text: user2603: Note this is a question from a lay reader.
  I've read in the popular press that ~1-4% of the genome of non-African Homo sapiens is inherited from Neanderthals, or that Melanesians derive a similar amount from the Denisovans.
  This seems like a lot, until you read (elsewhere!) that Neanderthals are 99.7% identical to humans, so most of the fraction inherited is identical in any case.
  Or taking it another way, reading that two individuals will typically have 99.9% identical DNA seems pretty similar, until you realise you are only 0.3% 'different' from a Neanderthal, or 15% 'different' from your dog.
  It seems to me this use of percentages is confusing, misleading, and open to abuse. When comparing species (for example) I would think that they should speak of differences in terms of  base pairs that we could not otherwise have had. 
  How should the lay (or popular science) press best communicate similarities or differences in genomes when talking about individuals, races, or species?
  
  user2609: I don't think there's any way to summarize data like this in a way that is both comprehensive in the "covering all relevant facts and concepts" meaning and in the "able to be understood" meaning. Relatedness is not a simple quantity that can be summarized in one statistic. There's what percentage of total genome is shared. There's percentage of coding genome shared (I would expect the non-coding portion of the genome to be disproportionately represented in similarities between species). There's in-group versus out-group variation (i.e. how does the variation between Neanderthals and modern humans compare to the variation within modern humans and within Neanderthals). Then there's more abstract concepts such as consanguinity index and metrics of genetic drift (i.e. species that separated more recently have less drift between them). 
  Ideally, a journalist would pick the statistic that is most relevant to the issue being discussed in the article, give an overview of how the statistic is calculated and what it represents, and explain why they think it is the most relevant statistic, and perhaps explain what some other statistics are and whey the journalist chose not to focus on those. But this would be a lot to expect from a journalist, and for a reader to go through. 
  Fact is, 87.6% of percentages are largely or completely meaningless. If someone claims that teenagers get into accidents 20% more often than the general public, does that mean that the number of accidents per teenagers is 20% more than accidents per general person? Accidents per mile driven is 20% more? Accidents per hour? Is it comparing all teenagers to the general public? Teenagers with driver's licenses to the general public with driver's licenses? Is number of accidents, or dollar amount of damages? Then you have things like Simpson's Paradox and selection bias. A percentage is supposed to be one number divided by another, and giving just that number is implicitly asserting that it summarizes the data. But generally speaking, knowing those two original numbers, or at the very least where those numbers come from, is an important part of interpreting the data.
  
  user29: I don’t think it’s misleading. Your question seems to be based on the mistaken assumption that the percentages you mention — 1%–4% Neanderthal origin, 99.7% similarity between individuals, etc — should somehow add up to 100%.
  As you note yourself, that’s obviously not the case. There was a similar question to the effect, “how can we share 99% of our genes with chimpanzees if we only share 50% of our genes with our mother and 50% with our father?” and the answer is fundamentally the same. Namely, that these numbers refer to different things. And the DNA or gene content we share with these individuals and groups of individuals isn’t additive, or mutually exclusive. Think of it as a Venn diagram:
  
  (Ratios obviously exaggerated, since showing a diagram where mother and father share 99% wouldn’t be very readable.)
  
  user37: 1–4% is from an evolution point of view. 99.7% is from a sequence point of view. Because they are measuring different things, they can be compatible with each other. The correct interpretation is: 1–4% of a non-African genome is inherited from Neanderthals and the sequence of this 1–4% differs from modern human sequence by 0.3%. PS: so, for each non-African, Neanderthals contributed 1–4% * 0.3% of base pairs not present in modern human. This sounds tiny, but even a single SNP may lead to severe disease. This tiny fraction has known functional impact to diabetes and high-altitude adaption.
  
  Others pointed out two related questions:
  
  How many genes do we share with our mother?
  Do apes and humans share 99% of DNA or 99% of genes? What is the difference?
  
  These questions are really about the ambiguity in the definition of "gene". Importantly, traditionally in popular science and population genetics, a gene could mean an allele. This makes differences.
  For example, by common uses of "gene" in biology, the answer to "how many genes do we share with our mother" would be nearly 100% – every human has nearly the same set of genes. However, clearly this is not what the asker wants. By gene, he/she really means allele. The expected answer is 50% – we inherit 50% of alleles from our mother.
  In the end, what is a "gene" exactly? I don't know. Biologists can often figure out the meaning of word "gene" in the right context, but non-biologists will sometimes have troubles with the ambiguity.
  
original_text: 2603: <p>Note this is a question from a lay reader.</p>
  
  <p>I've read in the popular press that ~1-4% of the genome of non-African <em>Homo sapiens</em> is inherited from Neanderthals, or that Melanesians derive a similar amount from the Denisovans.</p>
  
  <p>This seems like a lot, until you read (elsewhere!) that Neanderthals are 99.7% identical to humans, so most of the fraction inherited is identical in any case.</p>
  
  <p>Or taking it another way, reading that two individuals will typically have 99.9% identical DNA seems pretty similar, until you realise you are only 0.3% 'different' from a Neanderthal, or 15% 'different' from your dog.</p>
  
  <p>It seems to me this use of percentages is confusing, misleading, and open to abuse. When comparing species (for example) I would think that they should speak of differences in terms of  base pairs that we could not otherwise have had. </p>
  
  <p>How should the lay (or popular science) press best communicate similarities or differences in genomes when talking about individuals, races, or species?</p>
   2609: <p>I don't think there's any way to summarize data like this in a way that is both comprehensive in the "covering all relevant facts and concepts" meaning and in the "able to be understood" meaning. Relatedness is not a simple quantity that can be summarized in one statistic. There's what percentage of total genome is shared. There's percentage of <em>coding</em> genome shared (I would expect the non-coding portion of the genome to be disproportionately represented in similarities between species). There's in-group versus out-group variation (i.e. how does the variation between Neanderthals and modern humans compare to the variation within modern humans and within Neanderthals). Then there's more abstract concepts such as consanguinity index and metrics of genetic drift (i.e. species that separated more recently have less drift between them). </p>
  
  <p>Ideally, a journalist would pick the statistic that is most relevant to the issue being discussed in the article, give an overview of how the statistic is calculated and what it represents, and explain why they think it is the most relevant statistic, and perhaps explain what some other statistics are and whey the journalist chose not to focus on those. But this would be a lot to expect from a journalist, and for a reader to go through. </p>
  
  <p>Fact is, 87.6% of percentages are largely or completely meaningless. If someone claims that teenagers get into accidents 20% more often than the general public, does that mean that the number of accidents per teenagers is 20% more than accidents per general person? Accidents per mile driven is 20% more? Accidents per hour? Is it comparing all teenagers to the general public? Teenagers with driver's licenses to the general public with driver's licenses? Is number of accidents, or dollar amount of damages? Then you have things like Simpson's Paradox and selection bias. A percentage is supposed to be one number divided by another, and giving just that number is implicitly asserting that it summarizes the data. But generally speaking, knowing those two original numbers, or at the very least where those numbers come from, is an important part of interpreting the data.</p>
   29: <p>I don’t think it’s misleading. Your question seems to be based on the mistaken assumption that the percentages you mention — 1%–4% Neanderthal origin, 99.7% similarity between individuals, etc — should somehow add up to 100%.</p>
  
  <p>As you note yourself, that’s obviously not the case. There was a similar question to the effect, “<a href="https://biology.stackexchange.com/q/1981/166">how can we share 99% of our genes with chimpanzees if we only share 50% of our genes with our mother and 50% with our father?</a>” and the answer is fundamentally the same. Namely, that these numbers refer to different things. And the DNA or gene content we share with these individuals and groups of individuals isn’t additive, or mutually exclusive. Think of it as a Venn diagram:</p>
  
  <p><a href="https://i.stack.imgur.com/RaHa0.png" rel="nofollow noreferrer"><img src="https://i.stack.imgur.com/RaHa0.png" alt="enter image description here"></a></p>
  
  <p>(Ratios obviously exaggerated, since showing a diagram where mother and father share 99% wouldn’t be very readable.)</p>
   37: <p>1–4% is from an evolution point of view. 99.7% is from a sequence point of view. Because they are measuring different things, they can be compatible with each other. The correct interpretation is: 1–4% of a non-African genome is inherited from Neanderthals and the sequence of this 1–4% differs from modern human sequence by 0.3%. PS: so, for each non-African, Neanderthals contributed 1–4% * 0.3% of base pairs not present in modern human. This sounds tiny, but even a single SNP may lead to severe disease. This tiny fraction has known functional impact to diabetes and high-altitude adaption.</p>
  
  <hr>
  
  <p>Others pointed out two related questions:</p>
  
  <ul>
  <li><p><a href="https://biology.stackexchange.com/q/1981/166">How many genes do we share with our mother?</a></p></li>
  <li><p><a href="https://biology.stackexchange.com/questions/9172/do-apes-and-humans-share-99-of-dna-or-99-of-genes-what-is-the-difference">Do apes and humans share 99% of DNA or 99% of genes? What is the difference?</a></p></li>
  </ul>
  
  <p>These questions are really about the ambiguity in the definition of "gene". Importantly, traditionally in popular science and population genetics, a gene could mean an <a href="https://en.wikipedia.org/wiki/Allele" rel="noreferrer">allele</a>. This makes differences.</p>
  
  <p>For example, by common uses of "gene" in biology, the answer to "how many genes do we share with our mother" would be nearly 100% – every human has nearly the same set of genes. However, clearly this is not what the asker wants. By gene, he/she really means allele. The expected answer is 50% – we inherit 50% of alleles from our mother.</p>
  
  <p>In the end, what is a "gene" exactly? I don't know. Biologists can often figure out the meaning of word "gene" in the right context, but non-biologists will sometimes have troubles with the ambiguity.</p>
  