john hawks weblog

paleoanthropology, genetics and evolution

development

  • Microchimerism and selection

    Sat, 2013-02-09 11:37 -- John Hawks

    A recent article in Scientific American by Robert Martone explains some recent research on how fetal cells become integrated into mothers' brains for the long term: "Scientists Discover Children’s Cells Living in Mothers’ Brains"

    In this new study, scientists observed that microchimeric cells are not only found circulating in the blood, they are also embedded in the brain. They examined the brains of deceased women for the presence of cells containing the male “Y” chromosome. They found such cells in more than 60 percent of the brains and in multiple brain regions. Since Alzheimer’s disease is more common in women who have had multiple pregnancies, they suspected that the number of fetal cells would be greater in women with AD compared to those who had no evidence for neurological disease. The results were precisely the opposite: there were fewer fetal-derived cells in women with Alzheimer’s. The reasons are unclear.

    Sometimes people wonder what HLA is really for. Once in a while, having someone else's cells inside you isn't quite as harmless as the case discussed here. Being able to recognize your own cells may be your only means of defense.

    The kind of microchimerism described here lasts throughout a woman's postreproductive lifespan. The strength of selection varies across this timeframe. It was logical to hypothesize that the cells might have negative side effects on fitness, such as Alzheimer's risk, that manifest late in life. Mothers must suppress their immune responses to some extent during pregnancy, to avoid health risks to the developing embryo and fetus. That suppression cannot be cost-free; if it were, we would expect everybody to tolerate human foreign bodies as well as expectant mothers. Having roaming stem cells integrate themselves into neural tissue must not be good on average; if it were, we would have cells crawling their way into our brains all the time.

    I bet those cells worm their way into the brain so that your mother will love you better. The only thing wrong with that hypothesis is that it can't explain grandmas.

  • The workings of leprosy

    Fri, 2013-01-18 09:25 -- John Hawks

    Mo Costandi describes a paper with a really fascinating finding about the workings of leprosy: "Leprosy spreads by reprogramming nerve cells into migratory stem cells".

    Anura Rambukkana of the MRC Centre for Regenerative Medicine at the University of Edinburgh and his colleagues isolated Schwann cells from adult mice, grew them in Petri dishes and infected them with M. leprae. They found that the bacterium gradually turns off the genes that give Schwann cells their characteristic properties, and then activates another set of genes that transforms them into something resembling neural crest stem cells, which are only present in the embryo, and which migrate from the developing nervous along various routes to form a wide variety of tissues, including muscle, bone, cartilage, and the Schwann cells and sensory neurons of the peripheral nerves.

    On a scale of how parasites and pathogens manipulate our biological pathways to achieve their own ends, this one runs pretty deep. Exploiting our mechanisms of embryonic development to migrate through the body inside our own cells. Leprosy may be one of the oldest human pathogens, with its long slow course really well suited to spreading in small human communities with infrequent contacts among groups.

  • Metaphyseal fusion

    Sat, 2012-11-10 12:02 -- John Hawks

    Holly Dunsworth, whom readers will remember from my previous links to her work in genetics education, recounts a personal experience to show how the "incidentalome" isn't a particularly genetic issue: "Area Doctor Shatters Area Girl's Dream of Being Taller Than She Is. (A personal genomics parable)".

    "He said it so cavalierly, too," said Dunsworth. "I spent my whole life wondering how tall I'd grow to be, hoping and wishing I'd grow to be tall enough to really dominate on the basketball court. And my doctor didn't even warn me that he was about to deliver this dream-killing news, and he definitely didn't ask me if I even wanted to hear it in the first place."

    It's all in the metaphyses, you see.

  • Building bigger dolphin brains

    Tue, 2012-09-11 18:14 -- John Hawks

    Ed Yong reports on a new study demonstrating a history of positive selection on the gene ASPM in cetaceans. Bruce Lahn's group previously showed that this gene has been positively selected in primate lineages, including recent humans: "Same gene involved in bigger brains of dolphins and primates".

    Now, Shixia Xu from Nanjing Normal University has found that a gene called ASPM played an important role in the evolution of cetacean brains. The gene shows clear signatures of adaptive change at two points in history, when the brains of some cetaceans ballooned in size. But ASPM has also been linked to the evolution of bigger brains in another branch of the mammal family tree – ours. It went through similar bursts of accelerated evolution in the great apes, and especially in our own ancestors after they split away from chimpanzees.

    It seems likely that both primates and cetaceans—the intellectual heavyweights of the animal world—both owe our bulging brains to changes in the same gene. “It’s a significant result,” says Michael McGowen, who studies the genetic evolution of whales at Wayne State University. “The work on ASPM shows clear evidence of adaptive evolution, and adds to the growing evidence of convergence between primates and cetaceans from a molecular perspective.”

    Molecular mechanisms of convergence have proved to be very common in the evolution of different mammalian orders. Mechanistically, evolution seems to select the same pathways when the same general functional requirements are adaptive. It is interesting that cetaceans and primates have broadly similar social and communication constraints, but very different ecological constraints in other respects, such as diet, thermoregulation navigation and home range.

  • Fly larva growing in 3-D

    Thu, 2012-06-07 18:37 -- John Hawks

    I don't have any comments on this, it's just cool: "Fruitfly development, cell by cell"

    The groups behind the two articles both chose D.melanogaster embryos to image. “We understand how the fly embryo works better than any other, and that comes from 100 years of genetic studies,” says Michael Levine, who studies developmental genomics at the University of California at Berkeley and was not involved in the research. “We have a basic blueprint of gene interaction, and this imaging technology should take the abstract blueprint and turn it into a living, breathing embryo.”

  • Spielke profile

    Sat, 2012-05-05 12:25 -- John Hawks

    The New York Times has a long profile of developmental psychologist Elizabeth Spielke, whose work with babies has opened a window on early cognition ("Insights from the youngest minds"). The article is wide-ranging and worth sharing. I thought I'd make an note of Spielke's version of the "cathedral" model in which distinct cognitive functions are combined by executive consciousness into synthetic abilities. She denotes language as the functional glue holding the brain's abilities together:

    Dr. Spelke is also seeking to understand how the core domains of the human mind interact to yield our uniquely restless and creative intelligence — able to master calculus, probe the cosmos and play a Bach toccata as no bonobo or New Caledonian crow can. Even though “our core systems are fundamental yet limited,” as she put it, “we manage to get beyond them.”

    Dr. Spelke has proposed that human language is the secret ingredient, the cognitive catalyst that allows our numeric, architectonic and social modules to join forces, swap ideas and take us to far horizons. “What’s special about language is its productive combinatorial power,” she said. “We can use it to combine anything with anything.”

    She's in a position to test that by looking at prelinguistic children. I think there's much truth in the idea, but some functional integration must take place in any conscious organism, even without language. Language allows a complexity of expression, but complexity does not necessarily mean integration.

  • Baldness genetics

    Sun, 2012-03-25 17:29 -- John Hawks

    I've been doing some literature research on the genetics of baldness. Yes, I'm trying to work out what we can say about Neandertal phenotypes, if you're wondering. I share part of my androgen receptor gene with the Vindija Neandertals, and so I'm interested.

    Anyway, I was reading today a new paper that suggests the involvement of prostaglandin D2 in male pattern hair loss [1]. The paper gives a good, dense account of what is known about the mechanism:

    In AGA, large “terminal” hair follicles forming thick hair shafts miniaturize over time to small follicles that generate microscopic effete hairs (8). Follicle miniaturization is accompanied by a decrease in the duration of the growing phase of the follicle (anagen), which normally lasts several years to produce hair more than 1 m long, but which decreases to only days or weeks in AGA. This results in an increase in the percentage of resting (telogen) hair follicles containing microscopic hairs in bald scalp (4). In addition to these intrinsic changes to the hair follicle, infiltrating lymphocytes and mast cells have been identified around the miniaturizing follicle (9), especially in the area of the stem cell–rich bulge area (10). Sebaceous glands, which attach to each follicle, hypertrophy in bald scalp (8). In balding scalp, the number of hair follicle stem cells remains intact, whereas the number of more actively proliferating progenitor cells markedly decreases (11). This suggests that balding scalp either lacks an activator or has an inhibitor of hair follicle growth.

    The paper itself focuses on the molecular mechanism at work in a mouse model, and does not examine the genetics of risk within human samples. So no targets for me to look at yet. But the role of prostaglandins in sex development might have something to do with the reason male pattern baldness is such a common polymorphism in human populations worldwide.


    References

  • Anthropology 105, lecture 7: Eyes

    Sat, 2012-02-25 17:03 -- John Hawks
    Synopsis: 
    Illustrating phylogeny and evolutionary convergence using trichromacy and eye development

    Out of all the lectures in the course, this was one of my favorites to put together. I return to the topic of evolutionary developmental biology, first raised in the "Vertebrae" lecture, by extending from the Hox genes to toolkit genes, focusing on the role of Pax6 in eye development. Again, we see how model organisms like fruit flies and zebrafish are relevant to understanding human biology.

    Then, we zoom closer into the phylogeny of primates, considering the superfamilies and reminding students that New World monkeys, Old World monkeys and hominoids are all anthropoid primates. The anthropoids have a tremendously interesting difference with respect to color vision. Many New World monkey species have trichromacy in some individuals but many remain able only to see two colors. This is because one of the genes that codes for color-detecting pigments has different alleles. Heterozygotes can see three colors, homozygotes can see only two. By contrast, Old World monkeys and hominoids have trichromatic vision by virtue of a gene duplication in our ancestry, which generated two different genes that diverged in sequence to be sensitive to different wavelengths of light.

    The convergence of trichromatic vision reflects its adaptive value in anthropoids, which emerged from diurnal activity pattern, the need to detect young leaves for their protein content and low toxicity, and a coevolution of color vision with mating displays. At the same time, owl monkeys lost two-color vision in parallel with lorises and galagos, in this case reflecting the low adaptive value of color vision in nocturnal primates.

    Last, I discuss the polymorphism of eye color in living humans, which emerges due to the regulation of OCA2 in the surface layers of the iris.

    Study questions: 
    • Would you predict that the common ancestors of New World monkeys, Old World monkeys and hominoids had three-color or two-color vision?
    • Why is two-color vision so often lost in lineages that are active nocturnally?
    • Would it be possible to use zebrafish and fruit flies as models to understand human biology if we did not share common ancestors with these species? Why or why not?
  • Kidney recapitulation

    Thu, 2012-02-09 10:19 -- John Hawks

    Jerry Coyne reviews a case of recapitulation in human embryonic and fetal development: "Evidence for evolution: development of our kidneys".

    One example is the development of the human kidney, which is pretty much the same as the development of any mammalian kidney. It turns out that, in utero, we develop three separate kidneys in succession, absorbing the first two before we wind up with the embryonic kidney that will become our adult kidney. The first two of these reprise embryonic kidneys of ancestral forms, and in the proper evolutionary order.

    Yesterday during my Anthropology 105 lecture, I was discussing the successive replacement of different hemoglobin forms in embryonic and fetal development. This is not a case of recapitulation, but instead elaboration of function upon the duplication of genes. Amazing how complex the physiological solutions allowing normal development can be, each of them drawing upon the legacy of genes shared with ancient organisms.

  • Looking over a Neandertal's shoulder

    Sat, 2012-01-07 18:04 -- John Hawks

    A study by Di Vincenzo, Steven Churchill and Giorgio Manzi has fallen into the early drawer of the Journal of Human Evolution: "The Vindija Neanderthal scapular glenoid fossa: Comparative shape analysis suggests evo-devo changes among Neanderthals" [1]. The authors do a very nice job taking a long-studied anatomical feature and reframing its variation within a new context. Reading through its discussion, I find much to like in the way Di Vincenzo and colleagues deal with the variation of late Neandertals and integrate the concept of introgressive gene flow among Late Pleistocene populations.

    The glenoid fossa is the part of the scapula that articulates with the head of the humerus. It's the base of the "socket" in the ball-and-socket joint of the shoulder -- indeed, "glenoid" comes from the Greek word for "socket". Roughly shaped like a rounded teardrop, the glenoid is narrower in early hominins and relatively broad in recent people. Neandertals have an intermediate form compared to earlier and later humans.

    Figure 1 from Di Vincenzo et al. 2012, showing glenoid fossa of Vi-209

    Figure 1 from Di Vincenzo et al [1]. Original caption: "The scapular fragment VI-209 and its stratigraphic position (arrow) within the Mousterian layers of complex G of Vindija cave (left) according to Malez et al. (1980). On the right, the configuration of the 60 semi-landmarks used in the analysis is superimposed on the SGF profile. Sliding points are filled. The stratigraphic column is from Janković et al. (2006). Photograph by Milford H. Wolpoff."

    The main point of the study is that the Vindija glenoid specimen, Vi-209, has a more humanlike form than other Neandertals. Another conclusion based on the comparative sample is that the sample of glenoids from late Neandertals is intermediate between early Neandertals and recent people. Likewise, Upper Paleolithic and Mesolithic-era European specimens are intermediate between late Neandertals and recent people. Here's a graph with the first and second principal components of the variation; I've highlighted these groups.

    Figure 3a from Di Vincenzo et al. 2012

    Figure 2a from Di Vincenzo et al. [1]. Altered to include sample names: Krapina, "Classic" and West Asian Neandertals, Vi-209, and Upper Paleolithic/Mesolithic. X-axis is the first principal component of variation based on analysis of the whole sample, Y-axis the second principal component.

    The first principal component basically depends on the relative breadth of the glenoid fossa, with living people being much broader and Australopithecus (represented by Sterkfontein Sts 7 and Malapa MH2) being much narrower relative to the overall size of the fossa. The authors tested and rejected the hypothesis that the apparent trend could be a simple effect of size. This test was carried out relative to glenoid size, and since Australopithecus had relatively large shoulders compared to Homo, size does not vary much across the hominin sample. It would be useful to consider whether body size might matter, but body size would not by itself explain the relations of the later members of the genus Homo.

    The authors emphasize that the data are consistent with a single evolutionary trend within the genus Homo, so that the Neandertal-human difference should be interpreted within the context of this broader pattern. They propose a specific developmental hypothesis.

    Therefore, it seems reasonable that heterochronic factors related to the prolonged developmental pattern of our species (Smith et al., 2007a), which contrasts with the faster growth rates of Neanderthals and other ‘archaic’ hominins (Smith et al., 2007b; but see; Guatelli-Steinberg et al., 2005), led to longer periods of bone deposition along the inferior-lateral edge of the SGF [scapular glenoid fossa]. This could explain the observed variation along PC1 (and/or CV1) for different morphs of the genus Homo, reaching in H. sapiens the greatest extent in width of the SGF and, particularly, of its scapular portion. This is also consistent with the observation by Churchill and Trinkaus (1990) that much of the variability of the glenoid surface is a function of size variation of the joint itself, which can be viewed as forming a single functional matrix sensu Moss and Young (1960). Thus, the overall reduction in developmental rates in the genus Homo (relative to those of other hominoids) across the Pleistocene may account for the general evolutionary trend in SGF shape seen in the fossils, with more marked changes in developmental rates between archaic (including Neanderthals) and early modern humans, producing somewhat more dramatic differences between these groups in joint shape. Green et al. (2010) suggest that some of the differences between Neanderthals and modern humans in shoulder and thoracic morphology (particularly those related to clavicular length) are attributable to differences in the RUNX2/CBFA1 gene. The temporal pattern observed here would suggest that, with respect to SGF shape at least, that some differences are due to overall differences in developmental schedules (rather than specific differences in genes controlling development of the shoulder, such as RUNX2/CBFA1 or HoxC6).

    By suggesting at least one actual genetic substitution in recent humans, they lend some plausibility to the idea. I am more hesitant to accept the assumption that Neandertals had faster developmental schedules than recent people, although it could be true. This specific assumption is not necessary to support the idea of heterochronic change in the glenoid, which could be caused by much more focused developmental processes. If glenoid shape reflects heterochronic developmental changes, the data suggest that those changes were ongoing in global populations during the Holocene. Indeed, the difference between recent people in the study and Upper Paleolithic Europeans is as great as the difference between late Neandertals and Upper Paleolithic Europeans. The study's recent human sample covers a broad geographic distribution but is relatively small in numbers; a fuller comparison of recent people might uncover a more interesting pattern of change.

    The scapula has long figured in discussions of Neandertal genetic persistence. Neandertal scapulae often have a sulcus (groove) on the dorsal (back) aspect of the axillary border, and this feature is also found in a high fraction of early Upper Paleolithic skeletons [2] The axillary border morphology probably has no functional or developmental correlation with the glenoid morphology, so these features are best viewed as separate issues. I mention the axillary border only because of one significant commonality with the glenoid as considered here: We don't know how much variation in the trait may be explained by environment. Maybe the way an individual uses her arms when growing will affect the form of the scapula? With the axillary border, this question has occupied many researchers who tried to determine why some humans resemble some Neandertals and vice versa [3]. The current consensus is that a dorsal axillary sulcus probably reflects early developmental processes that are substantially influenced by genetics instead of shoulder activity pattern, but the consensus is not without detractors.

    In this study, the authors consider the role of introgressive gene flow among Pleistocene populations as a way to maintain the apparently continuous trend:

    The morphology of the SGF [scapular glenoid fossa] is unlikely to be under the genetic control of a single locus. Thus, it is more likely that regulatory genes controlling developmental rates overall produce pleiotropic effects throughout the skeleton. The introduction of these and other (non-regulatory) alleles into the Neanderthal populations of the Near East, and their movement by gene flow across Neanderthal demes into southern Europe (well in advance of the actual in-migration of modern humans) could account for mosaic morphology seen in the Vindija G3 Neanderthals, including the Vi-209 scapula. Introgression and subsequent gene flow would not be expected to have affected early Neanderthal populations (those predating the admixture), nor late Neanderthal populations from western (trans-Alpine) Europe, because they were separated by geographic barriers ( [Fabre et al., 2009] and [Degioanni et al., 2011] ), and/or protected from gene flow by distance (as hypothesized by Voisin, 2006).

    There is as yet no evidence that the Vindija Neandertal genomes have genetic introgression from the African populations from which present non-Africans derive most of their genetic heritage. Green and colleagues [4] tested explicitly for this kind of gene flow, from "modern" into Neandertal populations and found none.

    And yet, the latest Neandertals are consistently similar to recent people in ways that earlier Neandertals were not. The glenoid fossa of Vi-209 is not an isolated case, it joins many other characteristics in this sample (as noted in the quote above) and other Neandertal samples after 45,000 years ago.

    Frankly, I expect that the admixture estimates presented thus far will prove to be wrong. I could be wrong in this expectation, but there are many assumptions underlying genetic analyses of admixture, and it's easy for an incorrect assumption to give rise to an incorrect conclusion. I take the morphological evidence very seriously as a possible "reality-check" about the validity of genetic comparisons. After all, the morphological comparisons predicted introgression from Neandertals in the first place...

    Another reaction to the study by Zachary Cofran: "Evo-devo of the human shoulder?"

    Fabio Di Vincenzo and colleagues analyzed the shape of the outline of the glenoid fossa on the scapula (not to be confused with the glenoid on your skull), from Australopithecus africanus to present day humans. The glenoid fossa is essentially the socket in the ball-and-socket joint of your shoulder. The authors found that there is pretty much a single trend of glenoid shape change from Australopithecus through the evolution of the genus Homo: from the fairly narrow joint in Australopithecus africanus and A. sediba, to the relatively wide joint in recent humans. The overall size and shape of the joint influences/reflects shoulder mobility, so presumably this shape change hints that more front-to-back arm motions became more important through the course of human evolution (authors suggest throwing in humans from the Late Pleistocene onward).

    I think Cofran takes this in an interesting direction with respect to his own dissertation work on development in earlier hominins.


    References

    1. Di Vincenzo F, Churchill SE, Manzi G. The Vindija Neanderthal scapular glenoid fossa: Comparative shape analysis suggests evo-devo changes among Neanderthals. Journal of human evolution. 2011.
    2. Frayer DW. The persistence of Neandertal features in post-Neandertal Europeans. In: Bräuer G, Smith FH Continuity or Replacement? Controversies in Homo sapiens Evolution. Continuity or Replacement? Controversies in Homo sapiens Evolution. Rotterdam: Balkema; 1992. pp. 179–188.
    3. Trinkaus E. Kiik-Koba 2 and Neandertal axillary border ontogeny. Anthropological Science. 2008;116(3):231 - 236.
    4. Green RE, Krause J, Briggs AW, Maricic T, Stenzel U, Kircher M, Patterson N, Li H, Zhai W, Fritz MH, et al. A Draft Sequence of the Neandertal Genome. Science [Internet]. 2010;328:710–722. Available from: http://dx.doi.org/10.1126/science.1188021
    Synopsis: 
    A study of the glenoid fossa finds a pattern across the genus Homo, and similarities between a Vindija specimen and more recent humans

Pages

Subscribe to development

Neandertals

For years, I've worked on their bones. Now I'm working on their genes. Read more about the science studying these ancient people.

Denisova

From a finger bone of an ancient human came the record of a completely unexpected population. My lab is working on the science of the Denisova genome.

Acceleration

The advent of agriculture caused natural selection to speed up greatly in humans. We're uncovering some of the ways that populations have rapidly changed during the last 10,000 years.

Malapa

Just outside Johannesburg, the Malapa site is producing some of the most exciting finds in human evolution. This site is the headquarters of the Malapa Soft Tissue Project.