Resolution among major placental mammal interordinal relationships with genome data imply that speciation influenced their earliest radiations.
Resolution among major placental mammal interordinal relationships with genome data imply that speciation influenced their earliest radiations.
复制标题
DOI：
10.1186/1471-2148-8-162
复制
发表时间：
2008-05-27
影响因子：
3.4
通讯作者：
Janke A
中科院分区：
文献类型：
--
作者：
Hallström BM;Janke A
尽管进行了广泛的基因组分析，但胎盘哺乳动物树中的一些更深层次的分歧仍然没有得到最终解决。最近对200 kbp的蛋白质编码序列的分析只对劳氏兽（牛，狗，蝙蝠和鼩）之间的关系提供了有限的支持，可能是因为分歧只发生在几百万年内。一般认为，增加数据量和改进分类单元抽样可以提高对狭窄分歧的分辨力。因此，通过迄今为止最大的序列比对的重复基因组分析来检查这些和其他困难的分裂。越来越完整的胎盘哺乳动物基因组数据也允许开发一种新的和严格的数据搜索方法。严格的数据处理，递归BLAST，成功地从基因家族中删除了序列，包括那些来自众所周知的家族血红蛋白，嗅觉，肌球蛋白和HOX基因，从而避免了可能的旁系同源序列的比对。目前对来自22个物种的3，012个基因（2，844，615个核苷酸）的基因组分析为大多数关系提供了统计学上的显着支持。虽然使用基因组序列数据确认了一些主要的进化枝，但尽管比对的大小，树鼩、蝙蝠的位置以及Boreoeutheria、Xenarthra和Afrotheria之间的关系仍然存在问题。系统基因组分析的分歧时间的日期基本胎盘哺乳动物分裂在95-100万年前。以下的许多分歧只发生在几百万年（2-4）之后。与窄分歧的时间间隔的关系得到了意想不到的有限的支持，即使从基因组分析。狭窄的时间窗口内发生的一些胎盘分歧表明，不一致和有限的分辨率的哺乳动物树可能有其自然的解释在物种形成过程中，如谱系排序，物种杂交或杂交物种的渗入。这些过程模糊了系统发育分析，使得树的某些部分即使用基因组数据也难以解析。
A number of the deeper divergences in the placental mammal tree are still inconclusively resolved despite extensive phylogenomic analyses. A recent analysis of 200 kbp of protein coding sequences yielded only limited support for the relationships among Laurasiatheria (cow, dog, bat and shrew), probably because the divergences occurred only within a few million years from each other. It is generally expected that increasing the amount of data and improving the taxon sampling enhance the resolution of narrow divergences. Therefore these and other difficult splits were examined by phylogenomic analysis of the hitherto largest sequence alignment. The increasingly complete genome data of placental mammals also allowed developing a novel and stringent data search method. The rigorous data handling, recursive BLAST, successfully removed the sequences from gene families, including those from well-known families hemoglobin, olfactory, myosin and HOX genes, thus avoiding alignment of possibly paralogous sequences. The current phylogenomic analysis of 3,012 genes (2,844,615 nucleotides) from a total of 22 species yielded statistically significant support for most relationships. While some major clades were confirmed using genomic sequence data, the placement of the treeshrew, bat and the relationship between Boreoeutheria, Xenarthra and Afrotheria remained problematic to resolve despite the size of the alignment. Phylogenomic analysis of divergence times dated the basal placental mammal splits at 95–100 million years ago. Many of the following divergences occurred only a few (2–4) million years later. Relationships with narrow divergence time intervals received unexpectedly limited support even from the phylogenomic analyses. The narrow temporal window within which some placental divergences took place suggests that inconsistencies and limited resolution of the mammalian tree may have their natural explanation in speciation processes such as lineage sorting, introgression from species hybridization or hybrid speciation. These processes obscure phylogenetic analysis, making some parts of the tree difficult to resolve even with genome data.
登录
查看更多内容
影响因子：
3.7
作者：
Demuth JP;De Bie T;Stajich JE;Cristianini N;Hahn MW
通讯作者：
Hahn MW
影响因子：
1.1
作者：
Aguileta, Gabriela;Bielawski, Joseph P.;Yang, Ziheng
通讯作者：
Yang, Ziheng
影响因子：
1.9
作者：
Corneli, Patrice Showers
通讯作者：
Corneli, Patrice Showers
人类，狗和小鼠的系统基因组研究。
影响因子：
4.3
作者：
Cannarozzi, Gina;Schneider, Adrian;Gonnet, Gaston
通讯作者：
Gonnet, Gaston
影响因子：
3.6
作者：
GOODMAN M;CZELUSNIAK J;BEEBER J E
通讯作者：
BEEBER J E