The book sold very well, and while some anatomical experts hostile to Haeckel's evolutionary views expressed some private concerns that certain figures had been drawn rather freely, the figures showed what they already knew about similarities in embryos. The first published concerns came from Ludwig Rütimeyer , a professor of zoology and comparative anatomy at the University of Basel who had placed fossil mammals in an evolutionary lineage early in the 1860s and had been sent a complimentary copy. At the end of 1868 his review in the Archiv für Anthropologie wondered about the claim that the work was "popular and scholarly", doubting whether the second was true, and expressed horror about such public discussion of man's place in nature with illustrations such as the evolutionary trees being shown to non-experts. Though he made no suggestion that embryo illustrations should be directly based on specimens, to him the subject demanded the utmost "scrupulosity and conscientiousness" and an artist must "not arbitrarily model or generalise his originals for speculative purposes" which he considered proved by comparison with works by other authors. In particular, "one and the same, moreover incorrectly interpreted woodcut, is presented to the reader three times in a row and with three different captions as [the] embryo of the dog, the chick, [and] the turtle." He accused Haeckel of "playing fast and loose with the public and with science", and failing to live up to the obligation to the truth of every serious researcher. Haeckel responded with angry accusations of bowing to religious prejudice, but in the second (1870) edition changed the duplicated embryo images to a single image captioned "embryo of a mammal or bird". Duplication using galvanoplastic stereotypes ( clichés ) was a common technique in textbooks, but not on the same page to represent different eggs or embryos. In 1891 Haeckel made the excuse that this "extremely rash foolishness" had occurred in undue haste but was "bona ﬁde", and since repetition of incidental details was obvious on close inspection, it is unlikely to have been intentional deception.  :275–276;282–286
Darwin thought of natural selection by analogy to how farmers select crops or livestock for breeding, which he called "artificial selection"; in his early manuscripts he referred to a "Nature" which would do the selection. At the time, other mechanisms of evolution such as evolution by genetic drift were not yet explicitly formulated, and Darwin believed that selection was likely only part of the story: "I am convinced that Natural Selection has been the main but not exclusive means of modification."  In a letter to Charles Lyell in September 1860, Darwin regretted the use of the term "Natural Selection", preferring the term "Natural Preservation".