Category: speciation

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.

Revisiting an old paper

July 20, 2023 • 11:15 am

I was just reminded that in 2020 Hari Sridhar interviewed me about what is perhaps my most cited paper (1561 times to date, though my book Speciation with Allen Orr was cited almost six times as often), and certainly one of the few good ideas I’ve had in my life (the paper was also co-written with Orr). You can see the paper by clicking below, and there was a followup paper in 1997 with the word “revisited” tacked on the title below; that was written since new genetic-distance data had appeared.

Here’s the good idea as it came out in the interview:

HS: You were interested in Drosophila and the genetics of Drosophila right from the time of your PhD. What was the motivation for this particular piece of work?

Jerry Coyne: Well, the motivation is implicit in the paper. I was interested in the genetic basis of reproductive isolation in Drosophila. I realized that there were a lot of data out there on the genetic distances between different closely-related species of flies as measured by electrophoresis, and from reading a lot of the old literature – Patterson & Stone (1949, Univ. Texas Publ. 4920: 7-17), and The Genetics and Biology of Drosophila book series ‑that there is an immense amount of data on the crossability of flies, their sexual isolation, the sterility and viability of hybrids. And it came to me one day in Maryland – I can still remember this – that you could combine that different data using electrophoresis as the estimate of divergence time, and then the other parameters as estimates of the degree of reproductive isolation. By doing that, you could get some kind of estimate of the time course over which reproductive isolation evolves. After that, it was just a matter of compiling that data. It took a long time because it’s all in different places – papers, books and stuff. Nobody had thought to put them together before. It was just a matter of compiling the electrophoretic data with the crossability data and then seeing what came out of that. That was the motivation.

one more Q&A:

HS: At the time when you did this work, did you anticipate, at all, the kind of impact it would have on the field? Do you have a sense of what it mostly gets cited for?

JC: Yeah, it gets cited for the reason that we wrote it, actually. Well, two things. First, It gives an idea of the time course of speciation. But also, the result showing that sympatric species get reproductively isolated much more quickly, in terms of pre-zygotic isolation, than allopatric species, was unanticipated. It supports the idea that there’s either reinforcement or reproductive character displacement. I just said, well, let’s look at these data. Then we went back to all the original papers and looked at the ranges to see whether the species lived in sympatry or not. That was a lot of work too because, a lot of the time, range data is not presented as ranges.You have to look at where the flies were captured and, sort of, get an idea of whether the ranges overlapped or not. Those two aspects of the paper were important. Remember, the paper is incomplete because it leaves out a number of forms of reproductive isolation that could be very important in nature, like post-mating pre-zygotic isolation, sperm competition, ecological isolation and temporal isolation. Those aren’t included, because there’s no data. But the support for reinforcement that we showed, the high degree of pre-mating isolation between sympatric species as opposed to allopatric pairs, stimulated, stimulated, I think, work on reinforcement. Even in my own laboratory, my student, Daniel Matute, worked on reinforcement, I think, partly because of the data from this original paper. So it had a number of influences on the field. I don’t know how important it is. It’s a novel approach. It’s one that you can’t really us with most species because of the lack of crossability data. There have been a few other studies. Leonie Moyle did a similar study in tomatoes, I think, and Tamra Mendelson did a study on darters collecting information on genetic distance. The problem with darters and all other groups is that you just don’t have the ability to do laboratory crosses that you have in Drosophila. So Tammie was limited to about 12-13 species.

I’m sorry to say that I haven’t kept up diligently with other folks’ followup work, as there are more papers building on this one (e.g. here, here, and here). In general, I think, they’ve supported our main conclusions, especially the cool one that sexual isolation (mate discrimination) appears to evolve more quickly between groups that experience some period of “sympatry” (living in the same area) after speciation has begun. That in turn supports the idea of “reinforcement”: that if there is a reproductive penalty to hybridizing (e.g. producing hybrids that are sterile or weak), natural selection will build up mate discrimination so that the production of hybrids is less likely. (The idea is that you leave more of your genes to future generations when you produce healthy, conspecific hybrids, so any gene that favors mating with your own species will be favored.) And indeed, we found a strong pattern of heightened sexual isolation among species that are sympatric rather than allopatric (“geographically isolated”).

I liked the original idea of using genetic-distance data to figure out the time course of speciation (or rather, aspects of speciation: mate discrimination and hybrid sterility/inviability) because speciation is often very slow and reconstructing the process (and seeing if there are any generalizations to be made) can be done only by using proxies of divergence time, which in our case was the “genetic distance” calculated using gel electrophoresis. As I note in the interview, gel electrophoresis is pretty much dead, and DNA sequencing of fly species is the way to go.

A new book correctly criticizes the idea that some species are superior to others, but mistakenly claims that species aren’t real

January 29, 2023 • 10:10 am

The Berkeley News, the publicity site for the University of California at Berkeley, has a piece out announcing a new book that was published out in December (photo below). Since it was published by the venal and greedy Springer, the hardback of Speciesism in Biology and Culture will cost you only $159.

Click on the screenshot below to read about the book, which comprises nine essays rejecting humans’ view that we are the top and most important species, and that species can be ranked by their “superiority”. With that rejection I wholeheartedly agree. But there’s another theme, too: one which I think is misguided: species aren’t even real. Click below to read the article, which has a summary of the book.

Here are the book’s two themes:

In a new book, a group of scientists and philosophers places part of the blame on an attitude prevalent among scientists and the general public — the false belief that species are uniquely real, and that some species are superior to others.

To the researchers, this is analogous to racism — the fallacious belief that races exist as branches on the tree of life, and that some races are superior to others.

Now I agree that there is no hierarchy of species: we just happen to be the one that evolved a big brain with which we can control all other species, and an organ we can use to pat ourselves on the back as better than others. (A flea doesn’t have the capacity to see itself as superior to other species—but it can suck their blood!).

But the view that species are not “uniquely real” is a gross distortion. Species are far more real and discernible than human “races”, whose demarcation is somewhat subjective although even the “classic” races are not totally invented social constructs (they contain biological information).

If species weren’t real, however, there would be no problem of “the origin of species”, and nature would be a spectrum—a rainbow with no joints between its constituents. Orangutans, gorillas, and humans would all be arbitrary entities: “social constructs”. So would pigeons, starlings, robins, and cardinals. But I’m getting ahead of myself. A few more excerpts about the supposed non-reality of species:

Mishler has argued for decades against considering individual species as the most important grouping, particularly when discussing conservation. [JAC: actually, in the U.S. it is subspecies that are the units that must be conserved.] He laid out his arguments in a 2021 book, What, If Anything, Are Species? ( CRC Press), in which he proposed getting rid of taxonomic rankings altogether, including the binomial system for naming species that is used universally today. [JAC: As you know, this idea hasn’t caught on, nor will it.]

One key reason is that species distinctions are not equivalent across all branches on the tree of life. Bacteria that look identical may vary as much genetically as a dog from a cat, while some birds that live in totally different areas and look different can be nearly identical genetically. On the other hand, lineages — the sequence of organisms that have evolved from one another over millions of years — are consistent across all forms of life.

“Evidence shows that a species of amoeba does not mean the same thing as a species of fungus, animal or anything,” Swartz said. “And if species are not uniquely real, then where does that leave us? Is there anything that means the same thing across the tree of life? The answer to that question is: lineages. These are branches on the tree of life that maintain genealogical connections across time and space. They include children, or descendants, and their parents, or ancestors, on through animals broadly and their distant relatives. Lineages are branches across the tree of life.”

Throwing out the concept of species would eliminate the artificial dividing line that helps justify the belief that some species are more important. Instead, the authors maintain that humans are just one part of a genealogy connecting all living things. This interconnectedness forms an ecological web that sustains the planet and us, and that deserves to be protected equally with humans.

Mishler goes one step further, arguing that lineages should be respected — not for how they can benefit humans, but intrinsically, as part of the web of life. He detests the term “ecosystem services,” which implies that the natural world exists to service humanity.

. . .The authors point out that the standard definition of a species is a population that cannot breed with closely related populations. But Mishler said this definition is muddied by the fact that there is often wide variation within a breeding population; sometimes two separate species can and do successfully interbreed, and some species don’t breed at all.

. . .“Alan Templeton summarized it most succinctly: The trouble with species is too little sex and too much sex,” he said. “There are asexual groups that don’t do sex at all, but still have lineages. And then there are plants, like the orchid, which can just about be crossed with every other orchid, yet they’re bizarrely different from each other. So, reproductive compatibility, while a nice idea, just doesn’t work empirically.”

Species also can evolve because they get separated geographically or ecologically, not because of an inability to breed.

A more natural grouping is by lineage — ancestor-descendant pairs connected across time — or by clade, which consists of all the descendants of a creature.

Mishler and his colleagues have argued for years that species aren’t real, but their views haven’t gained any traction in the biological community beyond those few people who already reject the reality of species. Perhaps that explains this book.

The biological species concept (BSC), used by nearly all evolutionists, including me, is based on reproduction: a species consists of a group of populations whose members can exchange genes with each other, but cannot exchange genes with members of different species—where the different species live in the same area in nature—because there are barriers that impede genetic exchange between different species.

Now the entire first chapter of our book Speciation, by Coyne and Orr, is a defense of the BSC, a discussion of its problems (no, it’s not perfect), and an argument that it’s superior to all other species concepts because it gives us a handle on why organisms in nature don’t form a spectrum (see the Appendix for a discussion of alternative species concepts, including “lineage concepts” mentioned by Mishler).

First, the question of whether species are “real” is the same as the question “is nature a continuum or lumpy?”. That is, when we look at organisms like mammals or birds or trees in one place, do we see a continuum of variation that we can partition only subjectively, or are there discrete entities that are recognized widely as distinct? And for nearly all groups of sexually reproducing organisms, nature is lumpy. You already know this if you try to identify birds or mammals or other sexually reproducing organisms in the wild. We don’t have a spectrum of birds but, in one area, you see a series of discrete types that you can easily identify. Those groups (in one area; see below) are biological species: robins, starlings, pigeons, etc. etc., and are formally recognized with Latin binomials.  They are real, and you or Joe or Jill can easily slot what you see into a small number of bird groups—species. The lumpiness of nature in one area is, in fact, THE “species problem”, the problem that, despite the title of his book, Darwin didn’t answer. (He didn’t answer it because he had no knowledge of genetics and therefore no concept of reproductive barriers.) We need to explain why, in one area, we see a number of discrete forms and no intermediates (or only a few, which could be hybrids that are often sterile.)

The answer to the species question is that reproductive barriers, which are many (we have a chapter on each type in Speciation), keep species distinct by preventing any blurring that would occur with gene flow. Though hybridization between species in one area is more common than we used to think, in most groups it is rare, and if the hybrids are sterile or inviable, then they pose no problem for “blurring” species boundaries.

Now some caveats, for the BSC isn’t perfect:

a.) The BSC is meant to apply to sexually reproducing organisms because it’s based on genetic exchange between individuals or the lack thereof. In organisms like bacteria that are largely asexual, you can’t use it easily. Now whether those organisms form clumps as discrete as those seen in sexually-reproducing species isn’t clear: few people are interested in that topic, which I think is important. This issue is discussed at the end of the first chapter of Speciation.

b.) Two groups must usually live in the same place if you are to determine with certainty whether they are members of different species. If they do not form hybrids that are viable and fertile where they co-occur, they are different species. This is true, for example, of the lion and tiger, which used to co-occur in India before the lion was extirpated. They formed no hybrids in nature. (They sometimes do in zoos, but that’s because captivity can eliminate some reproductive barriers that occur in nature, like aversion to mating with other species. I call this the “prison effect”).

c.) If two similar species live in different places, it’s hard to tell if they’re different species or simply different populations of the same species. If you bring them together in the zoo or lab and they do not hybridize, or form sterile or inviable hybrids, then they are different biological species. But if they do form hybrids, even some fertile ones, the question is still unresolved, for, as I said, some true biological species hybridize in captivity but not in the wild. One can only guess in such circumstances. This kind of guessing is what biologists do when they designate very similar populations that live in different areas as “subspecies”. The “zoo or lab” tests are one-way: they can tell you that populations living in different areas are members of different species, but can’t tell you for sure that they’re members of the same species.

d.) Speciation is a process, usually occurring between geographically isolated populations of a single species. With no possibility of gene exchange, these populations begin to genetically diverge due to various processes like natural selection, sexual selection (a subset of natural selection), genetic drift, and so on. If that divergence occurs to the point that, when the different populations re-establish geographical contact, they do not exchange genes, then full speciation has occurred. But it need not occur: there are many time when populations aren’t isolated long enough to become reproductively isolated, and in that case they can re-establish contact and exchange genes. Those are not members of different species. (This re-establishment of contact is why human populations did not evolve into different species.)

Or, there could be some reproductive isolation but it’s not complete. In such cases we have to make a judgment, like calling them “incipient species” or “groups with incomplete reproductive isolation.” It turns out that there are evolutionary processes that, upon re-contact of incompletely isolated populations, can drive them, though natural selection, to evolve into different and full biological species. One such process is called “reinforcement”, and it’s been seen to work in both nature and the lab.

The upshot is that because the evolution of one species into two or more is a continuous process, there will be stages of the process in which there is some reproductive isolation but it’s not complete. (Geographically isolated populations will, if left long enough, nearly always become full species). That means that there will sometimes be problems establishing whether two populations are species or not. I like to say that spatially isolated populations become more and more “species-like” with time, and, when reproductive isolation is complete, finally attain the status of full biological species.

e.) The reality of species is also seen by common sense (the value of bird guides, for example), by the remarkable coincidence between indigenous people and outside scientists in recognizing the same groups existing in one location, and through using statistical methods to see if individuals fall into discrete phenotypic or genetic clusters. This is the very first topic we take up in our book, and provide ample evidence that clustering in one area is real, and that the same clusters are identified by both local residents and biologists from outside the area, establishing that the clustering is not simply the result of humans subjectively partitioning a continuuum of nature into discrete units.

If you think that species aren’t real, go outside for half an hour and look at birds. If you know your birds, do they form a continuum, or does each bird you see fall neatly into a group that has been recognized, described, and written up in bird guides? You already know the answer. Bird species are real, and that’s true in other groups of plants and animals.

I could go on, but if you can get hold of Speciation by Coyne and Orr, I’d suggest reading Chapter 1, which gives evidence for the reality of species. Since our book was taken over by Oxford University Press, it’s now as expensive as the one above, so try to get it from a library. Chapter 1 is, I think, accessible to the scientifically interested layperson. (The book, however, is written for professional evolutionists: grad students, advanced undergrads, or professional evolutionary biologists. I always tell my friends not to read it unless they’re willing to slog through the stuff meant for professional evolutionists.)

So yes, species are real in sexually-reproducing organisms, but there are intermediate cases because it’s a process that takes a lot of time—evolutionary time. Finding cases that are hard to decide does not negate the value of the BSC, for, in the end, it’s the genetic barriers between species that allow them to continue diverging from each other without “pollution” by genes from other populations. In other words, it is the evolution of reproductive barriers that produces the lumpiness of nature that we see in one area.

And that is the great value of the BSC: it explains why nature is lumpy, a question that wasn’t answered by evolutionists until around 1935 or so. It answers the species question, at least in sexually-reproducing organisms.  The concept of genetic barriers (reproductive isolation) gives a natural explanation for nature’s lumpiness, and thus the question of “the origin of species” in sexually reproducing groups boils down to the question of “the origin of genetic barriers. And that gives us something to work with at last! How do those barriers arise, and what is their nature? As I wrote in Speciation, I don’t know of a single study on the origin of species of plants or animals in nature that is not about the origin of genetic barriers and reproductive isolation. That’s how pervasive and useful the BSC has been!

As for the “lineage concept” of species, it’s deeply confused, and you can read the Appendix of my book to understand why. Just one point here: what lineages are we talking about? Lineages of genes are different from lineages of populations, and those differ from lineages of biological species. Species concepts based on using lineages of genes, for example, always wind up in a big muddle, and have not been used to answer the question of why nature is “lumpy.”  Insofar as lineages are constrained to remain separate, it’s because they’re reproductively isolated! But read the book to see more. Or look at any intro text on evolutionary biology, like this one.

In short, yes, I agree that no species is better than any other, or has any kind of natural hegemony over other species. That idea is crazy, though of course humans do kill and eat members of other species. But that doesn’t mean that we’re better than, say, cows—any more than lions are “better” than gazelles. So here I agree with the book’s authors.

But I think their view that species aren’t real is deeply misguided. It is, I think, an example of what I call “the reverse appeal to nature.” This is what I call the tendency to impose onto nature your own ideological or biological prejudices. The regular philosophical “appeal to nature” is the misguided idea that “what is natural is good”. (It’s similar but not identical to the “naturalistic fallacy,” which is “what we see in nature is what we ought to do.”)

The reverse appeal to nature simply stands that appeal on its head, saying “what we think is good must be what occurs in nature.” Another example of is using ideology to deny that there are two sexes in nature because you have an ideology that maintains that biological sex is a spectrum. You must thus claim that what exists in nature must be what your ideology tells you exists. This is why we see the pervasive ideological denialism of what is a palpable truth recognized by biologists. (And yes, there are only two sexes in humans and other animals.)

Perhaps the ideology behind the “species are not real” claim is that if you don’t think there should be a hierarchy of species, you can simply deny that species exist. But you don’t have to deny the existence of species to be kind to animals.

If you have questions about species or speciation, I’ll try to read the comments within a day and answer them. Or, best, consult this:

Readers’ wildlife lesson

October 14, 2022 • 8:15 am

Today we have another science-and-photo lesson from Athayde Tonhasca Júnior, whose captions are indented. I still have all the readers’ photos sent before, so don’t worry—yours will show up eventually. (I’m back in Chicago, but very fatigued.)

MISANDRIST BACTERIA

Athayde Tonhasca Júnior

J.K. Rowling and allies are battling hard against the Twitter mob, rabid activists and grovelling, dishonest academics to prevent women replaced with ‘birthing people’ or ‘individuals with a cervix’, and having their spaces encroached by penis-dangling non-birthing people. But at least female Homo sapiens don’t have bacteria as their enemies.

Bacteria are single-cell organisms found practically everywhere on the planet: your body alone harbours millions of them, mostly living quietly on your skin and inside your gut. But bacteria from the genus Wolbachia* have a specific niche: they spend their lives inside the cells of insects and other arthropods and are transmitted exclusively through the female germline—the cells that pass on their genetic material to the progeny.

*Insect-living Wolbachia comprise ten phylogenetic groups, and there’s no consensus as to whether they are lineages or species. So they are usually considered collectively: Wolbachia. The green dots show Wolbachia distribution in the tissues of some invertebrates © Pietri et al., 2016. MicrobiologyOpen 5: 923–936.

That’s a good strategy for those bacteria living inside a female host because they are transferred to her offspring via the eggs’ nutritious and protected cyto­plasm (the gooey solution that fills each cell). But bacteria in a male host are virtually doomed: they have little chance of being transmitted because sperm cells have almost no cytoplasm. For the Wolbachia‘s perspective, male hosts are a dangerous prospective. But these bacteria deal ruthlessly and efficiently with the problem: they make males irrelevant, or just get rid of them.

Wolbachia bacteria (bright spots) inside an egg of the parasitic wasp Trichogramma kaykai © Merijn Salverda & Richard Stouthamer, Microbe Wiki.

For some flies, beetles, wasps, moths, mites and isopods (woodlice relatives), Wolbachia-infected males mating with uninfected females are incapable of reproducing because the bacteria interferes with the paternal chromosomes, resulting in embryonic death. Mating with females carrying the same Wolbachia strain is not affected. The consequence is that Wolbachia-free females have lower chances of reproduction, while infected females can spread the bacteria through the population. This process, known as cytoplasmic incompatibility, is the most common effect of Wolbachia.

But there’s more. For some butterflies, true bugs (Hemiptera) and isopods, the bacteria turn genetic males into infertile or functional females by inhibiting the production of hormones that trigger the development of male sexual characteristics, a process known as feminisation. Interestingly, feminisation can be ‘cured’ by antibiotics that kill Wolbachia (e.g., Narita et al., 2007. Applied and Environmental Microbiology 73: 4332–4341).

Wolbachia’s cunning has no end: they take advantage of the reproductive system of Hymenoptera (bees, wasps and ants), where fertilized eggs contain two pairs of chromosomes and develop into females, whereas non-fertilized eggs contain one copy of each chromosome and develop into males. In some parasitic wasps, the number of chromosomes doubles in infected male egg cells. So voila, those eggs develop into females that reproduce asexually, giving origin to a new generation of infected female clones that can pass on the bacteria. And just like feminisation, asexuality can be ‘cured’ by treating wasps with antibiotics or heat, which kills the bacteria. In the laboratory, antibiotic ministrations over several generations induces wasp populations to revert to a sexually reproductive mode (e.g., Stouthamer et al., 1990. Proceedings of the National Academy of Sciences 87: 2424-2427).

A tiny Trichogramma dendroliti wasp laying eggs inside a moth egg. Some species in the genus are entirely female © Victor Fursov, Wikimedia Commons.

Last but not least, Wolbachia may resort to outright homicide: infected males of some beetles and butterflies are killed during embryonic or larval stages, resulting in populations heavily skewed towards females.

The mechanisms used by Wolbachia to manipulate their hosts remain largely unknown and speculative, even though this is a hot research topic. By whatever device, Wolbachia take control of their hosts’ reproduction for their own benefit, so they spread quickly throughout the population wherever they are introduced. [JAC: This manipulation of hosts is can be seen as an “extended phenotype” of the bacteria.]

That male-hating feeling: populations of the two-spot ladybird (Adalia bipunctata) and the Asian corn borer (Ostrinia furnacalis) are overwhelmingly females because most males are killed and feminised, respectively, by Wolbachia © Entomart (L) and Kembangraps, Wikimedia Commons.

You may think that such male-bashing shenanigans are oddities; but you would be wrong. It is estimated that 40 to 60% of all arthropod species are infected by Wolbachia. These are remarkable numbers, considering that these bacteria were unknown until 1924 when Wolbachia pipientis was first identified. And they are only one of the many microorganisms causing sexual aberrations in insects.

These facts and figures sound alarming; could Wolbachia be a risk to invertebrates? Highly distorted sex ratios could threaten populations or even whole species. But data from a variety of studies suggest that these bacteria are symbionts, that is, they have established a close and sustained relationship with their hosts. And as improbable as it sounds, these female chauvinistic bacteria can be good: there are instances of increased fertility, fitness and resistance against certain viruses in Wolbachia-infected hosts. Wolbachia may even be a factor in insect speciation (when populations evolve to become distinct species). If two populations become infected with different types of Wolbachia, males from either population may be unable to fertilize females from the other; with time, these two populations split into different species (Campbell et al., 1994. Insect Molecular Biology 2: 225-237).

The effects of these bacteria on their hosts have been used for our benefit. Viruses like dengue, Zika, chikungunya and yellow fever have hard times multiplying inside Aedes aegypti mosquitoes infected with Wolbachia. So researchers and mosquito control organisations are breeding Wolbachia-carrying mosquitoes and releasing them into areas of mosquito-borne diseases. Tests with modified mosquitoes have shown significant reductions of dengue incidence in Singapore, Brazil, and Indonesia. The potential for the management or control of other pests is enormous.

When infected male Aedes aegypti mosquitoes mate with wild females that are Wolbachia-free; their eggs will not hatch © Singapore National Environment Agency.

Considering the prevalence of Wolbachia, one would not expect pollinators to go unscathed. Indeed, honey bees, bumble bees, several solitary bees, wasps and hoverflies harbour the bacteria. Data for these groups are still scarce, but 66% of Germany’s native bees may be infected (Gerth et al., 2011. Systematics and Biodiversity 9: 319-327). We have the vaguest understanding about the implications of Wolbachia infections for pollinators, but we can assume they are susceptible to the same effects found in other invertebrates, i.e., cytoplasmic incompatibility, feminization, induced parthenogenesis and male killing. So many characteristics of our pollinating species such as sex ratios, biology, ecology, behaviour, distribution and phylogeny (their evolutionary history) could have been shaped or at least influenced by some bacteria whose workings we are just beginning to understand. Wolbachia is a good example of the vast area of known unknowns in the field of natural sciences.

A female Nasonia parasitic wasp. © M.E. Clark, Wikimedia Commons. The American species N. giraulti and N. longicornis infected with Wolbachia cannot breed with each other, but when both species were treated with antibiotics, interspecies mating produced hybrid offspring. This result suggests incipient speciation: reproductive isolation is already apparent, while genetic barriers have not yet been formed (Bordenstein et al., 2011. Nature 409: 707-710)

Revisiting an old paper, but a good one

October 13, 2020 • 9:30 am

I have to brag a bit in the title because if you say a paper is an “oldie,” you have to also say “it’s a goodie”. But I think this one is—it’s the first of two papers I wrote with my then-grad-student Allen Orr on the time course of speciation in Drosophila.  And it’s one of the few good ideas I’ve ever had. I don’t know how often it’s been cited—I don’t look up stuff like that—but it has been influential in inspiring others to do related work. I’m writing about this paper because I recently revisited it in an interview (see below).

Here’s a very brief summary of what we did. I realized one day, when I was at the University of Maryland, that there existed a tremendous amount of data about the sexual isolation and hybrid sterility/inviability of various Drosophila (fruit fly) species tested in the lab. There also existed, separately, a large amount of data on the “genetic distance” between these species as judged from gel electrophoresis. This genetic difference is a rough measure of the times since the species diverged. The more similar the electrophoretic profiles, the younger the species. (The actual real-time calibration of the distance is hard, as Drosophila has no fossil record, but we did our best.)

You could, I realized, take various pairs of species, see how much reproductive isolation they had between them—how much mating discrimination and whether the hybrids were viable and fertile—and correlate that with the genetic distance between members of each pair. If you plotted genetic distance against the degree of genetic isolation, you could get a “time course” of speciation, seeing which forms of isolation evolved earliest, what rate they evolved at, whether it would make a difference if the species lived in the same or different areas, and so on.

Of course there are lots of issues here, one being that measures of reproductive divergence between various pairs of species aren’t evolutionarily independent, so we had to do phylogenetic corrections. Further, sexual isolation and sterility/inviability are only two of the reproductive barriers that separate species, and we had to neglect types of genetic isolation that could operate in nature but couldn’t be measured in the lab (e.g., different preferences for food or microhabitats).

The results, though, were surprisingly clean and enlightening. For example, we found that sexual isolation—but not hybrid inviability—evolves ten times faster between species now found in the same area than those now found in different areas. This result, which has held up in repeats of our work, suggests that natural selection “reinforces”, or strengthens, mate discrimination between species when they live in the same place. That’s probably because there is a genetic penalty to be paid, in the form of hybrid problems, if you actually mate with the “wrong” species; and you only have that kind of selection operating in species that live in the same area, and have a chance to produce hybrids.

Here’s a graph from the second of our paper of papers showing two plots of the degree of sexual isolation between pairs of species (y axis) against their electrophoretic genetic distance (a measure of the divergence time between members of each pair). “Allopatric” taxa are pairs of species that are geographically isolated at present, while “sympatric” taxa are pairs of species that live in the same general area. (These data are phylogenetically corrected.) You can see that the degree of sexual isolation appears much earlier (at lower genetic distances) when the taxa live in the same area. This is a very striking result that is highly statistically significant. It suggests that natural selection operates on species living in the same place to “reinforce” their sexual isolation. You don’t see this difference for hybrid sterility or inviability, which are not expected to be reinforced by selection.

I digress, but it’s nice to think about this good old work.  Allen came on board the project at the beginning, and we spent several years collecting the data (which was scattered all over the literature), calculating statistics when only raw data were given, and analyzing the data. Thus the paper didn’t come out (in Evolution) until 1989, three years after we’d moved to Chicago.

Then electrophoretic data and reproductive-isolation data continued to accumulate, so in 1997 we published an update of the 1989 paper. The additional data confirmed the patterns we’d seen before. And now, since nobody does electrophoresis any more, and estimates of genetic divergence come from DNA sequences, we can’t do this analysis further. (DNA-sequence data does not exist for most of the species we used.)  Similar work has been done in fish and tomatoes, and at least two researchers have redone our analyses in flies using different techniques (the conclusions remain good).

The references to our two papers are given at the bottom, along with the links to them (free access).

This long introduction just wrote itself, when what I really want to do is call your attention to an interview I did about that first paper with Hari Sridhar at his site Reflections on Papers Past. Hari, a a post-doctoral researcher at the National Centre for Biological Sciences, Bengaluru (formerly Bangalore), India, has been interviewing scientists about well known papers in ecology and evolution since 2016.  He was kind enough to interview me about the first Coyne and Orr paper, and you can see the interview by clicking on the link below. I haven’t read the final version, which is a transcript of an audio conversation, so be aware that it’s spoken language. I did read a draft and corrected a few phrases that were unintelligible over the phone.

If you’re interested in papers in ecology and evolution, you might have a wander round Hari’s site; there are lots of interesting papers and interviews, many with people I know.

Click below to see the interview.

I want to add that although Allen was my grad student during much of the time we wrote these papers, it was a total collaboration. As with all my students, I don’t micromanage their work or ever tell them what research to do. Allen was interested in the project from the beginning, and contributed tons of work and many ideas to the two papers. And our collaboration continued in what I consider my most important scientific accomplishment, the book Speciation (Coyne and Orr, 2004; note that the book is now expensive but was about $50 when it first came out).

Here are Allen and I at the Evolution meetings in Portland in 2010. Allen was president of the Society for the Study of Evolution, and I was an incoming President, so he briefed me about the job. We had a great time in Portland, as that was before the city went nuts.

And as a measure of the fame of our work, you can’t get bigger than this. My collaboration with Allen was featured in the 2001 movie “Evolution” (a dreadful film!), as a scrawled reference on the blackboard behind two of the stars, David Duchovny and Orlando Jones. See below. It says “Read Coyne and Orr.  ‘Drosophila’ pp. xx8-450”. Note that the page numbers don’t correspond to either paper that we wrote, though it may refer to the book. But even in the book those pages don’t correspond to anything that would be a reading assignment.

Another ex-student of mine, Mohamed Noor, called me up and said he’d seen the movie and noticed a reference to our paper on the blackboard. I didn’t believe him, so I had to go see the movie myself. Sure enough, we were in there! Someone later sent me a screenshot (below).

I would call that real fame! Pity they got the page numbers wrong. I’ve always wondered who wrote that on the board and how they knew about our work.

_______________

Coyne, J. A. and H.A. Orr.  1989.  Patterns of speciation in Drosophila.  Evolution 43: 362-381.

Coyne, J. A., and H. A. Orr. 1997. “Patterns of speciation in Drosophila” revisited. Evolution 51:295-303.

More “evolutionary theory overturned” hype, but, as usual, it’s overrated

October 5, 2020 • 12:45 pm

Once again the magazines are hyping Big New Changes in Evolutionary Theory. This time, though, it’s the respected The Economist, which has a policy of not showing the authors’ names. They should have, for some authors should be given an education about their subject, or at least be held accountable for errors. I am surprised that the website has such a long article, though I don’t often read The Economist, so I was unaware that they did long-form science.

Unfortunately, this is not good long-form science because it distorts and exaggerates the evidence for the role of hybridization in speciation.

First, note the subtitle of the new article below (thanks to many readers for sending it to me). “The origin of species is more complex than Darwin envisaged.” That’s not even wrong. Darwin didn’t advance much of a theory of speciation in The Origin, as he had little idea of what a species was. And what he did say about speciation in that book was, as I note on the first page of my and Allen Orr’s book Speciation, “muddled or wrong.” Nobody touts Darwin as an expert on speciation, despite the title of his great book.

The modern theory of speciation began coalescing in the 1930s and 1940s with the works of Theodosius Dobzhansky and Ernst Mayr, supplemented by Ledyard Stebbins, whose big contribution was to show that in plants, a form of hybrid speciation called “allopolyploidy,” was important in forming new species. All of these authors took speciation to mean the origin of reproductive isolating barriers impeding gene exchange between separate species, with the barriers generally arising by selection causing evolutionary divergence between geographically isolated populations.  If substantial barriers arose as a byproduct of that evolutionary divergence, then speciation had occurred.

That view hasn’t changed much, although our view of how species arise has been a bit refined. But it surely hasn’t been “upturned,” as the article implies: what we know about speciation still rests on a scaffold erected 80 years ago. Yes, of course Darwin’s view of speciation has been completely revised, but we’ve known that for eight decades. It’s like saying, “How genetics has upturned the theory of inheritance,” with the subtitle, “The way heredity works is more complex than Darwin envisaged.”

And the major framework of Darwinism, the five-fold thesis that organisms evolved, that they did so slowly rather than instantly (and in a replacement rather than an individual transformation way), that there is a branching tree of life that began with one ancestral species, that all species, living or dead, have common ancestors, and that the mechanism for creating adaptations (the “match” between an organism, its way of life, and the environment) is due to natural selection—none of these five propositions are affected by the discovery that, as the article notes, hybridization is more common than we used to think. Yes, hybridization is more common than we used to think. What is not true—or at least is unevidenced and probably untrue—is that hybridization is a major cause of speciation in animals. (It is in plants.) But have a read below; The Economist piece is free:

The article was written to show the increasing prevalence of gene exchange between “species” in nature, and, more important, to emphasize that this gene exchange has been instrumental in creating new species. That is, there is a non-Darwinian form of speciation that involves not bifurcation of family trees, but exchange between branches of family trees, leading to new species. That is, here’s how we get new species, and one can say that it is indeed does not lie within the bifurcating-tree framework of Darwinism as limned above (figure from the Evolution paper below):

 

There are two ways this can happen. First, species can produce full hybrids and then the hybrid genome, forming a full population of hybrid individuals, can sort itself out into a new species—that is, a new group of populations that are reproductively isolated from the parental species. And this itself can take two forms. The first, allopolyploidy in plants, involves two plant species with different chromosome numbers (or arrangements) hybridizing, and that hybrid then doubles its number of chromosomes, forming an “allopolyploid” population that will be reproductively isolated from the two parental species. (Hybrids with the parents will produce sterile individuals with three sets of chromosomes.) In my book Speciation with Allen Orr, we show that this kind of speciation is pretty common, accounting for up to 4% of speciation events in flowering plants and 7% in ferns.

The second form of full-hybrid speciation is called “homoploid hybrid speciation”, and involves not an increase in chromosome number, but a normal diploid hybrid forming a population of hybrids, which then evolves into a population reproductively isolated from both parents. The Economist claims this is fairly common. But data I show below suggest it isn’t.

Finally, there is a third way that hybridization can contribute to speciation. That is through introgression: the occasional infusion of genes between species that could be used in adaptation and speciation. (To be part of speciation, those infused genes have to contribute to reproductive isolation between the new “part hybrid” species and its ancestors.) Thus we don’t get an entire population of full hybrids evolving into a new species; rather, speciation occurs in a population that’s taken up a handful of genes from another species through occasional hybrids.  This introgression has happened between modern Homo sapiens and the Neandertals on the one hand and the Denisovans on the other, but it hasn’t lead to new species. That form of introgression is roughly equivalent to mutation on a larger scale, introducing genetic variation that can be (and was, in the case of Neanderthals) used to adapt to environmental changes.

This form of “introgressive speciation”, too, is much rarer than The Economist says, and for the same reasons why homoploid hybrid speciation is rare: we simply don’t have many examples of parental genes in hybrids actually causing the reproductive isolation themselves, though they may cause new morphologies and traits in hybrids that can speciate by more conventional means. (That is, natural selection operates on hybrid or introgressed populations, producing reproductive isolation as a byproduct of the adaptive change, so that genes in the original parents aren’t the cause of reproductive barriers.)

This paper on birds in Evolution, published in 2014, sets out the criteria for homoploid hybrid speciation. Nearly all the examples cited in The Economist piece were already published by then:

Here are the authors’ criteria for homoploid hybrid speciation, the case most emphasized by The Economist:

. . . we define hybrid speciation as a speciation event in which hybridization is crucial in the establishment of reproductive isolation. Although we agree with previous reviews on the definition, we focus this piece on establishing standards for the genetic and phenotypic evidence required to demonstrate that homoploid hybrid speciation has occurred. To demonstrate that hybrid speciation has occurred given this definition, three criteria must be satisfied: (1) reproductive isolation of hybrid lineages from the parental species, (2) evidence of hybridization in the genome, and (3) evidence that this reproductive isolation is a consequence of hybridization. By contrast, a large number of empirical studies have simply used genetic evidence of hybridization (Criterion 2) as support for hybrid speciation (see below).

In our discussion, we evaluate the strength of evidence for homoploid hybrid speciation in studies published in the last decade against these three criteria. We argue that much of the evidence presented in proposed cases of homoploid hybrid speciation does not provide strong support for the hypothesis of hybrid speciation. In addition, we outline the evidence required to support hybrid speciation and suggest promising directions for future studies.

The criteria, though stringent, seem quite reasonable to apply to claims of hybrid speciation. I won’t go through all the analysis, but just present this graph of how many cases fit each of the authors’ three criteria. Plants are in dark green, fungi in lighter green, and animals in very light green. Note the y axis is number of studies, and it goes up to only fifty. The last column are the cases that fit all three criteria, that is, cases that might well represent homoploid hybrid speciation. Note how low the bar is!

For meeting all the authors’ criteria for homoploid hybrid speciation (last column), we have three cases in plants (all involve the superb work of Loren Rieseberg’s group on sunflowers in the genus Helianthus), none in fungi, and exactly one in animals, the hybrid butterfly species Heliconius heurippa. 

The “Big Bird” case of a hybrid species of Galápagos finch that starts out The Economist‘s article isn’t considered, but it, too, is a bit problematic, as it involves a very few finches that show some reproductive isolation but are in a population of very recent origin that hasn’t been examined in about a decade, as I recall. If that small population persists and remains reproductively isolated from the two other finches on the island, we’ll have one more case in animals. That would make a total of five cases of homoploid hybrid speciation among all three groups examined, and that’s a very small number. It’s certainly not enough cases to say that this kind of hybrid speciation has been at all common, much less ubiquitous. Now it may be that there are more cases that we simply don’t know about, but until we find them, we’re not justified in saying that they’re common, much less that “evolutionary theory is upturned.”

A related paper published in 2018 examines claimed cases of hybrid speciation in birds. Click on the screenshot to read it:

Author Jente Ottenburghs examines seven purported cases of hybrid speciation in birds, some of which are mentioned in the Economist piece.  He uses two criteria for whether bird speciation is homoploid hybrid speciation, the same type considered by Schumer et al. above. That is, these are cases in which a hybrid population is supposed to have evolved into new species. And, like Schumer et al., he judges the evidence on whether the reproductive isolation comes directly as a result of the hybridization, which is true hybrid speciation, or whether the hybrid population evolves reproductive isolation by more conventional processes, like natural selection acting on new mutations to create evolutionary divergence—with the byproduct of reproductive isolation—in geographically separated populations.

Ottenburghs finds only one convincing case of homoploid hybrid speciation in birds: the “Big Bird” case of incipient speciation in Galápagos finches. He finds just three cases in which species form after hybridization but the reproductive isolation is not the direct consequence of hybridization (Audubon’s Warbler, likely to be renamed by the Woke), the Golden-crowned Manakin, and the Italian Sparrow.  So even here, in a group where hybrid speciation is supposed to be common, we have fairly convincing evidence in only four cases.

The upshot.  Considering eukaryotes—I’m not dealing with bacterial “species” here, a complicated issue discussed in Speciation—we have at most five cases of true homoploid hybrid speciation, and then a few more cases of speciation after hybridization in which the reproductive isolation evolves by conventional Darwinian means. There is a difference between hybrid speciation and speciation that occurs via neo-Darwinian processes in a population of hybrids.

In other words, we don’t have near enough data to “overturn evolutionary theory”, or to say that new species often don’t form by a branching process. As far as we know, Darwin’s bifurcating tree is still good for nearly all eukaryotes.

Nor do we think that “Darwin’s concept of speciation as a slow and gradual process” is overturned by homoploid hybrid speciation, which, if it evolves via normal processes of selection and drift, could still be very slow. Yes, polyploidy is quick (a new species arises in three generations), and is not something Darwin considered. But allopolyploidy (the hybrid form of polyploid speciation) has been recognized as an important form of speciation in plants since at least 1950, when Ledyard Stebbins published Variation and Evolution in Plants, drawing plants into the Modern Evolutionary Synthesis. Well, that was 70 years ago. Allopolyploidy is important, but it’s old news.

But one thing we know now that we didn’t know before, and I think I’ve emphasized this, is that introgression—genes moving into species from other species—is more common than we used to think. This comes from the molecular innovations that have made such introgressions detectable. But that doesn’t mean that hybrid speciation is more common than we used to think. In fact, it may well be less common than we used to think.

It seems to me that The Economist‘s policy of not naming the authors of its pieces is not a good one for stuff like this, for the author, whoever he or she is, is represented as giving scientific facts and conclusions. If they’re exaggerated or misrepresented, the author should be held accountable.

 

The intellectual vacuity of New Scientist’s evolution issue: 2. The supposed nonexistence of species

September 27, 2020 • 11:30 am

Yesterday I began “deconstructing” (as the cool kids say) the claims in the new issue of New Scientist, below, stating that evolutionary theory needs a reboot.  I don’t intend to go through all 13 “novelties” that supposedly call for an “Extended Evolutionary Synthesis”, but I’ll tackle just a few this week, for “unpacking” (as the cool kids say) all the errors and distortions of the entire article would wear me out. And the rag magazine probably enjoys these posts as all they care about are clicks, not scientific accuracy.

Yesterday I criticized the magazine’s claim that “genetic plasticity”—the observation that the expression of genes and the traits they produce depend on the internal and external environment—is something novel that was just discovered recently, and that it refutes the widespread idea of genetic determinism.  Well, this kind of plasticity isn’t new (it’s been around for a century), it doesn’t refute “genetic determinism” construed in some ways, and almost no biologists accept the form of genetic determinism that New Scientist claims is widespread. Today we take up an area I know something more about: speciation.

Point 5 of their article is the assertion, in caps, “SPECIES DON’T REALLY EXIST.” That will be news to the many of us who already see Homo sapiens as a species that’s different from gorillas, orangs, and the two chimp species. It will also surprise those of us who can instantly recognize a local bird as a robin, a starling, a pigeon, a mallard, and so on. Field guides, after all, would be useless if species weren’t distinct.

For, as Ernst Mayr and Theodosius Dobzhansky recognized in the 1930s, nature is not a continuum in which one form blends imperceptibly into another. Rather, nature is “lumpy” if inspected in a single area, and the lumps correspond to species. (This and the other issues below are all discussed in the first chapter and Appendix of my book Speciation with H. Allen Orr.)

The issue is then not to define species a priori, forcing the lumps in nature into the Procrustean bed of that definition, but rather to conceptialize species: describe in words what they represent. In the first paragraph, then, author Colin Barras gets it wrong:

FOR most of history, we have had little trouble defining species. There was a general assumption that a finite number of distinct forms of life had existed unchanged since creation, each sitting in a clearly defined pigeonhole: human, housefly, hawthorn and so on. Within the past few centuries, and particularly after Darwin, evolutionary theory has emerged as a more satisfactory way to explain how species came into existence. Yet in doing so, it has made species far harder to define.

Well, the issue isn’t how to define species but to find out how to recognize them. And yes, evolutionary theory since the 1930s has provided not only a good criterion for recognition, but also a good explanation of how species come into existence: how the process of speciation works. The explanation is, contra New Scientist, intimately connected with how we conceptualize species, for if we don’t know what these discrete units of nature are, how can we possibly understand how they came into being? Yes, there are lots of new species “definitions” that have arisen in the last several decades, but only one has stood the test of time, and is recognized as an accurate conceptualization of nature’s lumpiness by evolutionists. It’s called the “biological species concept” (BSC), and is roughly this:

A species is a group of populations whose individuals have the ability to exchange genes with other members of the group where they coexist in nature. In contrast, individuals belonging to different species cannot exchange genes in nature: they are reproductively isolated from each other.

Thus the key to understanding why you have no trouble telling birds or insects apart in one plot of land is because they remain genetically distinct from one another, with the reproductive barriers (mate discrimination, hybrid inviability, and so on) preserving the differences that accumulate within each species as it adapts to its environment. In other words the species is the thing that evolves. Now of course some populations of a single species can evolve differently from others, and some species show a limited amount of gene exchange with other species: I deal with these complications in my book, which I urge you to consult for further information.

Things go really haywire in the next paragraph:

There are several aspects to the problem. One is that if we accept the idea of species evolving from other species, then we must allow that an ancestral species can gradually morph into one or more descendants. We would still like to place organisms in discrete categories, but doing so is difficult if species blur into one another through time. “As we have come to terms with evolution, it has highlighted a problem with the machinery in our heads we use for classifying,” says Frank Zachos at the Natural History Museum of Vienna in Austria.

Change in a single lineage over time is a non-problem. Of course lineages slowly transform over time, as ours did. If we evolved, for example, from Homo erectus, it becomes a purely arbitrary matter when to give the later segment of that lineage the name Homo sapiens. Everyone recognizes that this is a matter of naming, not of making a crucial and meaningful biological decision. As for the splitting of one species into several, which occurs via (usually) gradual differentiation of geographically isolated populations to the point where they can’t interbreed, it’s also arbitrary when you call the descend moieties “different species”. We know that when no gene exchange can occur, good biological species have come about, but at intermediate stages of the process, I prefer to say that populations are “becoming more and more species-like.” What New Scientist sees as problems here have been dealt with amply in the last 80 years.

Here’s another non-problem:

For Jody Hey at Temple University in Philadelphia, the more important problem is that biologists often have two objectives in mind when they define species: one is the traditional desire to divide nature into easily recognisable packages; the second is to explain, in evolutionary terms, how those species came into existence. “Humans have conflicting motivations towards species,” he says.

Some researchers argue that these two objectives can never be achieved simultaneously. Down the decades, biologists have come up with a few dozen clever ways to define species. Some make it easy to classify the organisms we encounter – by their physical appearance, for example – but tell us little about the evolutionary process itself (see “Sadistic cladistics”, page 49). Other definitions get to the heart of how species come to exist, but can be difficult to use in the real world.

But other researchers, including me and other evolutionists, do think these objectives can be achieved simultaneously. Are we mentioned, and our reasons given? Nope.

I’m a friend of Jody’s, and he’s a terrific scientist (and a reader here), but I disagree with him on this issue. If you read Speciation, you’ll see that the BSC in fact fuses these two objectives. You first conceptualize species as units of nature that have limited or no gene exchange between them where they co-occur. Then the second problem arises immediately, and comes with a built-in research program: “how do the reproductive barriers arise in the first place?” That is the problem of speciation, and the problem that Darwin, despite the title of his 1859 book, couldn’t solve, for he had no notion of species as reproductively isolated units. In fact, the two objectives have already been achieved simultaneously by evolutionists who accept the BSC. Somehow Colin Barras seems to have missed this. No species concept other than the BSC can explain the palpable lumpiness of nature, and also how it comes about.

The third issue, which comes up often, is that gene exchange between apparently distinct species occurs more often than we used to think. (We know this because we have DNA-based ways of detecting such exchange—”introgression”—that we didn’t have a few decades ago. So here’s the supposed problem of “hybrid bonanza”:

In principle, advances in genetic sequencing could have helped by indicating how genetically distinct different groups of organisms are and how long ago lineages diverged. But sequencing has arguably made the problem worse by revealing that interbreeding – more technically, introgression – between closely related “species” is common across the tree of life. “It does seem to be the rule, not the exception,” says Michael Arnold at the University of Georgia in Athens. Indeed, evidence of introgression stretches right to our front door: our ancestors interbred with various ancient hominins that might, in the eyes of some, count as distinct species.

Well, interbreeding is not ubiquitous (humans and orangs, for instance, don’t exchange genes with any other species), and even when hybrids are formed they sometimes are sterile or don’t mate back to one parental species, necessary for introgression. Hybrid ducks, for example, can be fertile, but introgression is limited because the hybrids look weird and aren’t seen as acceptable mates.  Yes, introgression is more common than we thought, but often it occurred in the distant past or, if it occurred more recently, is limited.  Yes, we had gene exchange with Neandertals and Denisovans, and it appears to have been more than rare, so I tend to see these groups as subspecies of H. sapiens rather than separate species. When there’s that kind of gene exchange, the problem becomes a judgment call. But this problem hasn’t persisted: now all H. sapiens belong to the same species, and there’s no question of an other species of hominin existing now.

In fact, if gene exchange were pervasive and ubiquitous, we couldn’t make family trees of plants and animals very easily: the gene exchange would blur out the twigs. But it hasn’t.

The article goes on:

Another problem is that looking at genes rather than observable features makes it easier to find new species, leading to what some researchers have called taxonomic anarchy. For instance, a biologist can argue that a previously recognised species should really be split into two or more “new” species, as happened when genetic analysis of the African elephant led to its being separated into savannah and forest-dwelling species.

This is a non-problem as well. If you insist on calling geographically isolated populations, like giraffes, as “different species” if they have a certain amount of genetic or morphological differentiation, then that’s also a judgment call, for one can never be sure what degree of genetic differences (usually judged by DNA differences) would correspond to reproductive isolation. If you don’t care about reproductive isolation, then you have no threshhold degree of genetic difference that is biologically meaningful.

The one sure criterion for species delimitation is this: “do the forms interbreed fairly extensively where they co-occur in nature?” If yes, then they’re members of the same species. If not, they’re members of different species. (One other way to demarcate separate species is that if you cross the forms in captivity and the hybrids are completely sterile or inviable, they are separate species, for hybrids would also be sterile and inviable in nature. But if two forms hybridize in zoos and produce fertile offspring, as lions and tigers sometimes do, then it’s a judgment call. In fact, lions and tigers co-occurred in the Middle East in historical times and there are no records of hybrids. Hybridization is an artifact of captivity, as it breaks down the reproductive barriers that kept these cats isolated in nature. Lions and tigers are different species because they don’t exchange genes where they cooccurred in nature.)

The giraffes, living in different parts of Africa, can’t be tested this way because they don’t co-occur, so calling them four different species on the basis of DNA differentiation is a purely subjective exercise (see my post on the giraffes here).

There is one way that looking at genes can help us find new species that aren’t “subjectively described.” This is when you find what seems to be a single species in one area, but then genetic analysis shows that there are actually two forms that each are “fixed” for a different set of genes or chromosome patterns. This is prima facie evidence of non-interbreeding, and we have what biologists call sibling species. Two of the species I worked with, Drosophila pseudoobscura and D. persimilis, for example, were originally thought to be a single species (you can’t tell them apart by looking at them), but research showed that each group is “fixed” for a different set of chromosome arrangements, and you don’t find both arrangements in any individual, so there are no hybrids.

The last bit:

To help add more rigour to the business of defining new species, earlier this year Zachos and other biologists proposed establishing the first single authoritative list of the world’s species. “Species” itself will remain a slippery concept, but at least we could all agree on where to draw the lines.

No, we won’t all agree on where to draw the lines. The giraffe is merely one out of many, many cases in which biologists will quibble about which populations are different species.

To summarize, New Scientist is wrong: species do exist, regardless of some introgression, and we understand not just what they represent—that is, why nature is lumpy rather than continuous—but also how the lumps come to be.