Can spammy links affect indexing?
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Meaning, if you have a lot of bad quality links (directories, blog comments) that are giving great rankings for some terms (on a homepage of a site), could the low quality of these links negatively affect the crawling frequency of interior pages or perhaps even give interior pages a ranking penalty?
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This is a topic I feel needs extensive testing. As you have said, although google has not commented on the subject to any great degree other than best practice (with respect to relevant linking) it would appear that there is methodology out there that would suggest the comparative quality of inbound links does have an effect - Eric Ward/Adgooroo are avid promoters of "domain profile" when it comes to inbound links.
The penalty side of things has only come into play recently with the PANDA update - many sites that rely only on syndicated content to exists have been penalised - as a result, perfectly legitimate sites that have syndicated content out with links in have suffered .
Of course the efficiency factor comes in to play too - both from the time and effort needed to gain a high quality link, over the "loads of links in 10 minutes" through directories/blog comments/syndication. We all know that 10 high quality, relevant .edu links will earn way more brownie points than 100 "easy" links from non-relevant sources.
I suspect if you took a large site with a high number of back links and reduced the number of spammy links - you might, over time, see an improvement in ranking. This is of course an assumption though, would be interesting to see if anyone has experimented.
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There is some discussion on this same topic you can take a look at: http://www.seomoz.org/q/few-high-quality-links-or-a-plethora-of-mediocre-links
Most SEO experts will share the same thought "you want to build your site over time with high quality links". I completely agree but many sites would like a boost to get started. Others have good content but due to heavy competition or other factors desire to perform better in SERP.
It is my understanding having a lot of low quality links can help a site, and cannot harm a site. For those who feel otherwise, I would appreciate the opportunity to further discuss the topic. I would love to see any information from Google or Matt Cutts on the topic.
The term "penalty" often used to describe these links or the site which receives them usually refers to the loss of link juice from the bad link. I am not aware of any negative effects outside of discounting the bad link.
The Pandora effect, or any drop of ranking, is due to the loss of juice from the offending links, not a penalty from Google. The site still benefited. For a time, they had higher rankings and more exposure to the public. During that period the site could have earned additional sales or picked up readers who otherwise may have not seen the site. Those additional customers and readers can directly lead to the site ranking higher then it would of if it never received the "bad" link.
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Just because you are getting great rankings for some terms, or better yet - THINK you are getting rankings for great terms due to bad quality links, does not mean that at some point you won't be harmed by them. And you could be harmed from them right now - or not necessarily harmed as much as hindered.
While Google does a questionable job at weeding out sites with lots of bad links, they're not completely helpless. And sites have been known to fall due to an over-abundance of bad links, though it's more that Google will discount them as a ranking factor before they actually penalize a site.
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