结合使用。然而，利用少量直系同源物的系统发育学方法在合并斜坡序列时应谨慎，因为单个斜坡序列可能提供冲突的信号。
Ramp sequences increase translational speed and accuracy when rare, slowly-translated codons are found at the beginnings of genes. Here, the results of the first analysis of ramp sequences in a phylogenetic construct are presented. Ramp sequences were compared from 247 vertebrates (114 Mammalian and 133 non-mammalian), where the presence and absence of ramp sequences was analyzed as a binary character in a parsimony and maximum likelihood framework. Additionally, ramp sequences were mapped to the Open Tree of Life synthetic tree to determine the number of parallelisms and reversals that occurred, and those results were compared to random permutations. Parsimony and maximum likelihood analyses of the presence and absence of ramp sequences recovered phylogenies that are highly congruent with established phylogenies. Additionally, 81% of vertebrate mammalian ramps and 81.2% of other vertebrate ramps had less parallelisms and reversals than the mean from 1000 randomly permuted trees. A chi-square analysis of completely orthologous ramp sequences resulted in a p-value < 0.001 as compared to random chance. Ramp sequences recover comparable phylogenies as other phylogenomic methods. Although not all ramp sequences appear to have a phylogenetic signal, more ramp sequences track speciation than expected by random chance. Therefore, ramp sequences may be used in conjunction with other phylogenomic approaches if many orthologs are taken into account. However, phylogenomic methods utilizing few orthologs should be cautious in incorporating ramp sequences because individual ramp sequences may provide conflicting signals.
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影响因子：
5.8
作者：
Posada, D;Crandall, KA
通讯作者：
Crandall, KA
DOI：
10.1073/pnas.0913033107
发表时间：
2010-01-05
影响因子：
11.1
作者：
Jun, Se-Ran;Sims, Gregory E.;Kim, Sung-Hou
通讯作者：
Kim, Sung-Hou
影响因子：
64.8
作者：
CRICK, F
通讯作者：
CRICK, F
影响因子：
10.7
作者：
Nguyen LT;Schmidt HA;von Haeseler A;Minh BQ
通讯作者：
Minh BQ
影响因子：
10.7
作者：
Kumar, Sudhir;Stecher, Glen;Tamura, Koichiro
通讯作者：
Tamura, Koichiro