Can Silos and Exact Anchor Text In Links Hurt a Site Post Penguin?

[UplinkSpyder]

Just got a client whose site dropped from a PR of 3 to zero. This happened shortly after the Penguin release, June, 2012.

Examining the site, I couldn't find any significant duplicate content, and where I did find duplicate content (9%), a closer look revealed that the duplication was totally coincidental (common expressions). Looking deeper, I found no sign of purchased links or linking patterns that would hint at link schemes,  no changes to site structure, no change of hosting environment or IP address. I also looked at other factors, too many to mention here, and found no evidence of black hat tactics or techniques.

The site is structured in silos, "services", "about" and "blog". All page titles that fall under services are categorized (silo) under "services", all blog entries are categorized under "blogs", and all pages with company related information are categorized under "about". When exploring the site's links in Site Explorer (SE), I noticed that SE is identifying the "silo" section of links (i.e. services, about, blog, etc.) and labeling it as an anchor text. For example, domain.com/(services)/page-title, where the page title prefix (silo), "/services/", is labeled as an anchor text. The same is true for "blog" and "about". BTW, each silo has its own navigational menu appearing specifically for the content type it represents. Overall, though there's plenty of room for improvement, the site is structured logically.

My question is, if Site Explorer is picking up the silo (services) and identifying it as an anchor text, is Google doing the same? That would mean that out of the 15 types of service offerings, all 15 links would show as having the same exact anchor text (services). Can this type of site structure (silo) hurt a website post Penguin?

[UplinkSpyder]

Hello EGOL, thanks for the resources. I bookmarked both for later reference, especially the article written by Marie Haynes.

I like to take a moment and update my findings. Earlier this morning, as I explored the subject site's hosting environment,  I found several backup copies of the site stored in "/home/alias". On a local host I restored the last backup and found that it did in fact undergo a restructuring of the URL's, not once but several times. Without looking further I suspect the site went through several (8) phases of restructuring and all within a period of 8 months making for linking and fluctuations in the SERP's.

This leads to another question which I posted here on this forum.

[UplinkSpyder]

Hello Cody, and thank you for responding to my question. Yes, I've examined all inbound links and the inbound links of the link grantors and found no purchased or low quality links on their sites.

[EGOL]

Here's Matt Cutts on internal anchor text...

http://www.youtube.com/watch?v=6ybpXU0ckKQ

Check out this YouMoz post for penguin and panda information...

http://www.seomoz.org/ugc/the-difference-between-penguin-and-an-unnatural-links-penalty-and-some-info-on-panda-too

[WhoWuddaThunk]

I wouldn't think so.  I have several sites that are 50,000+ pages with exact match links in the menu and footer that haven't had any problems.

Have you looked to see if any of the sites linking to that site have obvious purchased links?