Category: species

Colossal Biosciences responds to criticism of the Dire Wolf “de-extinction”, but not convincingly

April 13, 2025 • 9:45 am

Colossal Biosciences®, of course, recently announced the “de-extinction” of the dire wolf, which involved editing a gray wolf genome in 20 places (DNA bases), all edits involving 14 genes.  15 of the 20 sites change apparently involved substituting dire-wolf based nucleotides for wolf bases, while the other five, mainly involving coat color, were simply mutations already known to lighten the coat color in dogs and wolf, and the edits were based on dog and wolf DNA. These five edits made the dire wolf pups turn out white, though we’re not sure that the original dire wolves were white.  As for the other changes, well, we’ll have to see how they affect the three “dire wolves'” morphology when they grow up, as they’re just subadults now.

In the end, though—and I think Colossal should agree—they produced three gray wolves (Romulus, Remus, and Khaleesi), each with 15 DNA bases taken from a sequenced dire wolf genome.  This means that, because the wolf genome has nearly 2.5 billion base pairs, and because are over twelve million DNA base-pair differences between the dire wolf and gray wolf genome, there were tons of dire=wolf genome that was not edited into the egg used to produce the three faux dire wolves. A quote from Vox (archived here):

“The grey wolf genome is 2,447,000,000 individual bases (DNA letters) long. Colossal has said that the grey wolf and dire wolf genomes are 99.5% identical, but that is still 12,235,000 individual differences,” Nic Rawlence, a paleontologist at the University of Otago in New Zealand, told me in an email. “So a grey wolf with 20 edits to 14 genes, even if these are key differences, is still very much a grey wolf.”

Those 15 edits, then, constitute 0.0000012 of all differences between dire wolves and gray wolves, or .000012%.  As many science journalists have noted, Colossal has not produced anything close to a dire wolf, but simply a gray wolf containing a tiny, tiny fraction of the genes that differentiate the two species. Some of the genes they used may have been published in Colossal’s new preprint on the dire wolf (see below), but it gives little information about which genes they used. They clearly didn’t use genes that differentiated the physiology, digestion, or any behaviors that differentiated the two species, because those genes can’t be identified.  Yet surely if you want to “de-extinct” a species, you need more than just a few superficial changes in appearance to “resurrect” the extinct one. Well, that is apparently not Colossal’s view.

Much of the press around the Dire Wolf has been critical, with the exception of places like Time Magazine, which put one of the offspring on the cover with a photo and the word “extinct” crossed out (along with a photo saying “This is Remus” He’s a dire wolf”). But genuinely savvy journalists didn’t have to dig hard to find the hype in Colossal’s claims, some of which I myself pointed out at ABC News. I’d say that about two-thirds of the press stories have been sufficiently critical to raise doubts in the minds of readers.

That has clearly upset Colossal, which of course expected huge approbation and thje public’s acceptance that they had truly “de-extincted” the dire wolf. Instead they got the press kvetching about the company’s hype. (Granted, Colossal did accomplish good stuff like sequencing the dire wolf genome and making twenty edits to a gray wolf cell, which is a technical accomplishment although making multiple edits is pretty routine these days). What seems to have most upset Colossal and their chief scientific adviser, Dr. Beth Shapiro, is criticism of the claim that they had created a “new species” in the lab (the “dire wolf”) of course.

To evolutionary biologists who employ the “Biological Species Concept” (BSC)—one of over 20 such concepts, but the one, as I argue in my book Speciation with Allen Orr—the concept that makes the most evolutionary sense—the “dire wolf” is almost certainly not a new species.  If it were, it would be reproductively isolated from gray wolves (and dogs), so that if they were to cohabit in the same place, they could not produce fertile hybrids.  But I bet ten to one that if you put a bunch of grey wolves in the secret hidden pen where the three “dire wolves” are kept from prying eyes and are monitored by drones, they’d all hybridize and produce fertile puppies. End of the “new species” story.

Sadly, Colossal won’t do that experiment. But it doesn’t matter because Colossal has rejected the BSC in favor of the morphological or typological species concept, in which individuals are said to belong to different species because they look different.  This concept is next to useless because it’s completely subjective: how different do individuals have to look before they’re put in different species? (The evolutionist Ernst Mayr discussed the intellectual vacuity of morphological/typological species concepts beginning in 1942.)

Granted the BSC has its own problems (what do we do with geographically isolated populations who do not have the opportunity to interbreed?), but, as we show in our book, it does a lot of biological and evolutionary work, including giving us a research program for how species originate: why nature is lumpy instead of being a continuum. (The question of “What is the origin of species?” becomes “How do reproductive isolating barriers evolve?”, a question that is actually how people approach the origin of species when they do research.)

It’s clearly in Colossal’s interest to adopt the morphological species concept because they say they’ve produced an animal that looks different from gray wolves in a few traits. And so they can shout “We’ve got a new species!” from the rooftops. But many people aren’t buying it, and so this week Colossal sent out a press release to inquisitive reporters, which I quote below. It’s quite defensive! Bolding is mine.

We’ve been hearing critics call us “insane” for labeling Romulus, Remus, and Khaleesi “dire wolves” instead of “designer dogs” or “fancy gray wolves.” While we didn’t anticipate this would become the major talking point for a breakthrough in genetic engineering that will fundamentally transform biodiversity conservation, fine. Let’s go.

So many experts out there are demanding that species are defined solely by their DNA. That’s some version of “insane”. Even evolutionary biologists can’t agree on species definitions. Mammoth species? Defined by teeth ridges. Ancient bison? Horn shapes. And so arbitrarily that someone accidentally mixing up length and width measurements had zero impact on species classification. Brown bears and polar bears, humans and Neanderthals, wolves and coyotes are all different species unless you apply the most commonly taught species concept, which would classify them as the same species because they can interbreed and produce healthy, fertile offspring.

Getting dragged into arguments about species definitions is a distraction from the real achievement. This is the most significant advancement in gene-editing in history. Even our harshest critics admit it. As one of our founders stated, “this is the moon landing of synthetic biology.” Colossal identified 14 genes we could modify to resurrect the key traits that defined dire wolves, and then we did it. Why is the scientific community wasting time bickering about species concepts rather than celebrating this monumental achievement and its implications? It’s obvious most critics would rather complain than contribute. Through our dire wolf and woolly mouse announcements, Colossal has generated more attention and funding for conservation than anyone has in decades. That’s the kind of “insanity” the world needs.

We invested over a year collaborating with academic colleagues to improve the dire wolf paleogenome and decode the dire wolf’s evolutionary history. Our scientific manuscript has been submitted for peer review and posted to the preprint server–please go check it out. We generated high-quality ancient genomes from dire wolves that lived 13,000 and 72,000 years ago. Our analyses show that dire wolves interbred extensively with the lineage that ultimately evolved into gray wolves, suggesting that dire wolves and gray wolves are much more closely related than previously thought. This is contrary to the “scientific fact” that they were closer to jackals, which originated from a science writer’s misinterpretation of the previous paper. Our higher quality genomes allowed us to uncover the evolutionary history of dire wolves and dig more deeply into the genes under selection in their lineage. These discoveries enabled us to resurrect the traits that made dire wolves larger, stronger, and phenotypically unique: traits that are now embodied in Romulus, Remus, and Khaleesi.

Why did we stop at 14 genes and 20 edits? Because we didn’t need more and because we prioritize animal welfare. Every modification carries risk, and our primary goal was creating healthy animals with extinct traits. We meticulously evaluated each edit for safety and successfully birthed healthy animals that both resemble dire wolves and manifest the traits we targeted. Now critics are having meltdowns because we didn’t make hundreds or thousands of unnecessary, risky edits just to satisfy one particular interpretation of what constitutes a species? No thank you.

Yes, dog breeders have been transforming gray wolves into the animals that we rely on for work and companionship for thousands of years. Maybe tens of thousands. But the ability to dramatically alter an animal’s appearance and behavior in a single generation? That’s new. The implications for conservation are immense. This is the future. Show us what YOU’RE doing to ensure a world with wolves, poodles, pandas, whales, and (assuming agricultural advances) billions of humans. We’re convinced our brand of “insanity” is exactly what’s needed to get there.

We get it. We totally understand that some scientists are not comfortable calling these dire wolves because they feel like the wolves are not sufficiently genetically similar to a particular extinct individual to merit that name. That’s ok with us.  This is not a fight that we care about. We’re calling them dire wolves, and if you prefer something else (how about “Colossal’s dire wolves”?) that works too. And maybe also take a breath and think about what the birth of these technologies means to the future of our planet instead of nitpicking terminology.

That last sentence is pretty hostile, but reflects a certain defensiveness of Colossal about its achievements that does it no good. Will people like Paris Hilton, Tiger Woods, and Peter Jackson, who gave big donations to Colossal, think twice about what they funded. (Probably not; they’re rich as Croesus.) Colossal is saying, “we’re helping the environment; what are you doing?”

I’ve bolded two bits above. The first is their paper on the “dire wolf”, submitted for publication, which you can find on bioRχiv by clicking on the title below (download pdf here.) . The paper doesn’t say which edits were made from the dire wolf genome into the wolf genome, but that’s irrelevant when assessing if they’ve “de-extincted” the dire wolf.  It’s largely about phylogenetics, and shows that the dire wolf and gray wolf are separated by about 4.5 million years. It also gives the names of 80 genes whose DNA sequence shows that they seemed to be under positive natural (including sexual) selection in the dire wolf, and perhaps some of these genes were used in producing the faux dire wolf.  Note that they also claim they changed the behavior of the gray wolf through their edits, but I have seen no evidence of  that.

The second bit is their defense of using a morphological species concept. It’s clear that Shapiro and Colossal are buying into a morphological species definition that’s something like: “If we edit the genes of a living species so it superficially resembles an extinct species, having a few of its traits, then we’ve “de-extincted” the extinct species. Below they refer to the IUCN, the International Union for  the Conservation of Nature, a worldwide organization devoted to conserving habitat and species. They say they are using the IUCN’s definition of “de-extinction:, but they leave out the caveats that IUCN attaches to that word (it prefers “proxy”). This is unconscionable cherry-picking in defense of misleading scientific results.

When I posted on Twitter about the critical ABC News piece on de-extinction, because I was quoted, I got a comment from, of all people, the concerned scientists at Colossal:

But have a look at the IUCN SSC Guiding Principles on Creating Proxies of Extinct Species for Conservation Benefit”: page 1. Bolding is mine

Note on Terminology

The term “de-extinction” is misleading in its implication that extinct species, species for which no viable members remain, can be resurrected in their genetic, behavioural and physiological entirety. These guidelines proceed on the basis that none of the current pathways will result in a faithful replica of any extinct species, due to genetic, epigenetic, behavioural, physiological, and other differences1 . For the purposes of these guidelines the legitimate objective for the creation of a proxy of an extinct species is the production of a functional equivalent able to restore ecological functions or processes that might have been lost as a result of the extinction of the original species. Proxy is used here to mean a substitute that would represent in some sense (e.g. phenotypically, behaviourally, ecologically) another entity – the extinct form. Proxy is preferred to facsimile, which implies creation of an exact copy. The guidelines do not consider the application of techniques to address the conservation of extant species, such as cloning of extant rare species or the introduction of genetic variation into extant species that are at risk of inbreeding.

“De-extinction” is therefore here used in a limited sense to apply to any attempt to create some proxy of an extinct species or subspecies (hereafter “species”) through any technique, including methods such as selective back breeding, somatic cell nuclear transfer (cloning)2 , and genome engineering (see Section V). Where possible the term “proxy” will be used to avoid the connotations of “de-extinction”.

Note again that they say a “proxy” is this:

For the purposes of these guidelines the legitimate objective for the creation of a proxy of an extinct species is the production of a functional equivalent able to restore ecological functions or processes that might have been lost as a result of the extinction of the original species. Proxy is used here to mean a substitute that would represent in some sense (e.g. phenotypically, behaviourally, ecologically) another entity – the extinct form.

And they add that de-extinction is the attempt to create such a “proxy”, a word they prefer to “de-extincted.” But is the dire wolf a functional equivalent of the original dire wolf, “able to restore ecological functions or processes that might have been lost” through extinction?  Who knows? Even under the IUCN guidelines, Colossal hasn’t performed an act of de-extinction.

Here’s a defensive four-minute statement from Beth Shapiro, who I’m pretty sure had a hand in the press release above, as there are a lot of similarities (for example, the concentration on species concepts and the IUCN).

Colossal should really cool its jets on the “de-extinction” front. They are not helping themselves by being defensive and pretending that they did something that they didn’t. And their emphasis that their real goal was always to “restore ecological function and enhancing biodiversity” is not convincing given the history of what the company and its founders said.  Bringing back the dire wolf, the woolly mammoth, the dodo and the thylacine—such acts won’t do much to restore ecological function. And since the edited animals won’t be released, any “enhancing biodiversity” will be done by putting new forms of animals in zoos or reserves, which don’t constitute “nature.”

I think I see a d*g tail wagging behind Shapiro’s chair in the video.

Do “asexual” bacteria form biological species?

February 25, 2024 • 9:30 am

The Biological Species Concept, or “BSC,” was devised and refined by evolutionist Ernst Mayr in the 1930s and 1940s as a way to conceptualize the distinct groups—”species”—that we see in most plants and animals. It runs as follows (in my words), which also includes how we conceptualize different biological species.

A biological species consists of a group of populations that, where they coexist in nature, exchange genes through reproduction. Two populations that coexist in one area but do not exchange genes are considered members of different biological species. 

One of the advantages of the BSC is that it enables us to immediately solve the species problem that eluded Darwin: why is nature divided up into distinct clusters rather than existing as a continuum, clusters most visible where they coexist?  Under the BSC, the problem of the “origin of species” simply becomes the problem of “the origin of those barriers that prevent interbreeding”—and that is a tractable problem.  Again, see Coyne and Orr for our best take on how these clusters form.

Of course there are problems with this concept (it’s not an a priori definition, but an attempt to conceptualize in words what we see in nature). These problems include judging populations that live in different areas like islands of an archipelago, how we deal with groups that hybridize just a little where they coexist, and, most important for this article, what we do with species that are asexual, lacking the possibility of exchanging genes. We discuss all these issues in the first chapter of my book Speciation (2009) written with Allen Orr, but one issue we didn’t resolve properly was that of asexual organisms.

So what about those pesky “asexual” organisms? How can we conceptualize species in groups like bacteria? Well, the first thing we need to determine is whether they form distinguishable clusters like birds or turtles. If they don’t, then there’s no need to conceptualize nonexistent clumps. In our 2009 book, we reviewed the literature, which was scant at that time, and decided that the evidence was mixed about whether bacteria (considered asexual) formed species, but there are surely some clumps among them. So we restricted the rest of the book to sexually-reproducing organisms. Still, bacterial “species” are given names, like E. coli, but do all bacteria considered E. coli really comprise members of a distinct cluster? If so, how?

The literature has expanded since then, and the paper below, which I’d missed and which is now seven years old, makes a pretty good case that in bacteria, at least, there are species, and, more important, they are conceptualized in a way similar to that of the BSC. In other words, there are bacterial clusters, and each cluster is characterized by its ability to exchange genes among individuals. Members of different clusters, however, don’t exchange genes. In other words, bacteria do consist largely of genetically isolated clusters. The authors, though examining only bacteria (there are other asexually reproducing organisms, like bdelloid rotifers), conclude that life in general conforms to the BSC. That’s a bit too expansive a conclusion (see the title!), but their results for bacteria seem good.

Click to read, or see the pdf here.

The key to this paper is recognizing that bacteria are not in fact completely asexual, though they often reproduce that way. But they also have a form of sex in which genomes of two different individuals can sidle up to each other and recombine to produce new genes. This process, called homologous recombination, occurs via cell-to-cell contact or transfer of DNA through tubes (“pili”) connecting different individuals. This process is called conjugation.

Here’s a photo from Wikipedia showing two bacterial cells moving DNA through pili:

This file is licensed under the Creative Commons Attribution-Share Alike 4.0 International license.

This movement is one-way: the DNA (a single chromosome with double-stranded DNA) from one individual moves to the other. After that, there can occur a form of “sexual” reproduction in which different copies of the same gene can line up and recombine, producing a new gene. A similar process happens during meiosis (gamete formation) in sexually-reproducing organisms.

In bacteria this mixing-up between similar genes is called homologous recombination because it changes the composition of a gene by recombining its DNA with the DNA from a similar gene in another bacterium.  There are other forms of DNA exchange in bacteria in which a bit of DNA or a “plasmid” from one individual simply inserts itself somewhere else in the genome of another individual, but this is not recombination in the traditional sense, for it doesn’t involve two different copies of the same gene recombining to form a new gene.  The paper by Bobay and Ochman deals with homologous recombination,

Their method of determining whether two individuals in a named bacterial species can recombine their DNA in this way is complicated, and I’d best leave it for the experts here. But I will say that it involves showing that individuals in a group share the same variants in a given gene segment (10,000 bases were sequenced) as do other individuals in a group. For example, in one ten-base stretch of DNA, an individual may have  GTTACTCTAA, another would have GTTAGTCTAA, and another GTTACTCTAC, and still another GTTACTAC, representing combinations of DNA bases that could occur by recombination.

If you see this pattern among individuals of a named bacterial species, that’s indicative that homologous recombination—bacterial “sex”—is going on. This form of recombination is called “homoplasic” recombination because the variants all come via mutation from a single original genome present in the individual that founded the species.

One alternative is that we are dealing with two related species in which similar DNA sequences only look as if they’ve undergone homologous recombination because two groups shared a common ancestor and then the descendants had similar (“convergent”) mutations. This, called  “nonhomoplasic recombination”, is not caused by genetic exchange.

The authors have ways to distinguish these two types of recombination, and devise a ratio they call “h/m”, showing the ratio of the degree of homoplasic recombination (true sex) from nonhomoplasic recombination (independent mutations in different groups that superficially mimic sex).  The higher the h/m ratio, the more sex individuals in that group are having.

The authors calculated h/m ratios for 91 named bacterial “species”, using, of course, a large number of genomes sequences for each species, because one needs to survey the variation among individuals in that 10,000-base segment. (They also did simulations to verify that they could tell “h” from “m”.)  It turns out that over half of the 91 named bacterial species they examined conformed to biological species in which there was evidence of “h” recombination among individuals. Here’s one below, in which the h/m ratio increases. reaching an asymptote, as they looked at more strains. (This increases your power of detecting shared variants). 54 of the 91 named bacterial species looked like this, so the BSC holds for at least half of named bacterial species, and the authors sampled widely in bacteria.

A biological species in bacteria:

Here’s what was thought to be one species but, when they added more strains, they saw two clusters, one that behaved as like the one above, but the other, relative to the other group, showed very low h/m ratios, indicating that the two groups didn’t have homologous recombination between them. That is, they were different “biological species”. When they took out the low h/m group, B. pseudomallei behaved nicely. Here, then, we have two species that were given the same name, perhaps because they had similar morphologies or culturing requirements, or because the genetic distance between them (indicating the time of separation) was pretty low, suggesting a recent origin. These “cryptic species” were seen in 21 of the 91 named bacterial species.

Two biological species in bacteria that went under one name:

And the third group by itself had low h/m ratios no matter how many strains they included, so that there was no ability to assess gene flow at all—perhaps because these species simply don’t undergo any homologous recombination. Here’s one:

Thus 73/91 groups tested showed patterns consistent with a reproductive-isolation based species concept.

To test that their method did indeed detect groups analogous to biological species in more familiar animals, the authors did the same kind of h/m test for two pairs of related but clearly distinct biological species; one was the related species Drosophila melanogaster and D. simulans, and the other Homo sapiens and the chimp Pan troglodytes. As you see below, they were able to detect reproductive isolation between the group using a similar 10,000 base-pair fragment. (In all cases they looked at many replicates of the species on the left and a single sequence for the species on the right, which is why the “other” species forms a straight line: we have one sequence compared to many sequences in the other species, and all comparisons show a low h/m ratio.)

 

Humans vs. chimps, also good biological species:

The conclusion, then, is that the BSC is pretty good in conceptualizing species in bacteria: there are groups that exchange gene segments, and other groups (different “species”) that do not exchange DNA via homologous recombination. Remember: all of this was judged from looking at DNA sequences, not seeing gene exchange directly.

The big conclusion (from the paper):

That species can be universally defined based on gene flow implies that many of the same factors are operating in the process of speciation across all lifeforms. Differences in genomic properties (such as ploidy, recombination frequencies, and reproduction, and rates of gene acquisition) and demographic parameters (such as population sizes, geographic distribution, and rates of migration) will impact the pace at which microbes speciate relative to sexual organisms. However, the application of a single genomic-based BSC criterion to delineate species makes it possible to define species and study speciation under a similar framework across the tree of life.

Well, they need to look at other putatively asexual groups to see if this method also shows the existence of interbreeding groups reproductively isolated from other such groups, but at least for bacteria we see that many of them form clusters.  Two questions remain:

1.) What is “speciation” in bacteria, then?  One of the paper’s most intriguing results is that if you take pairs of bacterial “species”, the degree of reproductive isolation between them isn’t positively correlated with the time separating them, as judged by the “genetic distance”, or whole-genome divergence, between them. This is hard to understand because it implies that, unlike sexually reproducing organisms like fruit flies and mammals, reproductive barriers don’t form as a simple byproduct of the time of divergence from their common ancestor. This is the case because in those groups reproductive barriers are usually byproduct of divergence between populations by natural selection and genetic drift, which drive species apart genetically as time passes.

Why isn’t this the case in bacteria? I have no idea! My only suggestion is that “species formation” might be so quick in bacteria that you simply don’t get a correlation of time with reproductive isolation. That would imply that it’s virtually instantaneous.

2.) Why do bacteria form clusters?  In more familiar animals, clusters arise because after reproductive barriers arise, an interbreeding group is free to adapt to its environment without “pollution” from other species that would efface the clusters. The genetic divergence is reflected in not just reproductive isolation, but in the way organisms look or behave.  This may also be true in bacteria: each cluster might represent a group adapted to a particular ecological niche.  This would be hard to test for naturally-occurring bacteria, but might be tested in pathogenic bacteria, whose habitat (us) is more easily studied. As I recall, each bacterial species does its own thing in its own way, but that’s not really an answer to the question.

A final note: this paper was difficult, and I may have made some errors in summarizing its results. (I could read it only twice before I had to write about it here.) Perhaps the authors will read my summary and correct any mistakes.

_______________

Reference: Bobay LM, Ochman H. Biological species are universal across Life’s domains. Genome Biol Evol. 2017 Feb 10;9(3):491–501. doi: 10.1093/gbe/evx026.

Carl Zimmer on species and conservation

February 20, 2024 • 11:15 am

By Jerry Coyne and Greg Mayer

Yesterday Carl Zimmer wrote a piece for the NYT on species concepts and conservation. Both Greg and I, who discussed the piece and are coauthoring our take on it, found that while Zimmer does not take a position on species concepts (which is good thing), it does have a theme.  And the theme seems to be this: that conserving biological diversity depends critically on what biologists decide a “species” is.  Now this argument is not, in our view, correct, because you can conserve biological diversity regardless of your species concept, even though some biologists seem to feel that we must be conserving species.  If you take that latter point of view, which we see as misguided, then you’re screwed, as there are, as Zimmer notes, dozens of species concepts, and each will lead you to a different decision about populations of an animal or plant. Is a population of owls long isolated on an island a different species from its relatives? That is largely a subjective judgment.

As we mentioned above, Zimmer does not sign on to any particular species concept, which is okay, as different concepts are useful for different purposes.  But he often neglects to tell us when a judgment about whether a population is a different species (and presumably worth conserving) is pretty much subjective, which is often the case for populations that are geographically isolated from one another. That is, he implies that once we hit on a species concept, problems of subjectivity largely disappear, which isn’t the case.  We would recommend that readers take in chapter 7 of Why Evolution is True, which Jerry immodestly thinks is the best existing popular discussion of speciation, but since few are going to do that, we’ll briefly reiterate what we, as evolutionists, use as a species concept.

Click to read:

 

As Jerry emphasizes in WEIT, the species concept one uses depends on what question one is asking. To evolutionists, the main question about the diversity of nature is this: “Why is it lumpy?”  That is, why do animals and plants appear not as a continuum, but in pretty discrete groups.  Look at the birds out your window and see if you have any problem telling which is which. And so it is with most animals and plants—so long as they live in the same place, i.e., are “sympatric”. (For populations that are not sympatric, but live in different areas—i.e., “allopatric”—problems arise. and these are the problems that Zimmer describes in his piece.

At any rate, the explanation for the lumpiness in one area began to be solved when biologists adopted what we call the “biological species concept”, or BSC, devised by several biologists in the 1930s, notably Ernst Mayr. (Zimmer describes him as a “German ornithologist” but he really was a German-American evolutionist—the “Darwin of the 20th century”—who held forth on far more things than birds.) The BSC is basically this:

Two populations are members of different species if they live in the same area in nature but do not produce fertile hybrids in that area.

That is, they do not exchange genes because of what we call “reproductive isolating barriers” (RIBs) that prevent genetic interchange. These barriers keep populations distinct, and allow them to undergo evolutionary divergence without being held back by gene flow.  It is this feature—reproductive isolation—that leads to nature’s lumpiness, and it is the origin of these barriers that explains, to an evolutionist, the origin of species.

It turns out that these barriers usually form when populations evolve in different places. Then, when the evolutionary divergence has proceeded to the extent that there is reproductive isolation between the populations when they come back together in sympatry, we now have evolved two species from a single ancestor.  RIBs come in many forms: hybrid inviability, hybrid sterility (the mule), ecological isolation (related species prefer to live in different sub-areas of the environment, or are confined there, and thus do not meet), temporal isolation, so that populations mate at different times (common in marine organisms), and differences in mate preference, so members of each species prefer to mate with individuals of their own “kind,” forming substantial barriers to gene flow.

If we can understand how one ancestral species forms two populations that cannot exchange genes, then we’ve solved the problem of the origin of species—a problem that, despite the title of his great book, Darwin didn’t come close to resolving.   Now most evolutionists realize that the answer is the origin of RIBs. In fact, neither of us have ever found a scientific paper on how species form that doesn’t involve the origin of RIBs: a tacit but telling admission that the BSC is the answer to most questions about speciation.

The problems that Zimmer outlines largely involve animal populations that are geographically isolated from one another, so the BSC can’t really be applied: the populations don’t coexist. Some of them, like the giraffe populations, breed with each other like gangbusters in zoos, but that’s a very weak test of conspecificity, because some species that live in the same area without interbreeding have their RIBs broken down in captivity (this is true of many fruit flies and of species isolated by ecological preferences). One thing we can say is that if two populations in captivity produce hybrids, but that those hybrids are inviable or sterile, then, yes, they are members of different species. But breeding in captivity, something usually impossible to test, is at best a one-way test.

In 2016, Jerry wrote about the giraffes here: the populations, which look different, live in complete geographic isolation, but breed like crazy in zoos, producing viable and fertile offspring.  What do we call them? We don’t know, but we’d say that they’re subspecies rather than full species. It’s a judgment call. The non-BSC people have simply raised the rank of all the traditional giraffe subspecies to species. Nothing prevents people from wanting to conserve subspecies– we sure do! People tried desperately to conserve the two subspecies of white rhinos, well before it became fashionable to raise the subspecies to species.

The giraffes demonstrate the near impossibility of using a species concept when you want to conserve populations. Our own view would be to save all the populations, regardless of whether you call them species, subspecies, or simply different populations.
There are measures, other than breeding data, like genetic difference between populations, that can serve as a proxy for biological speciation. If we know that populations usually produce sterile hybrids when the difference in their DNA is greater than X%, then the “greater than X% criterion”, as used in European frogs by Christophe Dufresnes, is fine. Here’s what Zimmer says:

In recent years, Christophe Dufresnes, a herpetologist at Nanjing Forestry University in China, has used this concept to classify different species of frogs in Europe.

Some of the groups of frogs interbred a lot, whereas others had no hybrids at all. By analyzing their DNA, Dr. Dufresnes found that groups with a recent ancestor — that is, those that were more closely related — readily produced hybrids. He estimates that it takes about six million years of diverging evolution for two groups of frogs to become unable to interbreed — in other words, to become two distinct species.

“This is very cool,” Dr. Dufresnes said. “Now we know what the threshold is to deem them species or not.”’

Well, Dufresnes is still using a proxy for the BSC, but his concept of conspecificity: the “ready production of hybrids”, is a bit off. In fruit flies, species can readily produce fertile hybrids in vials in the lab yet they don’t do so in nature. Still, Dufresnes’ approach is better than just judging by genetic distance alone, or, worse, by the degree of morphological difference between isolated populations, which may be the worst way to make a species call.

Zimmer describes the intriguing finding that polar bears and brown bears have had several episodes of genetic exchange over the last 120,000 years even though they split from a common ancestor about half a million years ago.  What do we call them? Our view is that they are biological species that have had their ecological isolation (polar bears “prefer” to live in colder habitats) broken down several times by climate change. The fact that there is historical gene exchange doesn’t mean that reproductive barriers don’t exist, for speciation can be either fully or partly reversible if RIBs change—in this case by changes in ecological isolation caused by climate change.

But our point is that we don’t have to make a a strict call about whether brown bears and polar bears are different species before we can decide whether to protect them as separate entities, or only protect one of them. Conservation decisions shouldn’t rest heavily on a particular species definition; rather, we have to decide exactly what we want to conserve: nature’s lumps (biological species), geographically isolated populations of a single species, like the giraffes, or even just populations of a single species that differ by one or a few traits, like color. As Zimmer quotes:

“They [the two bears] clearly demand separate strategies for conservation management,” Dr. Shapiro said. “It makes sense to me to consider them distinct species.”

But separate management strategies do not demand that they be considered distinct species– US law allows protection of subspecies and “distinct population segments” of vertebrates. From the ESA: “(16) The term “species” includes any subspecies of fish or wildlife or plants, and any distinct population segment of any species of vertebrate fish or wildlife which interbreeds when mature.”  In other words, conservation strategies don’t depend on fixing on a hard definition of “species.”

Zimmer writes this on barn owls:

Even a common species like the barn owl — found on every continent except Antarctica, as well as remote islands — is a source of disagreement.

The conservation group BirdLife International recognizes barn owls as a species, Tyto alba, that lives across the world. But another influential inventory, called the Clements Checklist of Birds of the World, carves off the barn owls that live on an Indian Ocean island chain as their own species, Tyto deroepstorffi. Yet another recognizes the barn owls in Australia and New Guinea as Tyto delicatula. And a fourth splits Tyto alba into four species, each covering its own broad swath of the planet.

This is no big deal: it’s just the standard difficulty of ranking allopatric populations.  We can just call all the populations members of a “superspecies” and then try to keep all the populations from going extinct. This strategy will of course conserve both genetic diversity and the presence of endemic wildlife.

Zimmer mentions a botanist who is using a “triage” method:

Thomas Wells, a botanist at the University of Oxford, is concerned that debates about the nature of species are slowing down the work of discovering new ones. Taxonomy is traditionally a slow process, especially for plants. It can take decades for a new species of plant to be formally named in a scientific publication after it is first discovered. That sluggish pace is unacceptable, he said, when three out of four undescribed species of plants are already threatened with extinction.

Dr. Wells and his colleagues are developing a new method to speed up the process. They are taking photographs of plants both in the wild and in museum collections and using computer programs to spot samples that seem to cluster together because they have similar shapes. They’re also rapidly sequencing DNA from the samples to see if they cluster together genetically.

If they get clear clusters from approaches such as these, they call the plants a new species. The method — which Dr. Wells calls a “rough and ready” triage in our age of extinctions — may make it possible for his team to describe more than 100 new species of plants each year.

A triage approach is fine– there are many approaches to trying to document and preserve biodiversity quickly. But the clear implication that debates about species concepts delay publication is just wrong. The delays discussed by Wells are all about collecting decent samples of specimens, which takes time!  We have both written about the importance of museum collections, including continued collecting, for understanding and conserving biodiversity. So, we are all for accelerating collection and description of biological diversity — before it’s gone, and to try to prevent its loss.

We’ll come to an end now, but we find Zimmer’s discussion somewhat incomplete, and for the reasons we mentioned at the beginning. First, conservation need not depend on what biologists call a “species”. Second, for populations that are geographically isolated, any decision on species status will usually be arbitrary, and so we can leave aside applying fixed species concepts and instead decide what it is, exactly, that we want to conserve. We might want to save as much genetic variation as we can, or perhaps conserve morphological traits (based of course on genetic variation) that affect how a species looks or lives (e.g. coat color in mice), or even evolutionary history as reflected in genetic distance. But none of this relies particularly heavily on adhering to a particular species concept.

More calls for not naming species after people

March 14, 2023 • 9:30 am

I am so weary of people trying to change both the common and Latin names of species because doing so will magically render biology more inclusive. But I have yet to find a single person who left the field, or refused to enter it, because species were named after people, odious or otherwise.

In the case at hand, apparently all white people and men are odious, for the Nature Ecology & Evolution paper below, as well as a summary from Oxford University (click screenshot), are calling for the end of the practice of naming species after people, and mention whiteness and maleness several times—not as desirable traits! (Usually eponyms are meant as honorifics, taken from a famous biologist or a donor to research.)

For animals, you can change the common names of species if they’re found offensive (e.g., “gypsy moth” or “Bachman’s warbler”, which have been deemed offensive), but what you cannot do is change the Latin binomial of animals (e.g., Vermivora bachmanii has to stay), for doing so would play hob with the literature and with international scientific communication. (The botanical body for nomeclature has yet to weigh in on this issue.)

Clicking below, you’ll find the fourth or fifth article I’ve read that says exactly the same thing. I’m not going to critique these pieces in detail as I’ve done so previously. I’ll just excerpt some of the reasons why the authors think that animals shouldn’t be named after people, and add a few brief remarks. Click the screenshots read, though the first one is paywalled. (Judicious inquiry may yield a pdf.)

From the article:

Eponyms typically reflect benefactors, dignitaries, officials, the author’s family members and colleagues, or well-known cultural figures (Fig. 1) — a practice that persists today. From a contemporary perspective this is potentially problematic, as many of those honoured are strongly associated with the social ills and negative legacy of imperialism, racism and slavery. Moreover, 19th-century and early 20th-century taxonomy was largely dominated by white men who, by and large, honoured other men (funders, colleagues, collectors and so on) of their own nationality, ethnicity, race and social status. For example, a recent study has documented that over 60% of the eponyms given to the flora of New Caledonia have honoured French citizens and that 94% of the eponyms were named after a man.

. . . Attributing eponyms to species extends beyond the act of naming; it attaches the societal value system to which these individuals belong. It stakes a claim as to which knowledge system provides legitimacy to the existence of the species, while simultaneously diminishing the value and knowledge of the species within the context of those who may have interacted with it the most.

Any call for exceptional changes in how we name nature requires an exceptional rationale. In this respect, it is important to highlight that taxonomy provides the backbone for the study and conservation of biodiversity. There is already a common perception in many post-colonial nations that ecology and biodiversity conservation are Western constructs that are shaped by and for Europeans and that privilege Western perspectives over others. This perception is undoubtedly reinforced in many countries of the Global South by the existence of numerous species — some of which may be endemic or have local cultural value — that are named in honour of colonizers or people of colonial descent. In Africa alone, 1,565 species of birds, reptiles, amphibians and mammals (which represent a quarter of vertebrate endemics) are eponyms. Researchers from former colonies might feel justifiably uncomfortable, resentful or even angry at the constant reminders of imperial and/or political regimes that are reflected in the names of native and endemic species.

I will note here only three things. First, the fact that using eponyms would make people feel terribly uncomfortable (in a minority of case) is mere speculation by the entitled authors. I see this view as somewhat patronizing, as if Africans, for example, are too fragile to bear having beetles named after Cecil Rhodes. And really, how many people in any country would be offended by the common names of species, which of course differ from place to place? And NOBODY knows the Latin binomials: I doubt whether more than 2% of Americans, for example, could give the Latin binomial for more than one species (Homo sapiens, if they even know that one).

Second, changing the common names of species would involve having to go back through the literature and somehow add the new name, or publish a big list that people need to consult for translation. Renaming the Latin binomial, which is what scientists use when referring to a species, is prohibited by the International Commission for Zoological Nomenclature, and for good reason. So all you can do is get rid of the thousands and thousands of animal common names derived from humans.

At least you don’t have to determine whether a human was good or bad; you just efface the name, regardless of their sex, race, or accomplishments.

It’s likely that botanists will follow zoologists in prohibiting changes of Latin binomials, and for the same reason: to avoid messing up the literature and scientific communication.

Finally, if people want to eliminate all common eponyms, fine: let them go about doing it, but making sure that each animal (or plant) gets a name appropriate to its nature (appearance, location, etc.). In the end, though, wouldn’t that time (which would be considerable) be better spent actually doing something substantive to make science more inclusive?

Here’s the Oxford University p.r. piece on the above, which is free. Click to read:

An excerpt:

However, the reality is that the use of eponyms in the naming of species poses a wider, more problematic nature. Traditionally, eponyms typically reflect benefactors, academics  and officials affiliated with the individual who discovered a species – which is a practice that continues today. With science of the 19th and 20th century largely dominated by white men from colonising European nations, this meant many of those honoured are strongly associated with the negative legacy of imperialism, racism and slavery.

Another striking example of the dangers of overtly politicizing biological names is Anophthalmus hitleri, a cave beetle named after Adolf Hitler in 1933 that is currently threatened due to high demand from collectors of Nazi memorabilia. Due to codes around renaming species, whereby the first name given to a species is deemed its correct one known as the “Principle of Priority”, proposals to rename this species were rejected.

Now I’m not sure whether the author of this piece sees the extinction of the beetle as a good or bad thing, but I’ll show the beetle below.

TRIGGER WARNING: THE DEPICTION OF THIS BEETLE NAMED AFTER HITLER DOES NOT IMPLY ANY APPROBATION FOR ADOLF HITLER OR HIS GENOCIDAL POLICIES!!!! (And, after all, the Oxford piece showed it, so blame it on them.)

(From Oxford): Ophthalmus hitleri, a cave beetle named after Adolf Hitler that became a popular Nazi memorabilia collectors itemI have to say that although I’m a Jew and should be very very upset by seeing this beetle, it doesn’t bother me in the least. Some misguided people who admired der Führer named an insect after him, that’s all. The Oxford piece continues:

In a recent commentary published in Nature Ecology & Evolution researchers from various global Universities assessed the scientific names of all African vertebrates currently listed on the IUCN Red List. This revealed that 1,565 species of bird, reptiles, amphibians and mammals – around 24% of their sample – were eponyms, notably of white, male Europeans from the 19th and 20th centuries.

The authors argue that it is time to rethink the use of eponyms, and emphasise that whilst there currently isn’t a standard for changing species names, with technical and administrative barriers to doing so, renaming eponyms to better connect with local geography and culture could provide wonderful opportunities to highlight the importance of biodiversity conservation and to reinforce the deep links between nature and local societies.

Here are three photos and captions showing species that will have to be renamed; the captions presumably give some indication why. Note that what has to be changed is the Linnean binomial, which cannot be changed.

You can have your own say below; I’m too tired of performative ideology to repeat what I’ve said before.

h/t: Martim