Nitpick, but viruses are not organisms and so they don't have clades. That's why the paper you linked used the term "viral clades". Like how quasispecies is used rather than species for viruses.
I respectfully disagree. Viruses contain RNA, have reproduction dependent on DNA, and are subject to evolution, which is why they're still categorized in their own tree of "life" with kingdoms, phyla, families, genuses, species, strains, etc. There's no reason why you can't categorize a virus under a clade.
Someone reading this might be wondering how speciation can be measured with viruses, since viruses don't reproduce sexually. Well, we don't test whether different species of animals can reproduce with each other. There's no way to conduct such experiments at any meaningful scale. The vast majority of defined species are educated guesses, and in reality has very little to do with whether two groups of organisms can reproduce with each other. In a lot of cases, species are simply determined by the appearance or behavior of one group of organisms over another group of closely related organisms. The term "species" didn't even originally have anything specifically to do with reproduction; the word effectively meant "looks like", which is why the words "species" and "spectacle" share the first 4 letters.
> Well, we don't test whether different species of animals can reproduce with each other.
"They've been in the room an hour, sir. Nothing's happening."
"Hmmm... Ok, looks like polar bears and flamingoes are different species. Mark that down. Next on the list... swap out the flamingo for the barnacle. Be sure to keep watching closely."
They are definitely borderline; categories tend to fail to capture the continuous. But it is general scientific consensus that viruses do not meet all the criteria for life. They meet some, but not all. And no, they are not still categorized in their own tree of "life". We don't use kingdoms, phyla, etc. anymore. Your argument for viruses being life is clearly out of touch with modern biology, and since clades are by definitions groupings of organisms, and organisms by defintion are living things, no, you cannot say that "There's no reason why you can't categorize a virus under a clade". You have to either change definitions or show that viruses meet all criteria. But then if they did they wouldn't be viruses.
The species definition you brought up does not apply to asexual organisms, for them it's a matter of genomic analysis. As for sexual organisms, it is still a good definition because it is stricter and more "correct" than genomic analysis, although bioinformatics has been getting pretty good with the addition of more sophisticated statistical techniques that go past simple DNA-DNA hybridization.
That's not the strict definition. You are using an extremely loose definition. You are missing two key aspects. First, this defintion of species only applies to sexual organisms, and it's about sexual reproduction. Not just any kind of reproduction. Second, the offspring of said sexual reproduction itself must be fertile. So no, in no way can you ever say viruses are human with this definition.
Yes viruses are not alive and speaking strictly there are no clades or specieses. But I stopped beeing to strict with terminology like this on HN. Most people are not from this field and don't have broad prior knowledge and so it would just complicate and confuse unnecessarily.
Someone reading this might be wondering how speciation can be measured with viruses, since viruses don't reproduce sexually. Well, we don't test whether different species of animals can reproduce with each other. There's no way to conduct such experiments at any meaningful scale. The vast majority of defined species are educated guesses, and in reality has very little to do with whether two groups of organisms can reproduce with each other. In a lot of cases, species are simply determined by the appearance or behavior of one group of organisms over another group of closely related organisms. The term "species" didn't even originally have anything specifically to do with reproduction; the word effectively meant "looks like", which is why the words "species" and "spectacle" share the first 4 letters.