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Resolution among major placental mammal interordinal relationships with genome data imply that speciation influenced their earliest radiations

Hallström, Björn LU and Janke, Axel LU (2008) In BMC Evolutionary Biology 8.
Abstract
Background: 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... (More)
Background: 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. Results: 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. Conclusion: 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. (Less)
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author
organization
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type
Contribution to journal
publication status
published
subject
in
BMC Evolutionary Biology
volume
8
publisher
BioMed Central
external identifiers
  • wos:000257462400001
  • scopus:47349109604
ISSN
1471-2148
DOI
10.1186/1471-2148-8-162
language
English
LU publication?
yes
id
7f75cd23-00ab-4de4-8d48-ab5366cff2fa (old id 1257134)
date added to LUP
2008-10-14 15:31:24
date last changed
2017-08-27 04:30:58
@article{7f75cd23-00ab-4de4-8d48-ab5366cff2fa,
  abstract     = {Background: 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. Results: 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. Conclusion: 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.},
  articleno    = {162},
  author       = {Hallström, Björn and Janke, Axel},
  issn         = {1471-2148},
  language     = {eng},
  publisher    = {BioMed Central},
  series       = {BMC Evolutionary Biology},
  title        = {Resolution among major placental mammal interordinal relationships with genome data imply that speciation influenced their earliest radiations},
  url          = {http://dx.doi.org/10.1186/1471-2148-8-162},
  volume       = {8},
  year         = {2008},
}