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ERVs and common descent

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A significant problem in a nutshell with the orthologue argument for ERVs as evidence of common descent
(taken from here)
ERV deletions

(Incidentally, as the author acknowledges, the no. of missing ERVs in man on the left should be 7, of course, not 6 as is correct for the Orangutan.)

The same problem of missing deletions from potentially orthologous sites also applies to CERV 2.

Despite some intensive searching, I've only been able to find two candidate orthologous CERV 1 sites one Macaque to Pan Trog. (NW_001112574.1 vs. Contig33.125) and one Gorilla to Pan. trog. (AADA01328632.1 vs CABD02058267.1), and neither is anything like as persuasive as SA Smith's example for CERV 5 (post 193) in her blog taken from here. It has opened my eyes to the complexity and  difficulty of the search though.

Several interesting findings including genome-wide distribution of a non CERV fragment of NW_001112574.1 near to a CERV 1 site (coords 7346538-7350059) in Pan. trog., Homo sap., Macaque malatta (the origin of the sequence), Orangutan and Gor. gorilla.

Image of blast hit results:

Widespread peri CERV1 insertion site homology

A few details:

I searched for the pol gene of CERV1 (4544..5611 from NCBI's AY692036.1) in the macaque genome and then took contiguous sequences of the hits from this with adjacent non CERV containing sequence and blasted it against Pan Trog.
In the macaque contig NW_001112574.1 the a portion of CERV1 pol gene is found at 7352782-7351802(-), (though there's a gap in pol sequence from its 487th to 664th nucleotide).
Two non CERV containing adjacent fragments (I called a and b) from the macaque contig are also with the pol gene in the chimp contig for chromosome 2, Contig33.125 (AACZ03012828.1).
The fragments a and b are found at 7347266-7347577 and 7349461-7349794 in NW_001112574.1. None of 94 other chimp contigs shared either of these two non-CERV fragments from the macaque genome and CERV1 pol sequence.
A third non CERV fragment from the same macaque contig (which I called c) 7346538-7350059, near the pol sequence, was not in the chimp contig, but showed widespread distribution throughout the genome of several primates (nearly 3 k hits in man and 3,048 in orangutan). It was inside the regions of 15 different macaque genes.

The second interesting site was shared between the gorilla contig CABD02426596.1 and chimp AADA01328632.1 . Most of the shared sequence is from CERV1, but there is a non CERV1 region from 6129 to 6395 in the gorilla sequence also found in the chimp sequence at 800 to 1065 (Blast scores: 375 375 100% 3e-107 92%).


Frustrating and fascinating as this is, I lack the time and expertise to take the matter further presently.

Some other interesting recent reflections on ERVs here and here.

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