你对四个句子中逗号后的分词短语的分析都有错误。doing可能是动名词，也可能是现在分词。现在分词可能是定语，也可能是状语。现在分词作状语，可能是修饰谓语动词，也可能是修饰整个句子。你恰恰忽略了这几点，忽略了句子表达的逻辑一样，忽略了doing的逻辑主语为何。

1. The yield varies enormously, because a single tree, depending on its size and on climate and attitude, is able to produce.... 这里depending on不可能是定语，因为现在分词作定语，分词的逻辑主语必须是分词所修饰的那个名词。可是这个句子的逻辑意义是，一棵树结多少果子，取决于几个因素。而不是树取决于几个因素，换句话说，分词的逻辑主语并不是修饰tree的，而是修饰 a single tree is able to produce ... 这个句子的，所以depending on现在分词短语是修饰句子的句子状语。句子状语通常位于句首或句末，由于这里是because从句，就例外地把这个句子状语插入主语和谓语动词之间，用逗号分隔。

2. Employing many different techniques throughout his career, Michelangelo produced a great variety of art works, ranging from paintings, such as those in the Sistine Chapel, to sculpture, such as… 这里ranging from ... 为定语修饰art works, 但却不是定语从句的省略，因为如果用定语从句的话，应为which ranged from ... to... 即定语从句并不是进行体，不可能省略which 和 were。分词本身就可以作定语或状语，并非都是定语从句或者状语从句省略而来的。

3.Normally a bone becomes fossilized through the action of groundwater, permeating the bone, washing away its organic components and replacing them. 这个句子并没有错误，permeating..., washing away... and replacing... 这三个doing并不是现在分词，而是并列的动名词，作非限制性同位语，对the action of groundwater作补充说明。

4. banks are having troubles that are particularly acute in areas where real-estate values have dropped sharply and where industries have retrenched, eliminating thousands of high-paying jobs. eliminating 为结果状语，但不是修饰位于动词的，而是修饰修饰industries have retrenched这个分句的，即现在分词的逻辑主语，不是industries，而是industries have retrenched。这个分词短语可以改为which eliminates thousands of high-paying jobs. which的先行词为前面的分句内容。