Category: speciation

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

Railing about rails again: No, Science, it’s NOT THE SAME SPECIES!

May 17, 2019 • 8:45 am

UPDATE: Science has now corrected its post by issuing the addendum below.  As you’ll see in the comments below, author Alex Fox credits this post for the correction, which is gentlemanly of him. Thanks to reader Barry for the spot.

***************

It is a truth universally acknowledged that the two most prestigious science journals in the world are Science, published in the U.S., and Nature, published in England. One would think, then, that their science reporting would be more accurate than the slipshod stuff you see in the science pages of the major media (the NYT is an exception). But Science slipped up this time when reporting on the independent evolution of flightlessness on the island of Aldabra twice: in an ancient white-throated rail that colonized the island and went extinct when sea levels rose, and then in more modern times (i.e., several hundred thousand years ago) when birds from the same flying lineage colonized Aldabra again and once again evolved flightlessness. (Islands lack predators and so flying, which is metabolically expensive, can often be dispensed with to gain other advantages.)

A few days ago I wrote about how nearly all the major media—tabloids and respectable papers alike—mis-reported this finding, saying that the two flightless rails were really the same species, one that had been “resurrected” or “had come back from the dead.” In reality, the three white throated rails (Dryolimnas cuvieri) are designated as subspecies, so even that reporting is wrong. But that’s minor compared to the repeated claim (see my earlier post for screenshots of the distorted headlines) that the very same species had evolved twice.

This was a big boo-boo because calling the modern flightless rail and its extinct flightless analogue members of “the same species” depended only on the similarity of two bones: a wing bone and a leg bone. There was no other fossil evidence, of course, about what the extinct rail looked like, how it behaved, or anything about the rest of its skeleton, its habits, its DNA, or its physiology. It’s simply a misleading whopper to assert that the “same species” evolved twice.

Further, the species concept used by nearly all evolutionary biologists deems two individuals members of the same species if, where they meet in nature, they can mate and produce fertile offspring. It’s a concept based on reproductive compatibility and incompatibility. Doing such a test is not possible in this case because the extinct species never had a chance to cohabit with the modern species. Just as we can’t say whether modern Homo sapiens are members of the same biological species as Homo erectus (note that they’re even given different names, but that’s based on physical differences), so we can’t say whether the ancient and modern flightless rails are members of the same biological species—much less subspecies.

As someone who spent his whole career working on speciation, including species concepts, I was thus disheartened to see this news report in the journal Science:

Note that while the report does call this “iterative evolution” (“convergent evolution” would be clearer to evolutionists), and notes the independent evolution of flightlessness, it also passes on Gizmodo’s report that evolution had “resurrected the lost species.”

Nope, that’s not true. We know nothing about the genetics, morphology, behavior, and physiology of the extinct species compared to the new one. Science had no business talking about “resurrection”, but it did.

Of course only a petulant evolutionary biologist who works on speciation would single out this error. But it’s pretty bad when one of the world’s best science journals makes a totally unwarranted claim like this.

Epigenetics: the return of Lamarck? Not so fast!

August 26, 2018 • 11:00 am

I noticed that there’s a new book out by Peter Ward, a biology professor at the University of Washington who’s done a lot of work on nautilus cepalopods. (He’s also written several trade books in biology.) Here’s his new book, and, as you can see, the cover touts epigenetics as “Lamarck’s Revenge” (Jean-Baptiste Lamarck [1744-1829] was a French naturalist who proposed a theory of the inheritance of acquired characteristics.) The cover also promises to show how epigenetics is revolutionizing our understanding of evolution. Click on the screenshot to go to the Amazon site:

The book has been reviewed in several places, and I noticed that while it got a starred review on Kirkus, Publisher’s Weekly called it a “frustrating book” and has this in its review:

Ward references the classic study showing how starvation impacted one and perhaps two generations in the Netherlands following a WWII-era famine, but provides little hard evidence beyond that example. [JAC: see below for a discussion how even the famine study is flawed.] Without a proposed mechanism for such long-lasting effects and without data indicating such effects exist, Ward leaves readers with little more than suppositions.

And that’s the problem with the Lamarckian/evolutionary/revolutionary hypothesis. Environmentally induced changes to the DNA, usually produced by the placement of small methyl groups on DNA that affect what it does, are almost never inherited beyond one or two generations. This lack of stable change means that such environmental modifications cannot form the basis of permanent evolutionary adaptation. Ergo, it can’t revolutionize our view of evolution.  As the prescient Publisher’s Weekly reviewer noted, there’s just no evidence for the heritability of “Lamarckian” changes to the DNA.

I haven’t yet read Ward’s book, and don’t want to judge it by its cover, but the Nautilus site (the name is a coincidence, and that site was funded by Templeton) has reproduced an excerpt from Ward’s book, which is the article below on “fewer species”. Click on the screenshot to read it. And it gives me no confidence that Ward’s book presents a balanced view of epigenetics.

Lamarck’s Revenge, like David Quammen’s new book on phylogeny, seems to fall into the “Darwin was wrong” genre. (Darwin was supposedly wrong because modern evolutionary theory proposes that either mutations or genes transferred from other organisms are the variational basis for permanent adaptive change, and that the environment cannot itself influence DNA sequences in a permanent way. If environmental methylation did produce gene changes that could be both inherited and adaptive, and so spread through species, it would be a major change in how we view evolution.)

I should add that Darwin himself was “Lamarckian” because he thought the environment could somehow permanently modify heredity, and, as Matthew Cobb reminded me, Lamarck thought the changes occurred not through the environment, but through the animal’s “will.” Both men were wrong about heredity, but, as Matthew suggested, Ward’s book might better be called Darwin’s Revenge! After all, Darwin’s ideas were closer to these misguided epigenetic ideas than were Lamark’s theories.

Click and read:

 

Now the title doesn’t say much about Lamarck or the “evolution revolution”, but the article itself does. The title itself refers to work that Ward did with his colleagues on two species of Nautilus. One species, N. pompilius, occurs widely across the Pacific, while the closely related species N. stenomphalus is found only on the Great Barrier Reef. They were distinguished as different species by differences in morphology: they differ in whether they have a hole through the center of their shell, as well as showing big differences in both internal and external anatomy.

Ward, however says that they aren’t separate species because their DNA was identical using DNA-sequencing analysis (my emphasis):

We caught 30 nautiluses over nine days, snipped off a one-millimeter-long tip of one of each nautilus’ 90 tentacles, and returned all back to their habitats alive (if cranky). All the samples were later analyzed in the large machines that read DNA sequences, and to our complete surprise we found that the DNA of N. pompilius and the morphologically different N. stenomphalus was identical. No genetic difference, yet radically different morphology. The best way to interpret this is to go back to one of the most useful analogies in evolution: of a ball rolling down a slope composed of many gullies. Which gully the ball rolls down (corresponding to the ultimate anatomy or “phenotype” of the grown animal) is controlled by the direction of the push of the ball. In evolution, the ultimate morphological fate of an organism is caused by some aspect of the environment the organism is exposed to early in life—or, in the case of the nautiluses, while they slowly develop in their large egg over the course of an entire year before hatching. Perhaps it is a difference in temperature. Perhaps it is forces that the embryo encounters prehatching, or when newly hatched, the small nautiluses (one inch in diameter, with eight complete chambers) find different food, or perhaps they are attacked and survive, i.e., have two different kinds of predators. That’s why N. pompilius and N. stenomphalus are not two species. They are a single species with epigenetic forces leading to the radically different shell and soft parts. Increasingly it appears that perhaps there are fewer, not more, species on Earth than science has defined.

Well, the differences might not be genetic, but they might not be epigenetic either: the environment could simply change the development of the organism in different places without methylating or modifying its DNA in a heritable way, just as a plant given lots of fertilizer in one plot will grow taller than a plant grown without fertilizer in another plot. There’s no indication here that the differences in morphology of the two Nautilus species are caused by methylation of the DNA or histones, or by small RNA molecules—the three ways Ward says the environment might modify genes in a permanent way.

More important, when I looked up the paper on which this statement was based, I found, contrary to what Ward implied, they didn’t look at a lot of DNA in the two species, finding it identical. The paper (click on screenshot below), published in 2016, looks at only two genes in the mitochondria, and none from the nucleus:

An excerpt from the paper above:

Here, we report the genetic analysis of mitochondrial genes cytochrome c oxidase I (COI) and 16S rDNA, commonly utilized genetic tools for the phylogeographical studies of marine invertebrates, including cephalopods (Anderson 2000; Anderson et al. 2007; Dai et al. 2012; Sales et al. 2013a) from individuals across the known locations of Nautilus populations (Philippines, Fiji, American Samoa, Vanuatu, and eastern Australia – Great Barrier Reef). We chose COI and 16S because of their variability and success in past studies, and to align with sequences generated for this study with previous nautilus studies (Bonacum et al. 2011; Williams et al. 2012). We neglect nuclear genes (e.g., 28S or histone 3) because sequencing efforts have been limited in nautilus, precluding comparative analysis with past studies, and have been shown to be relatively uninformative for phylogenetic studies within this genus (Wray et al. 1995).

Now while the two species might indeed be one, you can’t conclude that from the identity of just two mitochondrial genes. And the Nautilus article at the top implies that a lot of DNA was examined. There may be substantial differences in other parts of the DNA that produce the morphological differences between the two (ergo these differences having a genetic rather than an epigenetic basis), and may even lead them to be reproductively isolated, ergo being two biological species.

I may have missed another paper looking at whole-genome sequences, but I doubt it. To me it seems that Ward is exaggerating his findings, and also implying that they extend to many species on earth, which might not be “biological” species because their differences are based not on DNA, but on developmental differences induced by the environment (and perhaps inherited via methylation). That might be true, but it’s an unwarranted extrapolation from a study of one organism.

Now Ward does mention one well known and important epigenetic property: the development of different cells and tissues in a single organism is often set off by epigenetic modifications that are themselves coded in the genome (i.e., the DNA of gene A says, “turn on/off genes B, C, D, and E under different internal environments”). Those differences are inherited through different cell divisions, which explains why, though all the cells in the body are genetically identical, they do different things and form different tissues. And those epigenetic changes are coded into the organisms’s DNA; they don’t come directly from the environment.

But that applies only to development of a single organism. It’s a very different thing to claim that environmental modification of the DNA of an organism is passed on through its gametes to its children, grandchildren, and so on, for that’s the only kind of environmental modification that can be involved in evolution. And the evidence says that this isn’t likely to happen. As I’ve said  repeatedly, methylation changes (and Ward notes this) are usually wiped out completely when gametes are formed, and we know of NO adaptation that is caused by environmentally-induced methylation of DNA or histones.

Yet in his popular article, Ward goes on to imply that this really does happen, and happens in human evolution as well. Here are a few excerpts (my emphases):

The methyl molecules are not physically passed on to the next generation, but the propensity for them to attach in the same places in an entirely new life-form (a next-generation life-form) is. This methylation is caused by sudden traumas to the body, such as poisoning, fear, famine, and near-death experience. None of these events come from small methyl molecules, but they cause small methyl molecules already in the body to swarm onto the entire DNA in the body at specific and crucial sites. These acts can have an effect not only on a person’s DNA but on the DNA of their offspring. The dawning view is that we can pass on the physical and biological effects of our good or bad habits and even the mental states acquired during our lives.

This is a stark change from the theory of evolution through natural selection. Heritable epigenetics is not a slow, thousand-year process. These changes can happen in minutes. A random hit to the head by an enraged lover. A sick, sexually abusive parent. Breathing in toxic fumes. Coming to God in religious ecstasy. All can change us, and possibly change our children as a consequence.

There is not a lick of evidence for any of that!

And there’s this:

. . . It has long been “truth” that the epigenome (the complement of chemicals that modify the expression and function of the organism’s genes, such as the methyl molecules that can glom onto specific genes during the life of the organism due to some environmental change) of the parent is reprogrammed (all epigenetic traces removed) twice: once during the formation of the gamete itself (the unfertilized egg, or a sperm waiting around to fertilize an egg) and secondly at conception. Erase and erase again. But now experiments definitively show that some of the chemicals added during the life of an organism do leave information in such a way that the offspring has [sic] their genes quickly modified in the same way that the parents did. The same places on the long DNA molecules of the newly born (or even the “not-yet” born) get the same epigenetic add-ons that one or both of the parents had. This is not supposed to happen. The revolution is the realization that it does. It happened to the nautilus. And it happens to you and me.

That is a gross exaggeration, and greatly misleading. If you want to see a good consideration and critique of the purported evidence for transgenerational epigenetic inheritance in humans, read this 2018 Wiring the Brain website post (click on screenshot) by Kevin Mitchell (note: he considers the overblown “Dutch famine” data as well):

Mitchell’s conclusion:

In my opinion, there is no convincing evidence showing transgenerational epigenetic inheritance in humans. But – for all the sociological reasons listed above – I don’t expect we’ll stop hearing about it any time soon.

He’s right on both counts: the evidence is horribly weak, and yet we still keep hearing about “Lamarckian” epigenetic inheritance, this time from Ward. After all, the message “Darwin was right” doesn’t sell books, but, in book publishing, “Darwin was wrong” is the scientific equivalent of “man bites dog”

As it says at the bottom of Ward’s article, these passages are from Lamarck’s Revenge. That doesn’t bode well for the book.

h/t: Nilou