john hawks weblog

paleoanthropology, genetics and evolution

development

  • 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.

  • Anthropology 105, lecture 4: Vertebrae

    Tue, 2012-02-07 17:57 -- John Hawks
    Synopsis: 
    Vertebrae, segmentation in body plans, and homology

    In this lecture, the key concepts are homology, serial homology, gene regulation, and the geological timeline. I introduce the vertebral column and the number of vertebrae of different types in humans, gorillas, orangutans and macaques. Looking at some data from Adolph Schultz, we examine the variation in vertebra count among humans and some other species of primates. To discuss the concept of variation in segment numbers, I turn to Hox genes and segmentation patterning in early embryos. Homology of the Hox genes between fruit flies, mice and humans mirrors the homology of segmentation, including vertebrae counts. Finally, I get to some Miocene apes and their lumbar vertebral anatomy, focusing on Nacholapithecus, Morotopithecus and Proconsul.

    This one stopped a bit short of where I wanted to go, but it's a neat combination of topics in anatomy and development.

    This is a continuing experiment in sharing the lectures for the course online. For my explainer, you can see Lecture 2: Feet.

    Study questions: 
    • What other parts of the body reflect serial homology?
    • The lecture used wings in birds as an example of homology. What other natural examples can you think of?
    • What is another natural example of convergence or parallelism?
    • Why can we use mice to learn about development in humans?
  • 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, and Manzi G. 2011. The Vindija Neanderthal scapular glenoid fossa: Comparative shape analysis suggests evo-devo changes among Neanderthals. Journal of human evolution.
    2. Frayer DW. 1992. 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. p 179–188.
    3. Trinkaus E. 2008. Kiik-Koba 2 and Neandertal axillary border ontogeny. Anthropological Science 116:231 - 236.
    4. Green RE, Krause J, Briggs AW, Maricic T, Stenzel U, Kircher M, Patterson N, Li H, Zhai W, Fritz MH, et al. 2010. A Draft Sequence of the Neandertal Genome. Science [Internet] 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
  • Taung

    Tue, 2011-10-25 00:38 -- John Hawks
    Synopsis: 
    A lab station introducing the Taung specimen and considering its age.

    The face, mandible and endocast from Taung, South Africa, was the first australopithecine fossil to be discovered. We now know that the fossil dates to the period between 2.5 and 3.0 million years ago, but at the time of its discovery, the precise date was not known; only that it was likely earlier than fossil evidence for human evolution outside Africa.

    The morphology of the specimen was therefore the strongest evidence about its relationships to humans and living apes. Interpreting the morphology means coming to terms with the developmental age of the skull.

    Assess the age and morphology of the individual:

    1. What dental age would you assign to Taung, based on your knowledge of human dental development?
    2. What differences are there between Taung and the chimpanzee?
    3. Imagine that Taung was the only australopithecine specimen ever discovered, as it once was. How would you support the argument that it was a hominid?
    Study terms: 
  • Aging juvenile fossil hominins

    Tue, 2011-10-25 00:27 -- John Hawks
    Synopsis: 
    Laboratory exercise giving the opportunity to examine the development of juvenile hominin jaws.

    The fossil record is not made up only of adults. We have abundant skeletal evidence from juvenile individuals of a broad range of ages. At this station you will find model mandibles and maxillae from human children of a range of ages. These provide a comparison for the casts at the station, each of which represents a fossil hominin specimen from Africa, between 3.6 million and 1.5 million years ago.

    The mandibles represent several different species. They include:

    1. OH 7, from Olduvai Gorge, Tanzania. This is the type specimen of Homo habilis, around 1.75 million years old.
    2. MLD 2, from Makapansgat, South Africa. This is an early specimen of Australopithecus africanus, around 2.7 million years old.
    3. LH 2, from Laetoli, Tanzania. An early specimen of Australopithecus afarensis, it is around 3.6 million years old.
    4. SK 47, from Swartkrans, South Africa. This is a juvenile specimen of Australopithecus robustus, around 1.5 million years old.
    5. A selection of other mandibles, including some adult mandibles of the same species, is also available. Examine these in comparison with the modern dental models. Which teeth are present in the fossil specimens? What teeth are in the process of eruption? What do they tell you about the ages of the individuals?

  • Tooth wear

    Sun, 2011-10-23 23:46 -- John Hawks
    Synopsis: 
    Laboratory exercise discussing the basics of dental attrition.

    Teeth have a close association with longevity. Enamel is the hardest substance in the body, but it does break, wear out, and is sometimes attacked by microbes. In Westernized contexts, we are all familiar with cavities, caused by acid-emitting bacteria in the mouth. But in many natural human societies, cavities (called caries) are rare. Instead, a lifetime of eating abrasive natural foods usually causes the teeth to wear down, a process called attrition.

    Dental attrition is very important in the anthropology of ancient peoples. It helps us to understand the food processing techniques — for example, the use of abrasive grinding stones to process grain in early agriculturalists. Dental wear also provides a way of understanding the ages at death of ancient skeletons. In Western societies, excessive tooth wear may be indicative of habitual behaviors such as grinding the teeth, or may result from biases in the chewing pattern to one side or part of the mouth.

    Differential wear describes a dentition in which one tooth is worn significantly more than its neighbors. A normal process of tooth wear results in differential wear, as first molars erupt at age 5 and develop many years of wear before the third molars erupt in the mid- to late teens.

    What to do: Examine the teeth at this station. How are they worn? Is there anything complicating their wear pattern, such as the presence of caries? Which individuals have differential wear? Which are worn the most?

  • Long bone development

    Sun, 2011-10-23 23:17 -- John Hawks
    Synopsis: 
    Laboratory exercise introducing bone development

    The long bones grow in parts. Early in fetal development, the bones are formed from cartilage. Bone tissue forms as special cells (called osteoblasts) lay down mineralized channels into the cartilage. Initially, the shafts, or diaphyses of the long bones begin to ossify. Later, the articular ends of the bone form their own centers of ossification, called epiphyses. Between the diaphysis and epiphyses remains a thin plate of cartilage, called the metaphysis.

    As the bone grows, the metaphysis constantly adds new cartilage, and the diaphysis continues to ossify into this cartilage. So the bone can grow even as parts of it have already become mineralized tissue.

    During the course of development, the bone tissue is recycled, gradually altering its shape. The hard cortical tissue can be invaded by cells that destroy the bone, called osteoclasts, only to have new bone laid down by secondary osteoblasts. The surface of the bone can be altered by having bone gradually removed, a process called resorption. Thus, bones remain living organs that can change their shape gradually, heal themselves, and adapt to new habits and needs.

    What to do: This station has many juvenile bones, including a model skeleton of a young child. Try to identify the shafts of the long bones.

    Study questions: 
    1. Why do you think the bones grow as they do, in parts? Why not just grow by adding more tissue at each end?
    2. How do you think you could use the pattern of bone development to determine the age of a skeleton?
  • Deciduous teeth

    Mon, 2011-10-17 23:59 -- John Hawks
    Synopsis: 
    Laboratory exercise introducing eruption of deciduous dentition in humans and primates.

    Like most mammals, humans have two sets of teeth. The first set is called the deciduous dentition, but you probably know these as "baby teeth."

    The human deciduous dentition includes two incisors, one canine, and two molars in each quadrant. When people lose their deciduous molars, these are replaced by permanent premolars. The permanent molars do not have deciduous teeth in their places before them.

    Deciduous teeth are abbreviated with a "d" and the tooth type and number in lowercase. For example, the deciduous lower first molar is a dm1; the upper left deciduous canine is luc.

    What to do: Consider the series of models at this station. They represent the mandibular dentitions of children at different ages during their development. Can you determine the order that the permanent teeth erupt and replace the deciduous teeth? For example, are the permanent incisors the first to erupt? The permanent molars?

    Part 2

    There are several kinds of primate represented at this station. These primates have different adult body sizes, and grow at very different rates. Nevertheless, their teeth erupt in sequences that are very much like the human dental eruption sequence.

    Yet, there are exceptions. Many primates erupt their canine teeth relatively late in their eruption sequence. In humans, the upper canine typically erupts before the second molars. In many primates, the canine is delayed in development compared to the second molars.

    What to do: Examine the primate dentitions at this station. Identify the deciduous and permanent teeth that you see in each. Try to think about what age a human would likely be, with the same teeth present. Can you find aspects of tooth eruption that differ between humans and these primates?

    Study terms: 
  • Chimp brains don't shrink with age

    Mon, 2011-08-22 00:07 -- John Hawks

    The Wall Street Journal reported on Chet Sherwood's work late last month: "Brain Shrinkage: It's Only Human".

    The human brain normally can shrink up to 15% as it ages, a change linked to dementia, poor memory and depression. Until now, researchers had assumed this gradual brain loss in later years was universal among primates.

    But in the first direct comparison of humans to chimpanzees, a brain-scanning team led by George Washington University anthropologist Chet Sherwood found that chimpanzees don't experience such brain loss. From that, researchers concluded that only people are afflicted by this oddity of longevity.

    The paper is in PNAS [1]. The press article doesn't really explain the findings of the paper very well. Sherwood and colleagues found that the age effect in their sample of humans was limited to ages older than any chimpanzee in their samples. So there's no evidence that humans and chimpanzees differ across the same ages. Now, whether we expect chimpanzees to shrink their brains at a younger age (because they develop and senesce faster) is an open question; I can see arguments both ways. Anyway, I think the study goes as far as gross morphological comparisons can take this question, and more detail will have to wait for us to understand the cellular mechanisms that influence brain size senescence.


    References

    1. Sherwood CC, Gordon AD, Allen JS, Phillips KA, Erwin JM, Hof PR, and Hopkins WD. 2011. Aging of the cerebral cortex differs between humans and chimpanzees. Proceedings of the National Academy of Sciences 108:13029 - 13034.

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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.