Category: speciation

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.

Today: Rosemary Grant gives an online talk on speciation

May 27, 2020 • 9:30 am

Rosemary Grant, along with her partner Peter Grant at Princeton, have done pathbreaking work on speciation, particularly in the finches of the Galápagos islands. (They’re a close team, and even share one Wikipedia page). Their work, for example, has revealed unexpected levels of hybridization between what were considered “good” species, and of course the duo, along with their students, are responsible for one of the classic demonstrations of natural selection in action: an evolutionary increase in beak size in Geospiza fortis following a drought that decimated small plants, leading to starvation of smaller finches with beaks that couldn’t handle bigger and harder seeds. Their work on the finches is described in the Pulitzer-Prize-winning book, The Beak of the Finch: A Story of Evolution in Our Time by Jonathan Weiner (1994).

At any rate, Rosemary is giving an online talk on speciation today, as announced by the tweet below.

The talk will take place between 5-6 pm British standard time, 11am-12 noon Chicago time, and 12 noon-1 pm. Eastern Daylight Time. It’s sure to be enlightening, and I’m pretty sure it will be accessible to non-biologists. And you can access it by clicking on the link below, which will take you to YouTube directly.

 

How often do bird species hybridize?

March 5, 2020 • 10:15 am

There are many reasons why we want to know how often distinct species hybridize, i.e., form individuals resulting from the mating of a male from one species with a female from a different species. For one thing, if this kind of mixing was very frequent, it would be hard to recognize distinct species as the hybrids would form a continuum between the parents. This isn’t a problem, as species (most notably in birds, as documented in my book Speciation with Allen Orr) remain pretty distinct. But if species remain distinct despite even pervasive hybridization, as seems to happen in some groups like ducks, this is evidence that the hybrids themselves are not mating back to the parental species and blurring species boundaries. And if that’s the case, then we can ask why hybrids are effectively sterile. This could be because they are physiologically sterile, like mules, or “behaviorally sterile”: hybrids could be capable of having offspring but might have the wrong appearance or behavior to attract mates, and so would remain unmated.

But hybridization can have other evolutionary effects. It can, for example, act as a form of “mutation”: if the hybrids are fertile, there’s a chance of genes being moved from one species to another, which could then be acted on by natural selection. This phenomenon, called “adaptive introgression”, is fairly well documented in our own species: “modern” Homo sapiens, for instance, shows several genes that came from Denisovans or Neanderthals (some, like me, consider these subspecies), and were probably driven to high frequency by natural selection. This paper gives a lot of examples of adaptive introgression between more well-demarcated species.

Birds are especially good candidates for estimating rates of hybridization, as they are widely observed, there’s a whole “citizen science” project (“eBird”) in which birders and bird lovers send in records of millions of birds, and hybrids are often easily recognized.

But up to now we had very little idea of how often hybridization occurs. The only estimate, and it’s not a great or systematic one, was one made by Ernst Mayr in 1963, who claimed that he observed only about one hybrid among every 60,000 museum skins he examined: a hybridization rate of 0.00167% (0.0000167). But this low value was a purely off-the-cuff “guesstimate”.

Now, in a new paper in Evolution, three researchers used eBird data to get a better estimate of how often bird species produce hybrids. You can access the paper for free by clicking on the link below, the pdf is here, and the reference is at the bottom. It turns out that hybridization, as estimated by citizen scientists, remains low—about the same order of magnitude as Mayr’s earlier estimate.

First, how do you know when a bird is a hybrid? It’s usually done by observing a weird bird that combines the morphological characteristics of two species who have the opportunity to hybridize. (It could be verified genetically, but that’s hard to do with wild birds.) However, the intermediacy, which is rare, is usually verified by experts, which is how hybrids find their way into the eBird database.

There’s a whole site devoted to bird hybrids, and that is its two-word name. I’ll show three pictures of putative hybrids from the site. Here, for example, is a picture from Bird Hybrids of a hybrid between a mallard and a black duck:

American Black Duck x Mallard hybrid, Ottawa River, Ottawa (Ontario, Canada), 7th April 2016 – copyright Gordon Johnston (photo ID: 2787)

Here’s a likely hybrid between a Great Blue Heron and a Great Egret:

Great Blue Heron x Great Egret hybrid, Fort de Soto Park, Pinellas County (Florida, USA), 17th August 2016 – copyright Dave Norgate (photo ID: 2976)

And a hybrid between a Greater white-fronted goose and a Canada goose, showing the Canada goose parental species:

Greater White-fronted Goose x Canada Goose hybrid (same bird as in photo ID 1844 above; with Richardson’s Canada Goose hutchinsii), location not given (probably Colorado, USA), 25th December 2013 – copyright Cathy Sheeter (photo ID: 1845)

There are several ways to calculate hybridization rates. The simplest is just the number of hybrid birds found divided by the total number of birds observed. But bird species vary in their numbers, and if a numerous species hybridizes a lot, that could give you an overestimate of how often members of all species produce hybrids. To correct for that, you can calculate a per species hybridization rate: the total number of species that have produced hybrids divided by the total number of species observed. (You can also do this for hybridization rates between bird orders or bird families.) This of course will be higher, because a species is counted as hybridizing even if it produces only a single hybrid. Alternatively, you can take each species, calculate its hybridization rate with all other species, and then average that across all species to get an estimate of how often an average bird species produces hybrids. (That was not done in this paper.)

There are of course errors introduced by using observations from eBird. One is the assumption that hybrids are recognized as hybrids just as often as pure-species birds are recognized as pure. That’s not unlikely given that hybrids are often distinct, but it may lead to underestimates if very similar-looking species, like warblers, produce hybrids that, because the parents are similar, aren’t easily seen as hybrids. Conversely, hybridization may be overestimated because birders may report this exciting event more than once, so the same hybrid is counted multiple times. Time of year also matters, as hybrids are best recognized when the parental species are in their breeding plumage: during the mating season. I won’t go into detail about how the authors dealt with these issues, except to mention that they used location information to rule out hybrids that were reported multiple times. You can read the paper for the caveats and biases.

The methods: the authors used eBird observations reported between January 1, 2010 and December 31, 2018: nine years of data. Observations were restricted to the contiguous U.S. and submissions were scrutinized and vetted by experts.

Here are the results, all of which confirm Mayr in suggesting that bird hybridization is rare.

1.) The overall hybridization rate was calculated from 212,875 hybrids reported among 334,770,194 birds, or a rate of 0.064%. That is forty times the rate that Mayr reported.

2.) The corrected hybridization rate eliminating possible multiple sightings of the same hybrid: 0.076%, about the same as the uncorrected rate.

3.) The hybridization rate eliminating species that were very prone to hybridization. Eliminating the 10 most frequently hybridizing species, mostly ducks and gulls, which hybridize like gangbusters, brought the hybridization rate down to 0.009%, about 5 times higher than Mayr’s rate. It turns out that the families Anatidae (ducks) and Laridae (gulls) contributed 83% of all bird hybrids in the dataset.

4.) The species hybridization rate: 242 species were implicated in forming hybrids out of 1146 species available giving a frequency of 21% of species forming hybrids at all.

5.) The order hybridization rate. There are 25 orders of birds in the U.S.; 16 of these had species involved in at least one hybridization event, giving a rate of 64%. Here’s a plot of the wide variation in hybridization rate among bird orders. You can see that the two orders Anseriformes, which contains ducks, geese, and swans, and Charadriiformes, which includes gulls, comprise the bulk of hybridization among birds.

6.) The family hybridization rate. there are 95 bird families in the U.S., and 35 had species involved in hybridization, giving a rate of 37%.

The upshot. Correcting for multiple reports of hybrids and eliminating the sluttiest species of birds, the researchers got a rate of about 5 hybrids per 60,000 species: five times higher than that of Mayr—but Mayr’s value was unreliable to begin with. This still means, however that bird hybrids are rare. Here are the data shown graphically in the paper, with the hybridization rate going down as the sluttiest species are removed (oy, the mallards!):

Are there any implications beyond this? Yes. First, there are observations by my colleague Trevor Price and his associate Michelle Bouvier that crosses in captivity between members of different genera and even families can produce viable hybrids, at least in the “lab”. The absence of such hybrids from nature means either that prezygotic isolation (mating discrimination and other impediments to gene flow that operate before copulation) is very strong, or that viability of hybrids in nature is much lower than observed in captivity. (It’s probably a combination of both factors, but I suspect that mate discrimination is quite strong in the wild, and can be overcome by forcibly confining birds in captivity.)

Second, the genetic data from birds, particularly mitochondrial DNA, shows that species remain quite distinct, with species-specific DNA sequences as judged from their “bar codes”.  This shows that despite even the low rates of hybridization, hybrids are not putting foreign genes into other species very often.

h/t: Luana

_____________

Justyn, N.M., Callaghan, C.T. and Hill, G.E. (2020), Birds rarely hybridize: A citizen science approach to estimating rates of hybridization in the wild. Evolution. Accepted Author Manuscript. doi:10.1111/evo.13943

My last research paper. Part 3: Significance

January 29, 2020 • 11:00 am

In the past week I’ve written two posts about what I think will be the last “research paper” I write, i.e., a paper in which I actually did work at the bench (pushing flies). I’ve covered the paper at some length because I think the experiment is cool, because the results were conclusive, and because it’s an experiment that many evolutionary geneticists have wanted to do in their careers, but couldn’t because it would take too long to get results within a single grant-funding cycle. It’s the kind of experiment that you do out of pure curiosity: to find out what happens.

Here’s the paper again; clicking the screenshot takes you to it (if it doesn’t, ask for a pdf):

Part 1 was a description of the study: its aims and methods, which corresponds roughly to the “Introduction” and “Methods and Materials” section of the published paper (and of most published science papers). In that post I described how we made “hybrid swarms” of two pairs of sister species, each pair comprising one widespread Drosophila species living on a continent and an endemic sister species restricted to an oceanic island (D. simulans/D. mauritiana and D. yakuba/D. santomea). Each swarm began with 50% of the DNA, organelles, and cytoplasm from the two parental species, and we made 8 replicate swarms for each pair.

The object was to simply find out what happened when we “mogrelized” two species into a gemisch and then let the population go, without any experimenter-imposed selection over 20 generations. Would the mixture evolve back to one of the parental species? If so, which one, and was that reversion repeated in all eight replicates? Or would we simply get a mixture that persisted over time, without much happening? Alternatively, could we even get a new species—a “diploid hybrid species” that was reproductively incompatible with its two parental species? These questions bear on the compatibility of two species’ genes in a single mixture: are the genes of a species “coadapted“, that is, do they work well together but can’t tolerate the presence of genes from another species? Or is there broad tolerance for genes from a close relative?

In Part 2, posted yesterday, I described what happened (the “results” section of the paper). In short, the results were conclusive and replicable: all the swarms in both replicates reverted back to a parental species—in both cases the “dominant” mainland species (D. simulans in one case and D. yakuba in the other).  This reversion was seen in several morphological traits that distinguish males from each of the parental species, in the mating behavior of the flies, in their reproductive relationships (fertility) when crossed to the two parental species, and in the sequences of the DNA itself. Since all the trait and behavioral differences are surely based on differences in DNA, all the results are mutually supportive.  Nevertheless, foreign DNA was not completely eliminated from the swarms after 20 generations, but that’s only a year in the lab and it might have been further weeded out by selection over longer stretches of time.

So what does this all mean? I’ll use subheadings here.

Selection caused each of the hybrid swarms to revert to a constitution pretty much that of one parental species. In no case did we get anything like a new hybrid species: in every case the swarm reverted to looking and acting like the mainland-species parent, and its DNA sequence was on average about 93-94% that of the dominant species, with the rest of the genome showing some DNA from the minor species.

This means that some form of selection eliminated the island-species’ genes from the mix over time. We don’t know what kind of selection that is (see below), but surely a lot of it had to do with incompatibilities between the species that lead to hybrid sterility and mate discrimination. These will be eliminated no matter what environment you test the flies in, as such selection is largely independent of the environment. It just involves getting rid of genes that produce malfunctioning hybrids. And the elimination of those genes will also eliminate any DNA linked to those genes, whether it be neutral or also bad. This is the “hitchhiking effect” caused by the fact that genes sit next to each other on chromosomes, and if you eliminate one section quickly it will eliminate the adjacent genes from the population as well. What surprised me is how quick the reversion was, and how repeatable it was: not just that all the replicates reverted to the same parent, but because the sections of DNA that “allowed” foreign genes tended to be the same among replicates.

This leads to the next question:

Why did the populations always revert to the mainland species?  There are several possibilities here, and the short answer is that we just don’t know. Here are all the alternatives (several of these could, of course, operate together).

a. The island species, comprising smaller populations, might be more inbred than the mainland species. If that’s the case, the island species might have had high frequencies of deleterious genes, as such genes tend to reach higher frequencies in smaller populations. (This is why small, inbred groups of humans, like the Old Order Amish and the Dunkers, show a high frequency of genetic disorders.) In such a case the “healthier” genes from the less inbred mainland species would replace these deleterious genes. I consider this unlikely because the island species are still present, at least today, in appreciable numbers, which would make them less prone to “inbreeding depression”. Further, that depression would have to have affected nearly every area of the island species’ genomes.

b. Mainland species are more ecologically generalized than island species, as the latter live in a restricted environment while the former roam over many diverse habitats. (D. santomea, for example, is restricted to the high-altitude mist/rain forest of Saõ Tomé while D. yakuba can live in open forests, grasslands, and savannas). This means that mainland species may have genomes that comprise “jack-of-all trades” genes, and thus would be more likely to replace the island species’ genes in a foreign laboratory environment. Several ecologists have proposed that island endemics are often more narrowly adapted than are their mainland relatives.

c. The mainland species was more fit in the particular environmental conditions we used (standard cornmeal/agar/yeast medium, rearing at 24°C, 12 hour light-dark cycles, and high humidity), but in other conditions the island species’ genes could have been more fit. For example, D. santomea prefers cooler temperatures than D. yakuba, and perhaps if we left the swarms at, say 18° C, the swarm would have reverted to D. santomea. This remains to be studied.

d. The genomes of the island species may simply contain more genes that cause hybrid incompatibilities than do the mainland species. This would lead to the more rapid elimination of “island” genes, and thus reversion to the mainland species. There is a bit of evidence for this in one of these pairs, but not for the other.

Why were there parallel regions of the genome that retained “foreign” genes from the island species? As I mentioned last time, some regions of the genome, like the middle of the right arm of the second chromosome in the D. santomea/D. yakuba swarm, and the tip of the left arm of the third chromosome in the D. mauritiana/D. simulans swarm, more readily retained genes from the island species, though not at high frequencies. We don’t know why this is, but it indicates a parallelism in the selective forces acting on the different replicates. The retained regions could have contained “neutral” genes from the island species, or island-species genes might even have been subject to positive selection in these locations, driving them towards high frequencies. Since the island-species genes didn’t really attain high frequencies (we saw no cases of regions that had two copies of island-species genes), I suspect these are just regions that don’t have a lot of genes that affect the fitness of the hybrids.

Further, the X chromosome had the lowest retention of foreign-species genes. This is in line with our previous observations that X chromosomes have more genes causing hybrid problems, for because they are present in only one copy in males, and can also express both dominant and recessive genes that cause hybrid problems.

Are there parallels in the amount and nature of introgression (gene admixture) between what we saw in the lab and what occurs in nature? We can answer this question in only one pair: D. yakuba/D. santomea. That’s because these species co-occur in a narrow “hybrid zone” at about 1000 m high on São Tomé, and hybrids are formed naturally. We can thus see how much foreign genome goes from one species to the other in nature.

The answer to that is: very little. There are only a few regions of each species that contain small amounts of genes from the other species, suggesting that even in nature foreign genes are not tolerated well. But the regions of the genome where we see some gene “pollution” in nature aren’t the same as the ones that show it in our lab experiment. (In nature, low amounts of gene exchange have occurred pretty evenly across the genome, while we find them concentrated in particular areas in the lab.) This could reflect either the fact that selection wasn’t finished in our swarm, or that the nature of selection in the wild differs from that in the lab, so that different foreign genes would be tolerated.

A few caveats. Our study does not show that the formation of a new species after hybridization is impossible: after all, we used only four species of Drosophila (hybrid species are unknown in that genus), and new hybrid species are known in other groups, like butterflies and sunflowers, though for diploid species they aren’t common. (Some people say they are common, but the evidence for that is very weak.)

Further, we used only two strains in each hybridization: one from each species. Though the strains weren’t inbred, it’s possible that if we started with other genetic material from these species, we’d get different results. We were constrained to use only a few strains because we had to get their DNA sequences to be able to determine which DNA in the swarms came from which species. That would have been much harder if we used more genetically heterogenous starting material. We also had to eliminate chromosome inversions in these strains whose presence would have impeded gene exchange, so were constrained to use these “homosequential” strains.

And, as I mentioned above, even with these strains the results may have differed had we reared them under different lab conditions—say using different food or different temperature. Such studies should be done, but I doubt they will be given the difficulty of doing our own research using four species, one strain of each, and under a single laboratory condition.

But the consistency of the results in our study shows that, at least under our experimental conditions, not much foreign DNA is tolerated in even closely related species.

Here are the nine species in the D. melanogaster subgroup (a male from each). D. santomea (e) is in the middle, notable for its derived lack of pigmentation. And so endeth this series of posts.

From Lachaise et al. (2000)

 

The Washington Post refuses to correct scientific errors

January 7, 2020 • 11:30 am

Two days ago I analyzed an article about hybrid parrots that had just appeared in the Washington Post. It was grossly misleading in assuming that two parrots of different “species” (they weren’t—one was a hybrid) had mated and produced, lo, a parrot of another “new species” (also wrong). I tweeted my correction to the Washington Post, but, to be sure they saw it, I also contacted the author of the post and her editor through another editor, pointing them to my correction.

In the meantime, I made a bet with a reader (you know who you are!) that they would not correct the errors. The reader said that they would.

I figured I’d let two days go by before looking for a correction or update, and that is now. And there is no correction, as you can see by clicking on the screenshot below.

Now granted, the story was by a local-issues journalist with no apparent scientific training, but it still contains scientific claims—claims that are wrong. And their responsibility is to correct them. As it is now, many readers think that a hybrid is the same thing as a new species, even though a single individual cannot be a new species (later there were two, but of course both were hybrids in an aviary).

What’s heartening is that many of the article’s 265 comments so far point out to reporter Vargas that the parrot chicks are not a new species but simply hybrids, and that breeders regularly produce hybrid parrots that they call “hybrids” and not “new species.”  But even all those comments on top of a post by a petulant biologist won’t force the Post to admit its errors. FAKE NEWS, FOLKS!

And. . . I win my bet!

Not even wrong: The Washington Post botches a biology story

January 5, 2020 • 8:45 am

A misguided science story just appeared in the Washington Post. Read on.

I will claim some expertise in this critique because my field of study is speciation. Indeed, I literally wrote the book on speciation in collaboration with Allen Orr. But regardless of my “science cred”, Theresa Vargas, a local reporter for the Post, apparently has very little. She has a degree in sociology from Stanford and another from the Columbia University School of Journalism. That doesn’t automatically disqualify her for writing science-based journalism. But the article below does, for, as they say, “It’s not even wrong.” (Click on screenshot; if it’s paywalled judicious inquiry might yield a transcript.) The errors, glaring to a biologist, could have been avoided had Vargas simply picked up the phone and called an ornithologist or someone who studies speciation. You would never see Carl Zimmer, for instance, writing a story so full of errors.

First, a didactic digression by yours truly:

What is a “species”? Some (but not all) biologists use the “Biological Species Concept” (BSC), which conceptualizes a species as a group of interbreeding individuals who are reproductively isolated from members of other such interbreeding groups when they co-occur in nature. That is, members of different species cannot exchange genes in the wild, so that a gene in one species, while it can spread to all other members of its own species, cannot get into another species—barring rare events like “horizontal gene exchange” mediated by parasites or viruses.

The barriers that prevent reproduction between co-occurring species are many, and can involve preference for different microhabitats, lack of sexual attraction so that individuals don’t mate even if their hybrids could be fertile, the use of different pollinators (in plants), different mating periods (“temporal isolation”) and sterility or inviability of any hybrids that do form. All of these factors—collectively called “reproductive isolating barriers” (we summarize them in two chapters of our book—keep different species distinct. Three caveats here:

1.) Sometimes there are intermediate cases in which speciation is not an all-or-none phenomenon. During the evolution of reproductive barriers, there is a long time period when the barriers aren’t yet complete, and gene exchange between incipient species is possible. Or, there may be rare cases in which two fairly distinct groups form occasional hybrids in the wild (ducks are one group that does this). However, if those hybrids are sterile, or can’t find mates, then the hybridizing species are indeed true species. In our book we call these forms “species-like”, and emphasize that speciation is a process that eventually leads to the complete cessation of gene flow in most cases. In such cases delimiting species is a rather arbitrary task. But many species in nature—probably most—cannot form fertile and viable hybrids with others (think human and chimp or pigeon and starling), and there’s no subjectivity in delimiting species.

2.) Sometimes species that are distinct in the wild can hybridize in confinement, as in zoos or farms, and even form fertile hybrids. This does not mean that they are members of the same species, for jailing animals can break down reproductive barriers—like habitat preference or distaste for cross-mating—that would keep species separate in the wild. For example, tigers and lions once had overlapping ranges in India, but hybrids were never found. But in zoos they occasionally hybridize, forming “ligers” or “tiglons”; and some of the female hybrids are fertile. But lions and tigers are not the same species merely because you can force the production of fertile hybrids in zoos. What is important is what happens in the wild when species co-exist. (If they don’t live in the same area, it’s sometimes difficult to tell. You can crossbreed these in the zoo or lab, and if the hybrids are sterile or inviable, that tells you that they would be separate species even if they lived in the same place. But this is a one-way test: zoo hybrids infertile or dead = different species; zoo hybrids viable and fertile = can’t tell.)

3.) The reproductive criterion of the BSC is accepted by nearly all evolutionary biologists, though some miscreants, mainly systematists, have other criteria. Allen and I explain in Chapter 1 and the Appendix of our book why we don’t think these criteria are good, and why they aren’t useful in explaining the Big Question of Speciation: why is nature “lumpy”, with distinct and usually easily identifiable groups, rather than forming a continuum? That is the true question of the origin of species, and one Darwin didn’t answer in his famous book. (He had no notion of species as reproductive units.)

Those caveats aside, let’s briefly look at Vargas’s story.

In the TC Feathers Aviary in Chantilly, Virginia (where my sister and her husband reside) live two parrots. Kirby is a male harlequin macaw, and Suzie is a female military macaw.  They were of very different size and appearance, as you can see below:

They roamed free in the store, and eventually mated. They produced an egg, and it hatched into what Vargas calls a “new species”. It was dubbed “Kuzie” (a hybrid name), and grew up into a bird with intermediate traits. Here’s Kuzie as a chick:

And as an adult:

The hook in this story, which apparently entranced many readers (see the comments), was the romance between members of two supposedly different species, and the production of a cute chick born before the eyes of the customers. (The birds are not for sale.) The attraction and production of a chick between two very different birds seems to be good news in these troubled times, and that’s the way the article was written. (Perhaps they are seen as members of different bird “ethnicities”.)

But everything in the article about the birds themselves, save the fact that they reproduced, is wrong.

1.) The parents are not members of separate species. While the military macaw (Ara militaris) is indeed a real species, the father, a harlequin macaw, is himself not a member of a recognized species but a hybrid. As The Spruce Pets notes:

Harlequin macaws are only produced in captivity. This bird is known as a first-generation hybrid because it is bred from two “true” species of macaw, the blue and gold macaw [JAC: Ara ararauna, the “blue and yellow macaw”] as well as the greenwing macaw [JAC: Ara chloropteris, usually called the “red-and-green macaw“] . The result is a bird with the coloring and characteristics of both parent birds.

But Vargas calls the parents members of different species, not even mentioning that Kirby is a hybrid bird.

There are love stories, and then there is the love story of Suzie and Kirby. Theirs is a rare pairing, one that both defies nature and resulted from it. The two are species of parrots that don’t normally mate. Kirby is a harlequin macaw, and Suzie is a military macaw.

Nope. Even though Kirby was a fertile hybrid, he wasn’t a member of a species different from Suzie’s. Kirby was a “hybrid,” pure and simple.

2.) The chick is not a “new species.” So the hybrid male mated with a pure-species female, producing a male chick that had genes from three species (A. ararauna, A. chloropteris, and A. militaris). That’s truly a mule of a bird. It is a triple hybrid, but what it is not is a member of a new species. But Vargas calls it that in the headline and implies it in the text:

Kuzie, they realized, wasn’t just the product of an unusual love story. He was the product of an unusual love story that might have created a one-of-a-kind species.

Later Kirby and Suzie produced another chick, this time a female called Millie. So there are now two hybrid individuals (they don’t necessarily have the same species’ gene complement because the hybrid father produces sperm having different genes from its own two parental species).

Are the hybrids fertile? Could Millie and Kuzie produce their own chicks? Who knows! But even if they could, that says nothing about them becoming members of a new species. They are, like Kirby, hybrids. (Occasionally a new species of plant or butterfly can form in nature after hybridization, but that’s in nature, and, while common in plants, is exceedingly rare in animals.)

So what we have is a cute human interest story that is dead wrong from a biology point of view. But who cares—except for a petulant biologist like me?

In fact, I made a “get off my lawn” comment after the story (screenshot below), which, says Matthew, was like cracking a walnut with a hammer. (I’d add that it was a bad walnut).  I wrote it in the heat of science passion, so it’s not especially well written and is also a wee bit intemperate!

One more point. Vargas’s story is almost like a religious tale in the sense that the truth is irrelevant because the story makes people feel good. That’s evident in the 200 readers’ comments after the story. Here’s just one:

Of course I will inform the Post, as I’m a curmudgeon, and most likely they will ignore me and not correct the story. So it goes. Cute stories drive out true stories (Coyne’s Law of Science Journalism.)

h/t: Carl

A misguided philosopher claims that species don’t exist

July 17, 2019 • 9:15 am

I won’t say that philosophers in general have nothing to contribute to debates about the nature of biological species, but this philosopher certainly does: Henry Taylor, a fellow in philosophy at the University of Birmingham. His paper in The Conversation (click on screenshot below) not only says that the most used species concept in evolutionary biology—Ernst Mayr’s “biological species concept” (henceforth “BSC”)—is not only wrong, but that we should in fact have no species concept. Ignoring nature completely (has he been outdoors?), he concludes that nature is not divided into the discrete groups that gave rise to the notion of species. Rather, he thinks, nature—like some ideologue’s notion of biological sex—is a continuum. In fact, he concludes that “there is no such thing as ‘the human species’ at all.”

Well cut off my legs and call me Shorty! My whole life I’ve been interacting with (and mating with) what I thought were specimens of Homo sapiens. Now I find that I’m mistaken: we form a continuum with other species. Could I have mated with a chimpanzee or a badger by mistake?

Taylor’s list of publications gives exactly one (forthcoming in Synthese) related to the notion of species, and manages to make a big to-do about a geographically isolated population of brown bears that can hybridize with brown bears and polar bears. That is one of his beefs about the BSC, which I discuss below the screenshot:

The BSC is not really a definition, but, as I emphasize in my book Speciation—written with Allen Orr—an attempt to encapsulate in words the palpable lumpiness in nature that we see before us.  And nature, at least in sexually-reproducing species, really is lumpy: it’s not the continuum, or “great interconnected web”, that Taylor sees. In Chapter 1 of Speciation, I give three lines of evidence for the reality of species: they aren’t just artificial constructs, or subjective human divisions of a continuum, but real entities in nature. Yes, there is some blurring in both sexual and asexual organisms, but by and large species exist as “lumps” in the pudding of Nature. If this were not so, biologists would be wasting their time studying species, and field guides would be of no use. There is no blurring, for instance, between our species, chimpanzees, and orangutans, nor between starlings, hawks, and robins on my campus. And so it goes for most of nature. Some hybrids may be formed between species, but they are often sterile or inviable, and so don’t blur the boundaries between groups.

What Mayr and others (e.g., Theodosius Dobzhansky) did was simply to describe what kept these lumps separate from one another where they coexist in the same location. And that factor was reproductive isolation: the existence of genetic barriers to hybridization that kept two species living in one place from forming fertile hybrids, and thus kept their gene pools separate. The BSC is this:

Members of different species are unable, when they live together in the same area, to hybridize and form fertile offspring: they are “reproductively isolated”.  Members of the same species are able to mate and produce fertile offspring with other members of the same species. 

Coexistence, or “sympatry”, is important in this determination because geographically isolated populations that show some differences can’t be fully tested under the BSC since they don’t encounter each other in a state of nature, and some species that hybridize in captivity don’t do so when they encounter each other in the wild (e.g., lions and tigers, which used to coexist in India).

There are of course intermediate cases—groups that are more or less “species-like”—depending on how much hybridization and gene flow they experience. But for sexually reproducing organisms, these cases are the exception (see Chapter 1 of Speciation). And of course, as we emphasize in the book, the BSC cannot be applied to species that lack sexual reproduction—like many species of bacteria. In those groups one may have to use other species concepts.

The advantage of the BSC is that it gives us an empirical program for studying how lumpiness arises in nature: it arises by the formation of genetic barriers, almost always between isolated populations that experience divergent evolution to the extent that, eventually, gene flow becomes impossible. (The barriers to gene flow aren’t directly selected for in most cases: they are simply byproducts of divergent evolution.) As I pointed out in my chapter, virtually everyone studying speciation in biology (as opposed to defining species), studies the origin of reproductive barriers. That’s a tacit admission that speciation does have something to do with reproductive isolation.

I won’t go on here: I recommend Chapter 1 of Speciation (it’s accessible to the layperson who knows a bit of biology), and, if you want to see the failures of other species concepts, read the Appendix.

Now, why does Taylor reject the BSC, and along with it all species concepts? He gives two reasons.

1.) Polar bears and grizzly bears, once living in different places (“allopatric”) are now meeting each other in nature due to the global-warming-induced disappearance of the cold habitat to which polar bears were once restricted. There is some hybridization between the two groups that now meet, and some of the hybrids are fertile.

Taylor says this shows that the two bears weren’t reproductively isolated, and thus weren’t species. But this is bogus: the two groups were biological species, isolated by what we call “ecological isolating barriers”: genetically based preferences for different habitats that kept two species from encountering each other. (The genetic basis of habitat segregation is important here: two groups isolated simply because they’re on different islands aren’t necessarily biological species because their spatial segregation is due to the contingencies of geography and not to evolution.) Thus the polar and grizzly bears were separate species, but their genetic barriers broke down due to climate change, making the differential habitat preference nonfunctional.

Species may not be permanently different: all of us recognize that groups that remain distinct in nature can, in the future, exchange genes because their genetic barriers have been circumvented by environmental change. Plants kept apart in nature because they are serviced by different pollinators (“pollinator isolation”) may, in the future, suddenly begin hybridizing if one of the pollinators goes extinct. Changes in habitat can efface genetically based ecological preferences, and so on. If you put lions and tigers together in zoos, this breaks down both the geographic and sexual preferences that kept them separate when they used to coexist in India. They can then hybridize and form fertile “ligers” or “tiglons”. Does this mean that lions and tigers are the same species? No, because the change in habitat (artificial confinement in this case) has broken down their genetically-based isolating barriers.

To say that the BSC is bogus because polar bears and grizzly bears now hybridize in some places is to throw out the baby with the ursine bathwater. And this isn’t even an intermediate case: it’s a case where a barrier has been effaced by climate change.

2.) Taylor then trots out the old canard (if ducks can trot) that organisms that don’t interbreed can’t be subject to the BSC. DUH! This is something I discuss at length in Speciation. Taylor:

The [BSC] definition makes use of the notion of interbreeding. This is all very well with horses and polar bears, but smaller organisms like bacteria do not interbreed at all. They reproduce entirely asexually, by simply splitting in two. So this definition of species can’t really apply to bacteria. Perhaps when we started thinking about species in terms of interbreeding, we were all just a bit too obsessed with sex.

Indeed, it’s hard (but not entirely impossible) to imply a reproductively-based species concept to bacteria. But different species do exchange genes, and there have been several attempts to discern bacterial species using reproductive criteria. The question hinges on whether there’s a problem to explain in bacteria: are they “lumpy,” like sexually-reproducing species, or do they form more of a continuum, and thus there’s not a biological observation that needs explaining? This question isn’t yet settled.

And that’s it: Taylor’s lame effort to topple the BSC—a concept that was not even meant to apply to asexual organisms.  He then throws into the mix Darwin’s own confusion about what species really were (this is well known) and on that basis wants us to deep-six all species concepts and all ideas that species even exist as discrete entities independent of human judgment. (Tell that to a robin who is courting other robins but not pigeons! Animals are themselves good taxonomists!)

Here you go:

Scrapping the idea of a species is an extreme idea: it implies that pretty much all of biology, from Aristotle right up to the modern age, has been thinking about life in completely the wrong way. The upshots of this new approach would be enormous, both for our scientific and philosophical view of life. It suggests that we should give up thinking about life as neatly segmented into discrete groups. Rather, we should think of life as one immense interconnected web. This shift in thinking would fundamentally reorient our approach to a great many questions concerning our relation to the natural world, from the current biodiversity crisis to conservation. [JAC: Yeah, what would we now conserve if all of nature is one interconnected web? Would we need to conserve everything?]

And, in a way, this kind of picture may be a natural progression in biological thought. One of the great discoveries of evolutionary biology is that the human species is not special or privileged in the grand scheme of things, and that humans have the same origins as all the other animals. This approach just takes the next step. It says that there is no such thing as “the human species” at all.

That last sentence is risible: there is no species Homo sapiens?! Does Taylor know that we cannot form fertile offspring with any other species (yes, it’s been tried with our closest relative: inseminating female chimps with human sperm produces bupkes). And it’s not the “next step” in dethroning humans as the pinnacle of evolution to then say that they don’t exist as a group.

The danger here is that those who don’t know much about biology and evolution will read Taylor’s piece and think he’s onto something. He isn’t: these criticisms of the BSC have been made many times before, and dispelled equally many times—I do it in my book, which is 15 years old. The palliative for Taylor’s nonsense—and here I have to be a bit self-aggrandizing—is to read Chapter 1 and the Appendix of Speciation.

h/t: coel