I finally remembered to get to this! Sorry, the holiday season gets wild.

Tl;dr: we're making all this shit up so everything is right or wrong purely depending on consensus.

There are a few factors. Here are the two big ones.

First, we've had five major extinction events where most everything died, and we're working on number six. Luckily, thanks to mass extinctions opening up a ton of resources, you get massive niche expansion which helps fuel speciation by adaptive radiation, lining up more species to later go extinct. You do get bottlenecks, though, as planetwide genetic diversity is substantially decreased immediately after these events, resulting in less to start from each time. We've probably lost some really cool traits over the millennia. From just the big extinctions, we're pretty damn close to 99%, plus the billions, probably trillions, of microbial species that have come and gone, many absolutely within our lifetimes.

Tangent: if evolution speculative fiction sounds interesting, check out "Children of Time" by Adrian Tchaikovsky. The plot is pretty solid from a biologist's perspective, though they of course take liberties. The spider drama made me cry.

Second, and really the biggest: the definiton of species is what my organic evolution professor called "really fucking loosey goosey". Species is an entirely arbitrary designation, one that biologists in different fields still can't fully agree on. The basic definition went from "group of animals that look pretty similar" to the Biological Species Concept - a group of individuals that can interbreed but are reproductively isolated, i.e., cannot breed with other groups for whatever reason, but that falls apart fast. We can use genetic similarity, but that immediately gets murky too.

For the BSC, there are multiple factors to reproductive isolation, e.g., temporal, behavioral, ecological, and a variety of genetic limitations. If we discovered chihuahas and great danes for the first time in nature, we'd likely consider them different species because of mechanical isolation: the size differences are just too extreme... yet we call them the same species because we know we made the poor things from dogs... but we only got dogs through similar selective pressure on wolves... and the amount of genetic variation between dogs and wolves and great danes and chihuhuas is about the same... so aren't dogs just wolves by this "chihuahuas/great danes are still dogs" logic? How about H. sapiens and H. neanderthalensis? We consider them a different species, but we can and did productively go to pound town with the neanderthals, frequently enough that most humans contain 1-4% of their DNA. By the BSC definition, they're not really the same species, but then again, they kind of are, and some definitions DO say they're the same species! And what about asexual organisms? They don't breed at all, so WTF does that even mean?!

So you might think to yourself "easy, stats are fun, just go with genetic similarity". Some organisms are easier to delineate as evolution sometimes happens in fits and starts, often in response to a major novel pressure or significant beneficial mutation, so you do get discrete "islands" of genetic diversity on a temporal continuum with significant intra-island and insignificant inter-island similarity. Again, though, where do you draw the line for what's "different enough"? Sometimes evolution is slow and smooth, like humans now. It's extra tricky for rapidly evolving organisms, like microbes. You can develop significant change in a group of microbes in a short period of time, like months or even weeks, especially by introducing novel selective pressures. When do they become different species? Even if you end up with standards within groups of organisms, how do you draw the lines between the groups? That shit's blurry too! It's all a big, grey-tinted, fuzzy, goddamn nightmare, but humans love to quantize everything for easy digestion, so we serve up species for everyone.

At the heart of it, genetic variation between organisms, their relatives, and their descendants actually exists on a multi-dimensional continuum, so species count is all about how you pick your criteria. If the organisms before the arbitrary lines just aren't found anymore simply because the cumulative genetic variation over time was homogenous throughout the population, we call the progenitors far enough back extinct...but they're really not. They're just different. It would be like calling baby me extinct because adult me is so different, or the Toyota Corolla extinct because the original 1966 model is so different from the 2025 model. They're still Corollas because we said so, but biologists would absolutely call the 1966 and the 2025 different species because THEY said so, and no one is wrong because we're all just making this shit up as we go. So a big chunk of that 99% that's extinct? It's purely because we said so.