Hi everyone,
I am thinking about using JSDM for small mammals communities in Europe following HMSC package. When performing these kind of analyses for birds, I obtained the phylogenetic correlation matrix from http://birdtree.org/. However, in http://vertlife.org/ it seems that mammal phylogenetic subsets are not available for now. Is there any other source where I can find this kind of information?
thanks!
Hello, Teresa. About data base of Mammoth you can give your question to some people from Russia, where this topic is well developed. Below I attach an abstract from 2006 article and here is email of one author [email protected]
Article Complete Mitochondrial Genome and Phylogeny of Pleistocene M...
PLoS Biol. 2006 Mar;4(3):e73. Epub 2006 Feb 7.
Complete mitochondrial genome and phylogeny of Pleistocene mammoth Mammuthus primigenius.
Rogaev EI1, Moliaka YK, Malyarchuk BA, Kondrashov FA, Derenko MV, Chumakov I, Grigorenko AP.
Author information
1Brudnick Neuropsychiatric Research Institute, Department of Psychiatry, University of Massachusetts Medical School, Worcester, Massachusetts, USA. [email protected]
Abstract
Phylogenetic relationships between the extinct woolly mammoth (Mammuthus primigenius), and the Asian (Elephas maximus) and African savanna (Loxodonta africana) elephants remain unresolved. Here, we report the sequence of the complete mitochondrial genome (16,842 base pairs) of a woolly mammoth extracted from permafrost-preserved remains from the Pleistocene epoch--the oldest mitochondrial genome sequence determined to date. We demonstrate that well-preserved mitochondrial genome fragments, as long as approximately 1,600-1700 base pairs, can be retrieved from pre-Holocene remains of an extinct species. Phylogenetic reconstruction of the Elephantinae clade suggests that M. primigenius and E. maximus are sister species that diverged soon after their common ancestor split from the L. africana lineage. Low nucleotide diversity found between independently determined mitochondrial genomic sequences of woolly mammoths separated geographically and in time suggests that north-eastern Siberia was occupied by a relatively homogeneous population of M. primigenius throughout the late Pleistocene.
Comment in
- Reading the evolutionary history of the woolly mammoth in its mitochondrial genome. [PLoS Biol. 2006]
PMID: 16448217 PMCID: PMC1360101 DOI: 10.1371/journal.pbio.0040073[Indexed for MEDLINE] Free PMC Article
Dear Teresa:
Nathan Upham ([email protected]) has a species level phylogeny for all (most) extant mammal species. I assume his tree will be the one to be uploaded in vertlife.org
Cheers,
Miguel
Thanks everyone for your answers :) I will contact Nathan and take a look to GenBank. Thanks Evgeny, but I am looking for small mammals communities in Europe.
Teresa
Teresa Morán-López the Nathan Upham's paper is finally publushed. Check it out: Article Inferring the mammal tree: Species-level sets of phylogenies...
Best,
Miguel
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