Hallström Björn M, Janke Axel
Department of Cell and Organism Biology, Division of Evolutionary Molecular Systematics, University of Lund, Sölvegatan 29, S-223 62 Lund, Sweden.
BMC Evol Biol. 2008 May 27;8:162. doi: 10.1186/1471-2148-8-162.
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.
尽管进行了广泛的系统基因组分析，但胎盘哺乳动物谱系中一些更深层次的分歧仍未得到确凿解决。最近一项对200千碱基对蛋白质编码序列的分析，对劳亚兽总目（牛、狗、蝙蝠和鼩鼱）之间的关系仅提供了有限的支持，这可能是因为这些分歧发生的时间间隔仅在几百万年之内。一般认为，增加数据量和改进分类群抽样可以提高对细微分歧的分辨率。因此，通过对迄今为止最大的序列比对进行系统基因组分析，对这些以及其他难以区分的分支进行了研究。胎盘哺乳动物日益完整的基因组数据也使得开发一种新颖且严格的数据搜索方法成为可能。
严格的数据处理方法——递归BLAST，成功地从基因家族中去除了序列，包括来自血红蛋白、嗅觉、肌球蛋白和HOX基因等知名家族的序列，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3012个基因（2844615个核苷酸）进行的系统基因组分析，为大多数关系提供了具有统计学意义的支持。虽然一些主要分支通过基因组序列数据得到了确认，但尽管比对规模很大，树鼩、蝙蝠的位置以及北方真兽高目、异关节总目和非洲兽总目之间的关系仍难以确定。对分歧时间的系统基因组分析表明，胎盘哺乳动物的基部分歧发生在9500万至1亿年前。随后的许多分歧仅在几百万年（200万至400万）后发生。即使是系统基因组分析，对于分歧时间间隔较短的关系，得到的支持也出人意料地有限。
一些胎盘哺乳动物分歧发生的时间窗口很窄，这表明哺乳动物谱系的不一致性和有限的分辨率可能在物种形成过程中，如谱系分选、物种杂交的基因渗入或杂交物种形成，有其合理的解释。这些过程模糊了系统发育分析，使得即使有基因组数据，谱系中的某些部分也难以解析。
