Razib Khan One-stop-shopping for all of my content

April 25, 2018

Whales and complex speciation

Filed under: Evolutionary Genomics,Speciation — Razib Khan @ 10:07 pm


“Reader request”, what’s going on with this new crazy baleen whale paper, Whole-genome sequencing of the blue whale and other rorquals finds signatures for introgressive gene flow. First, putting “blue whale” in the title is genius, since blue whales are awesome and people will read the paper with that in the title (most people don’t know what “rorquals” are). Second, this paper was interesting because it highlighted the importance of thinking across different ecologies when attempting to understand evolutionary processes.

Since I don’t think too much about speciation, a lot of my thought is derived from the fifteen-year-old book Speciation (good book, too bad it doesn’t seem to be in print anymore!). The authors of Speciation are evolutionary geneticists and emphasize allopatric speciation and the biological species concept. They’re instrumentalists. Basically, you separate populations and they eventually diverge until they’re no longer interfertile. Then you get species.

The problem is that in the oceans allopatric speciation isn’t as straightforward, the seas are open three-dimensional spaces after all. This opens up the likelihood that a lot of oceanic speciation is sympatric speciation (think cichlid fish). Something like this seems to apply to large non-toothed whales in this study.

Though the gray whale is phenotypically very distinct from others in the study above, it turns out that phylogenetically they are within the rorqual clade. The authors suggest that the gray whale distinctiveness is a function of adaptation to a benthic lifestyle. They’re bottom feeders.

The topology at the top of this post illustrates that there seems to have been a lot of complexity and gene flow as the rorquals diverged early on so that it’s not really a simple bifurcating phylogenetic tree. We’ve seen this story before. Remember Genetic evidence for complex speciation of humans and chimpanzees?

I think the moral of the story is that large mammalian species which are the basis of the biological species concept don’t really fit under that paradigm too easily. Even this study is probably not going to be the last word on rorqual phylogenetics.

February 27, 2018

The tall and long tales that elephants tell (also, ancient DNA never forgets)

Filed under: Speciation — Razib Khan @ 1:01 am

The new paper on ancient DNA from elephants, mammoths and mastodons, A comprehensive genomic history of extinct and living elephants, is pretty cool. It leverages next-generation sequencing and ancient DNA, to reconstruct the demographic history of several species of elephants, extant and extinct.

The major core finding is that ancient DNA along with better data from extant species suggests that straight-tusked elephant of Europe (P. antiquus), which went extinct 50,000 years ago, seems to have been an evolutionary synthesis of sorts. A substantial portion of its ancestry as from a deeply diverged lineage of elephant. But another fraction seems to derive from a branch of the African forest elephants, in particular, the West African variety. Finally, earlier on there was also admixture with an Asian pachyderm related to the woolly mammoth.

You can see from the figure at the top that the divergence between these lineages is on the order of hundreds of thousands to millions of years.

This section from the conclusion is a huge takeaway:

Our genomic analyses of present-day and extinct elephantids revealed a history of multiple major interspecies admixture events. Evidence for gene flow among closely related mammalian species is not unprecedented. Examples include cases of unidirectional gene flow [e.g., from polar bears into brown bears (47), similar to the Columbian mammoth gene flow into woolly mammoths observed in our study]; emergence of admixed species [e.g., North American wolves with ancestry from coyotes and gray wolves (48), similar to the straight-tusked elephants in our study]; different extents of gene flow [e.g., between gray wolves and Eurasian/African golden jackals (49), and between bonobos and central/eastern chimpanzees (50), as in the case of straight-tusked elephants and west African forest elephants/woolly mammoths in our study]; extended periods of gene flow during the initial diversification of species [e.g., between eastern and western gorillas (39), Sumatran and Bornean orangutans (39), and the ancestors of humans and chimpanzees (39, 51), like those inferred from most pairwise species comparisons in our study]; and adaptive introgression [e.g., in the great cats of the genus Panthera (52)], which could have played an important role in the evolution of elephantids as well. Our results in elephantids thus add to the growing weight of evidence in favor of the view that capacity for hybridization is the norm rather than the exception in many mammalian species over a time scale of millions of years.

Big speciose mammal lineages seem to have hybridzed a lot. Should this surprise us? Probably not.

Placental Invasiveness Mediates the Evolution of Hybrid Inviability in Mammals:

A central question in evolutionary biology is why animal lineages differ strikingly in rates and patterns of the evolution of reproductive isolation. Here, we show that the maximum genetic distance at which interspecific mammalian pregnancies yield viable neonates is significantly greater in clades with invasive (hemochorial) placentation than in clades with noninvasive (epitheliochorial or endotheliochorial) placentation. Moreover, sister species with invasive placentation exhibit higher allopatry in their geographic ranges, suggesting that formerly separated populations in mammals with this placental type fuse more readily on recontact. These differences are apparently driven by the stronger downregulation of maternal immune responses under invasive placentation, where fetal antigens directly contact the maternal bloodstream. Our results suggest that placental invasiveness mediates a major component of reproductive isolation in mammals.

Monkeys and apes (including humans), have very invasive placentas. Afrotheria, somewhat less so. Placental invasiveness isn’t the only criteria to predict or gauge the viability of hybridization, but it’s a major one.

I’ve stated before that genomics didn’t really change our understanding in a qualitative way in relation to evolutionary biology. Yes, stupid arguments about selectionism vs. neutralism really don’t happen anymore because there’s a mad scramble for data, as opposed to rhetorical tactics. But, perhaps in the area of understanding speciation with regards to mammals genomics has really changed things. That is, it’s a lot more about reticulation and a lot less about bifurcation.

To a great extent the “biological species concept” (BSC), which to the general public is the scientific species concept, is mammal focused. If plant geneticists had the catbird seat I think we’d have a different view of what species were. As it is, that’s not what happened. Species are human constructs and reify a certain Platonic sense of categories and kinds. What genomics is showing us here is even in the “best case” circumstances of the BSC, in mammalian lineages, when evaluated over reasonable time spans species barriers are highly porous.

January 29, 2018

Species are what you want them to be

Filed under: Speciation,species,Species concepts — Razib Khan @ 8:55 pm

What is a species? I don’t know. And honestly, I don’t really care too much.

Species is just a semantic label I place on a set of individuals related to a phylogeny. There tends to be a correlation in genetic variants between these creatures. For sexual organisms, which does not include all organisms, it generally denotes the ability to produce fertile offspring between any two pairs of the opposite sex.

Over ten years ago I read Speciation by Jerry Coyne and H. Allen Orr. As evolutionary geneticists with an interest in taxonomy they take the “species problem” somewhat seriously, but ultimately they’re instrumentalists. “Species” are not the ultimate goal of their scholarship from what I can tell. Rather, species are instruments, semantic tools to smoke out evolutionary processes which shape and determine the pattern of biological variation we see around us. The “origin of species” is less important in relation to the species themselves, as opposed to why we can create categories of species out of the specialized morphological diversity around us.

Not everyone agrees with this position. And not everyone has the same opinion about species. On the whole plant systematists and ecologists will take a different tack on the species problem than evolutionary geneticists. Evolutionary geneticists who work with plants will have a different view from those who work on animals, let alone those who work with bacteria.

The point then is that species are social constructs whose utility and nature varies by discipline. I’m not being a solipsist here. Nature is real. And genetic and phenotypic variation is real. But in some ways the labels we give it can become matters of emphasis.

Of course, I am aware this is an idiosyncratic view. For Carl Linnaeus, the cataloging of species, natural kinds, was cataloging the Creation of God. If you are a Creationist, as most pre-modern people were, then species in their variety and number reflect the will and intention of God. Their study and enumeration would be a glimpse into the mind of the divine.

This doesn’t come out of a vacuum. The religious and Creationist thought simply systematized deep intuitions about the nature of things and biological categories. One doesn’t have to be a genius to make a story about why it would be adaptive to promiscuously and compulsively categorize nature around you. Religious thinkers were simply reshaping and firming up ideas which were in the air.

And this probably brings up why questions about “species” crop up over and over in the comments. And this is why a few times a year I have to put this post up….

May 5, 2011

Why the Amazon Rainforest is species rich

Filed under: Amazon Rainforest,Amazonia,Diversity,Ecology,Environment,Speciation — Razib Khan @ 3:08 pm


A monkey frog

The Pith: The Amazon Rainforest has a lot of species because it’s been around for a very long time.

I really don’t know much about ecology, alas. So my understanding of evolution framed in its proper ecological context is a touch on the coarse side. When I say I don’t know much about ecology, I mean that I lack a thick network of descriptive detail. So that means that I have some rather simple models in my head, which upon closer inspection turn out to be false in many specific instances. That’s what you get for relying on theory. Today I ran into a paper which presented me with some mildly surprising results.

The question: why is the Amazon Rainforest characterized by such a diversity of species? If you’d asked me that question 1 hour ago I would have said that it was a matter of physics. That is, the physical parameters of a high but consistent rainfall and temperature regime. This means the basic energetic inputs into the biome is high, and its consistency allows the organisms to plan their life schedule efficiently, maximizing the inputs. All ...

April 20, 2011

Evolutionary pressures, within and without

Filed under: Ecology,Evolution,Extinction,Radiation,Speciation — Razib Khan @ 12:16 am


Foraminifera, Wikimedia Commons

The Pith: The tree if life is nourished by agon, but pruned by the gods. More literally, both interactions between living organisms and the changes in the environment impact the pulsing of speciation and extinction.

No one can be a true “Renaissance Man” today. One has to pick & choose the set of focuses to which one must turn one’s labor to. Life is finite and subject to trade offs. My interest in evolutionary science as a child was triggered by a fascination with paleontology. In particular the megafauna of the Mesozoic and the Cenozoic, dinosaurs and other assorted reptilian lineages as well as the hosts of extinct and exotic mammals which are no more. Obviously I don’t put much time into those older interests at this point, and I’m as much of a civilian when I read Laelaps as you are. More generally when it comes to evolution I focus on the scale of microevolution rather than macroevolution. Evolutionary genetics and the like, rather than paleontology. This is in part because I lean toward a scale independence in evolutionary process, so that the ...

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