Site wide links removal

[jazavide]

A website of mine has about 4,000 backlinks of which 2,500 of them are coming from one website to the homepage and about 6 internal pages.  These have been built up over about 5 years, mainly via article posts.

The site was recently hit via penguin 2.0 but has only had natural links built so i'm wondering if the sitewide links are in fact the issue?

The website linking to mine is an authority source within its niche but the concern is the amount of backlinks coming from this one site and if it may now be seen as having a negative impact.  When ive reviewed the links from this one site via a backlink removal tool about 80% seem fine and suggestions are to remove about 20% of the backlinks.

Would you keep all the sitewide backlinks or remove them?
Have you come across a similar situation and how did it affect ranking/traffic?

[jazavide]

Anyone else looking at same issue or has feedback/comments?

thanks

[Carson-Ward]

Authority links are only one part of the equation. Regardless of source, Penguin looks quite heavily at anchor text. If the majority of anchor text pointing to your site is exact-match non-branded stuff, then it's entirely possible that Google could look on this as an attempt to manipulate rankings artificially. Without seeing more, I can only tell you that it's happened before and may be possible, especially if many of your links are from the same site.