Bears in a forest of gene trees: phylogenetic inference is complicated by incomplete lineage sorting and gene flow.
Bears in a forest of gene trees: phylogenetic inference is complicated by incomplete lineage sorting and gene flow.
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DOI：
10.1093/molbev/msu186
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发表时间：
2014-08
影响因子：
10.7
通讯作者：
Janke A
中科院分区：
文献类型：
--
作者：
Kutschera VE;Bidon T;Hailer F;Rodi JL;Fain SR;Janke A
熊是一个哺乳动物亚科，包括六个形态和生态不同的现存物种。以前的系统发育分析串联核基因不能解决所有的关系，熊，似乎与线粒体同源性冲突。进化过程，如不完整的谱系排序和基因渗入，可能会导致基因树的不一致和复杂的系统发育推断，但没有考虑在系统发育分析的串联数据。我们产生了一个高分辨率的数据集，常染色体内含子从每个物种的几个人和Y染色体标记。在基于聚结的系统发育和基因流估计方法中，我们解释了种内变异，追溯了个体等位基因的系谱历史。核基因座之间存在相当大的异质性，核基因座和线粒体基因座之间存在不一致性，一个具有分歧时间估计的物种树表明，熊在不到2个月的时间内实现了多样化。与亚洲熊物种的一个分支内的复杂分支顺序一致，我们确定了从亚洲黑熊到懒熊的单向基因流。此外，从棕色到美国黑熊检测到的基因流可以解释美国黑熊在线粒体和核遗传学中的冲突位置。这些结果强调，即使在长达数百万年的时间尺度上，不完全的谱系排序和基因渗入都是突出的进化力量。复杂的进化模式不能被严格的分叉模型充分捕获，只有在合并框架中分析多个独立遗传的位点时才能完全理解。因此，基因树之间的系统发育不一致需要被认为是一个有生物学意义的信号。
Ursine bears are a mammalian subfamily that comprises six morphologically and ecologically distinct extant species. Previous phylogenetic analyses of concatenated nuclear genes could not resolve all relationships among bears, and appeared to conflict with the mitochondrial phylogeny. Evolutionary processes such as incomplete lineage sorting and introgression can cause gene tree discordance and complicate phylogenetic inferences, but are not accounted for in phylogenetic analyses of concatenated data. We generated a high-resolution data set of autosomal introns from several individuals per species and of Y-chromosomal markers. Incorporating intraspecific variability in coalescence-based phylogenetic and gene flow estimation approaches, we traced the genealogical history of individual alleles. Considerable heterogeneity among nuclear loci and discordance between nuclear and mitochondrial phylogenies were found. A species tree with divergence time estimates indicated that ursine bears diversified within less than 2 My. Consistent with a complex branching order within a clade of Asian bear species, we identified unidirectional gene flow from Asian black into sloth bears. Moreover, gene flow detected from brown into American black bears can explain the conflicting placement of the American black bear in mitochondrial and nuclear phylogenies. These results highlight that both incomplete lineage sorting and introgression are prominent evolutionary forces even on time scales up to several million years. Complex evolutionary patterns are not adequately captured by strictly bifurcating models, and can only be fully understood when analyzing multiple independently inherited loci in a coalescence framework. Phylogenetic incongruence among gene trees hence needs to be recognized as a biologically meaningful signal.
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DOI：
10.1016/j.cub.2011.05.058
发表时间：
2011-08-09
期刊：
Current biology : CB
影响因子：
--
作者：
Edwards CJ;Suchard MA;Lemey P;Welch JJ;Barnes I;Fulton TL;Barnett R;O'Connell TC;Coxon P;Monaghan N;Valdiosera CE;Lorenzen ED;Willerslev E;Baryshnikov GF;Rambaut A;Thomas MG;Bradley DG;Shapiro B
通讯作者：
Shapiro B
kretzoiarctos gen。十一月，巨型熊猫进化枝的最古老成员。
影响因子：
3.7
作者：
Abella J;Alba DM;Robles JM;Valenciano A;Rotgers C;Carmona R;Montoya P;Morales J
通讯作者：
Morales J
影响因子：
4.9
作者：
Good, Jeffrey M.;Hird, Sarah;Sullivan, Jack
通讯作者：
Sullivan, Jack
影响因子：
4.9
作者：
Clement, M;Posada, D;Crandall, KA
通讯作者：
Crandall, KA
影响因子：
10.7
作者：
Bidon, Tobias;Janke, Axel;Hailer, Frank
通讯作者：
Hailer, Frank